30. Harhaj, E. W., Good, L., Xiao, G. & Sun, S. C. Gene expression profiles in HTLV-I-immortalized T cells: deregulated expression of genes involved in apoptosis regulation. *Oncogene* **18**, 1341–1349 (1999).

31. Smith, M. R. & Greene, W. C. Identification of HTLV-I tax trans-activator mutants exhibiting novel transcriptional phenotypes. *Genes Dev.* **4**, 1875–1885 (1990).

32. Xiao, G., Harhaj, E. W. & Sun, S. C. Domain-specific interaction with the I kappa B kinase (IKK)regulatory subunit IKK gamma is an essential step in tax-mediated activation of IKK. *J. Biol. Chem.* **275**, 34060–34067 (2000).

33. Dardenne, E. et al. RNA helicases DDX5 and DDX17 dynamically orchestrate transcription, miRNA, and splicing programs in cell differentiation. *Cell Rep.* **7**, 1900–1913 (2014).

34. Geissler, V., Altmeyer, S., Stein, B., Uhlmann-Schiffler, H. & Stahl, H. The RNA helicase Ddx5/p68 binds to hUpf3 and enhances NMD of Ddx17/p72 and Smg5 mRNA. *Nucleic Acids Res.* **41**, 7875–7888 (2013).

35. Mizuguchi, M. et al. Induction of cell death in growing human T-cells and cell survival in resting cells in response to the human T-cell leukemia virus type 1 Tax. *PLoS ONE* **11**, e0148217 (2016).

36. Tranchevent, L. C. et al. Identification of protein features encoded by alternative exons using Exon ontology. *Genome Res.* **27**, 1087–1097 (2017).

37. Weimann, T. K., Wagner, C., Goos, M. & Wagner, S. N. CD44 variant isoform v10 is expressed on tumor-infiltrating lymphocytes and mediates hyaluronan-independent heterotypic cell-cell adhesion to melanoma cells. *Exp. Dermatol.* **12**, 204–212 (2003).

38. Ponta, H., Sherman, L. & Herrlich, P. A. CD44: from adhesion molecules to signalling regulators. *Nat. Rev. Mol. Cell Biol.* **4**, 33–45 (2003).

39. Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. *Nucleic Acids Res.* **37**, W202–W208 (2009).

40. Cermak, T. et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. *Nucleic Acids Res.* **39**, e82 (2011).

41. Laurent, F. X. et al. New function for the RNA helicase p68/DDX5 as a modifier of MBNL1 activity on expanded CUG repeats. *Nucleic Acids Res.* **40**, 3159–3171 (2012).

42. Kar, A. et al. RNA helicase p68 (DDX5) regulates tau exon 10 splicing by modulating a stem-loop structure at the 5' splice site. *Mol. Cell Biol.* **31**, 1812–1821 (2011).

43. Dardenne, E. et al. Splicing switch of an epigenetic regulator by RNA helicases promotes tumor-cell invasiveness. *Nat. Struct. Mol. Biol.* **19**, 1139–1146 (2012).

44. Rosewick, N. et al. Cis-perturbation of cancer drivers by the HTLV-1/BLV proviruses is an early determinant of leukemogenesis. *Nat. Commun.* **8**, 15264 (2017).

45. Nakahata, S. et al. Loss of NDRG2 expression activates PI3K-AKT signalling via PTEN phosphorylation in ATLL and other cancers. *Nat. Commun.* **5**, 3393 (2014).

46. Bai, D., Ueno, L. & Vogt, P. K. Akt-mediated regulation of NFkappaB and the essentialness of NFkappaB for the oncogenicity of PI3K and Akt. *Int J. Cancer* **125**, 2863–2870 (2009).

47. Yamagishi, M. et al. Polycomb-mediated loss of miR-31 activates NIK-dependent NF-kappaB pathway in adult T cell leukemia and other cancers. *Cancer Cell* **21**, 121–135 (2012).

48. Sithole, N., Williams, C. A., Vaughan, A. M., Kenyon, J. C. & Lever, A. M. L. DDX17 specifically, and independently of DDX5, controls use of the HIV A4/5 splice acceptor cluster and is essential for efficient replication of HIV. *J. Mol. Biol.* **430**, 3111–3128 (2018).

49. Lin, C., Yang, L., Yang, J. J., Huang, Y. & Liu, Z. R. ATPase/helicase activities of p68 RNA helicase are required for pre-mRNA splicing but not for assembly of the spliceosome. *Mol. Cell Biol.* **25**, 7484–7493 (2005).

50. Camats, M., Guil, S., Kokolo, M. & Bach-Elias, M. P68 RNA helicase (DDX5) alters activity of cis- and trans-acting factors of the alternative splicing of H-Ras. *PLoS ONE* **3**, e2926 (2008).

51. Moy, R. H. et al. Stem-loop recognition by DDX17 facilitates miRNA processing and antiviral defense. *Cell* **158**, 764–777 (2014).

52. Mori, M. et al. Hippo signaling regulates microprocessor and links cell-density-dependent miRNA biogenesis to cancer. *Cell* **156**, 893–906 (2014).

53. Delebecque, F., Pramberger, K., Prevost, M. C., Brahic, M. & Tangy, F. A chimeric human T-cell lymphotropic virus type 1 with the envelope glycoprotein of Moloney murine leukemia virus is infectious for murine cells. *J. Virol.* **76**, 7883–7889 (2002).

54. Mallinjoud, P. et al. Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin. *Genome Res.* **24**, 511–521 (2014).

55. Anders, S., Pyl, P. T. & Huber, W. HTSeq-a Python framework to work with high-throughput sequencing data. *Bioinformatics* **31**, 166–169 (2015).

56. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. *Genome Biol.* **15**, 550 (2014).

57. Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. *Nat. Biotechnol.* **34**, 525–527 (2016).

58. Messeguer, X. et al. PROMO: detection of known transcription regulatory elements using species-tailored searches. *Bioinformatics* **18**, 333–334 (2002).

59. Yeo, G. & Burge, C. B. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. *J. Comput. Biol.* **11**, 377–394 (2004).

60. Barrett, T. et al. NCBI GEO: archive for functional genomics data sets-update. *Nucleic Acids Res.* **41**, D991–D995 (2013).

61. Consortium, E. P. An integrated encyclopedia of DNA elements in the human genome. *Nature* **489**, 57–74 (2012).

62. Zheng, R. et al. Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. *Nucleic Acids Res.* **47**, D729–D735 (2018).

63. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. *Nat. Methods* **9**, 357–359 (2012).

64. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). *Genome Biol.* **9**, R137 (2008).

65. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. *Bioinformatics* **26**, 841–842 (2010).

66. Zhu, L. J., Holmes, B. R., Aronin, N. & Brodsky, M. H. CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems. *PLoS ONE* **9**, e108424 (2014).

67. Ran, F. A. et al. Genome engineering using the CRISPR-Cas9 system. *Nat. Protoc.* **8**, 2281–2308 (2013).

## Acknowledgements

This study makes use of data (EGAS00001001296) generated by Department of Pathology and Tumor Biology, Kyoto University²⁴. We gratefully acknowledge support from Laurent Modolo at the LBMC for bio-informatic advice, and from the PSMN (Pôle Scientifique de Modélisation Numérique) of the ENS de Lyon for computing resources. This work was supported by the Ligue Contre le Cancer (Comité de la Savoie, de la Drome et du Rhône), the Fondation ARC (ARC PJA20151203399), and the Agence Nationale pour la Recherche (program EPIVIR and CHROTOPAS). L.B.A. was supported by Ligue Contre le Cancer; G.G., by ANR CHROTOPAS; M.T., by a bursary from the French Ministry of Higher Education and Science; F.M., C.F.B, and D.A., by INSERM; and E.W., by Hospices Civils de Lyon and Lyon I University (France).

## Author contributions

Conceptualization, L.B.A., D.A., and F.M.; resources, A.G. and E.W.; experiments, L.B.A., P.M., M.T., and G.G.; technical support, E.C. and M.B.; bioinformatics, J.B.-C., H.P., N.F., and S.L.; formal analysis, L.B.A., M.T., G.G., and F.M.; supervision, D.A. and F.M.; funding acquisition, C.F.B., D.A. and F.M.; writing—original draft, F.M.; writing—review and editing, L.B.A, M.T., G.G., C.F.B., D.A., and F.M.

## Competing interests

The authors declare no competing interests.

## Additional information

Supplementary information is available for this paper at https://doi.org/10.1038/s41467-020-16853-x.

Correspondence and requests for materials should be addressed to D.A. or F.M.

Peer review information *Nature Communications* thanks Neil Perkins, Claus Scheidereit and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Bibliographie
Ahn, J.H., Davis, E.S., Daugird, T.A., Zhao, S., Quiroga, I.Y., Uryu, H., Li, J., Storey, A.J., Tsai, Y.-H., Keeley, D.P., Mackintosh, S.G., Edmondson, R.D., Byrum, S.D., Cai, L., Tackett, A.J., Zheng, D., Legant, W.R., Phanstiel, D.H., Wang, G.G., 2021. Phase separation drives aberrant chromatin looping and cancer development. Nature 595, 591–595.
https://doi.org/10.1038/s41586-021-03662-5

Akhade, V.S., Arun, G., Donakonda, S., Rao, M.R.S., 2014. Genome wide chromatin occupancy of mrhl RNA and its role in gene regulation in mouse spermatogonial cells. RNA Biol. 11, 1262–1279. https://doi.org/10.1080/15476286.2014.996070

Allfrey, V.G., Faulkner, R., Mirsky, A.E., 1964. ACETYLATION AND METHYLATION OF HISTONES AND THEIR POSSIBLE ROLE IN THE REGULATION OF RNA SYNTHESIS. Proc. Natl. Acad. Sci. U. S. A. 51, 786–794. https://doi.org/10.1073/pnas.51.5.786

Ameur, A., Zaghlool, A., Halvardson, J., Wetterbom, A., Gyllensten, U., Cavelier, L., Feuk, L., 2011. Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat. Struct. Mol. Biol. 18, 1435–1440.
https://doi.org/10.1038/nsmb.2143

Ameur, L.B., Marie, P., Thenoz, M., Giraud, G., Combe, E., Claude, J.-B., Lemaire, S., Fontrodona, N., Polveche, H., Bastien, M., Gessain, A., Wattel, E., Bourgeois, C.F., Auboeuf, D., Mortreux, F., 2020. Intragenic recruitment of NF-κB drives splicing modifications upon activation by the oncogene Tax of HTLV-1. Nat. Commun. 11, 3045.
https://doi.org/10.1038/s41467-020-16853-x

Anderson, M.G., Dynan, W.S., 1994. Quantitative studies of the effect of HTLV-I Tax protein on CREB protein--DNA binding. Nucleic Acids Res. 22, 3194–3201.
https://doi.org/10.1093/nar/22.15.3194

Andersson, R., Enroth, S., Rada-Iglesias, A., Wadelius, C., Komorowski, J., 2009. Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res. 19, 1732–1741. https://doi.org/10.1101/gr.092353.109

Ansari, A., Hampsey, M., 2005. A role for the CPF 3'-end processing machinery in RNAP II-dependent gene looping. Genes Dev. 19, 2969–2978.
https://doi.org/10.1101/gad.1362305

Arnulf, B., Villemain, A., Nicot, C., Mordelet, E., Charneau, P., Kersual, J., Zermati, Y., Mauviel, A., Bazarbachi, A., Hermine, O., 2002. Human T-cell lymphotropic virus oncoprotein Tax represses TGF-beta 1 signaling in human T cells via c-Jun activation: a potential mechanism of HTLV-I leukemogenesis. Blood 100, 4129–4138.
https://doi.org/10.1182/blood-2001-12-0372

Ashburner, B.P., Westerheide, S.D., Baldwin, A.S., 2001. The p65 (RelA) Subunit of NF-κB Interacts with the Histone Deacetylase (HDAC) Corepressors HDAC1 and HDAC2 To Negatively Regulate Gene Expression. Mol. Cell. Biol. 21, 7065–7077.
https://doi.org/10.1128/MCB.21.20.7065-7077.2001
Auweter, S.D., Oberstrass, F.C., Allain, F.H.-T., 2006. Sequence-specific binding of single-stranded RNA: is there a code for recognition? Nucleic Acids Res. 34, 4943-4959.
https://doi.org/10.1093/nar/gkl620

Ballard, D.W., Böhnlein, E., Lowenthal, J.W., Wano, Y., Franza, B.R., Greene, W.C., 1988. HTLV-I tax induces cellular proteins that activate the kappa B element in the IL-2 receptor alpha gene. Science 241, 1652-1655. https://doi.org/10.1126/science.241.4873.1652

Bangham, C.R.M., 2018. Human T Cell Leukemia Virus Type 1: Persistence and Pathogenesis. Annu. Rev. Immunol. 36, 43-71. https://doi.org/10.1146/annurev-immunol-042617-053222

Banigan, E.J., Mirny, L.A., 2020. Loop extrusion: theory meets single-molecule experiments. Curr. Opin. Cell Biol., Cell Nucleus 64, 124-138.
https://doi.org/10.1016/j.ceb.2020.04.011

Barash, Y., Calarco, J.A., Gao, W., Pan, Q., Wang, X., Shai, O., Blencowe, B.J., Frey, B.J., 2010. Deciphering the splicing code. Nature 465, 53-59.
https://doi.org/10.1038/nature09000

Barutcu, A.R., Wu, M., Braunschweig, U., Dyakov, B.J.A., Luo, Z., Turner, K.M., Durbic, T., Lin, Z.-Y., Weatheritt, R.J., Maass, P.G., Gingras, A.-C., Blencowe, B.J., 2022. Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns. Mol. Cell 82, 1035-1052.e9.
https://doi.org/10.1016/j.molcel.2021.12.010

Batsché, E., Yaniv, M., Muchardt, C., 2006. The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat. Struct. Mol. Biol. 13, 22-29.
https://doi.org/10.1038/nsmb1030

Baydoun, H.H., Bai, X.T., Shelton, S., Nicot, C., 2012. HTLV-I Tax Increases Genetic Instability by Inducing DNA Double Strand Breaks during DNA Replication and Switching Repair to NHEJ. PLoS ONE 7, e42226. https://doi.org/10.1371/journal.pone.0042226

Baydoun, H.H., Cherian, M.A., Green, P., Ratner, L., 2015. Inducible nitric oxide synthase mediates DNA double strand breaks in Human T-Cell Leukemia Virus Type 1-induced leukemia/lymphoma. Retrovirology 12, 71. https://doi.org/10.1186/s12977-015-0196-y

Bergqvist, S., Alverdi, V., Mengel, B., Hoffmann, A., Ghosh, G., Komives, E.A., 2009. Kinetic enhancement of NF-κB-DNA dissociation by IκBα. Proc. Natl. Acad. Sci. U. S. A. 106, 19328-19333. https://doi.org/10.1073/pnas.0908797106

Berlivet, S., Paquette, D., Dumouchel, A., Langlais, D., Dostie, J., Kmita, M., 2013. Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs. PLoS Genet. 9, e1004018. https://doi.org/10.1371/journal.pgen.1004018
Bernal-Mizrachi, L., Lovly, C.M., Ratner, L., 2006. The role of NF-κB-1 and NF-κB-2-mediated resistance to apoptosis in lymphomas. Proc. Natl. Acad. Sci. 103, 9220-9225.
https://doi.org/10.1073/pnas.0507809103

Bertero, A., Fields, P.A., Ramani, V., Bonora, G., Yardimci, G.G., Reinecke, H., Pabon, L., Noble, W.S., Shendure, J., Murry, C.E., 2019. Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. Nat. Commun. 10, 1538. https://doi.org/10.1038/s41467-019-09483-5

Bex, F., McDowall, A., Burny, A., Gaynor, R., 1997. The human T-cell leukemia virus type 1 transactivator protein Tax colocalizes in unique nuclear structures with NF-kappaB proteins. J. Virol. 71, 3484-3497. https://doi.org/10.1128/JVI.71.5.3484-3497.1997

Bex, F., Murphy, K., Wattiez, R., Burny, A., Gaynor, R.B., 1999. Phosphorylation of the Human T-Cell Leukemia Virus Type 1 Transactivator Tax on Adjacent Serine Residues Is Critical for Tax Activation. J. Virol. 73, 738-745.

Bex, F., Yin, M.J., Burny, A., Gaynor, R.B., 1998. Differential transcriptional activation by human T-cell leukemia virus type 1 Tax mutants is mediated by distinct interactions with CREB binding protein and p300. Mol. Cell. Biol. 18, 2392-2405.
https://doi.org/10.1128/MCB.18.4.2392

Beyer, A.L., Osheim, Y.N., 1988. Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes Dev. 2, 754-765. https://doi.org/10.1101/gad.2.6.754

Bhat, P., Honson, D., Guttman, M., 2021. Nuclear compartmentalization as a mechanism of quantitative control of gene expression. Nat. Rev. Mol. Cell Biol. 22, 653-670.
https://doi.org/10.1038/s41580-021-00387-1

Bickmore, W.A., 2013. The spatial organization of the human genome. Annu. Rev. Genomics Hum. Genet. 14, 67-84. https://doi.org/10.1146/annurev-genom-091212-153515

Bielli, P., Busà, R., Di Stasi, S.M., Munoz, M.J., Botti, F., Kornbliytt, A.R., Sette, C., 2014. The transcription factor FBI-1 inhibits SAM68-mediated BCL-X alternative splicing and apoptosis. EMBO Rep. 15, 419-427. https://doi.org/10.1002/embr.201338241

Billman, M.R., Rueda, D., Bangham, C.R.M., 2017. Single-cell heterogeneity and cell-cycle-related viral gene bursts in the human leukaemia virus HTLV-1. Wellcome Open Res. 2, 87. https://doi.org/10.12688/wellcomeopenres.12469.2

Bird, G., Zorio, D.A.R., Bentley, D.L., 2004. RNA Polymerase II Carboxy-Terminal Domain Phosphorylation Is Required for Cotranscriptional Pre-mRNA Splicing and 3'-End Formation. Mol. Cell. Biol. 24, 8963-8969. https://doi.org/10.1128/MCB.24.20.8963-8969.2004

Bogenberger, J.M., Laybourn, P.J., 2008. Human T Lymphotropic Virus Type 1 protein Tax reduces histone levels. Retrovirology 5, 9. https://doi.org/10.1186/1742-4690-5-9
Bonev, B., Cavalli, G., 2016. Organization and function of the 3D genome. Nat. Rev. Genet. 17, 661-678. https://doi.org/10.1038/nrg.2016.112

Borghini, L., Lu, J., Hibberd, M., Davila, S., 2018. Variation in Genome-Wide NF-κB RELA Binding Sites upon Microbial Stimuli and Identification of a Virus Response Profile. J. Immunol. 201, 1295-1305. https://doi.org/10.4049/jimmunol.1800246

Boumpas, P., Merabet, S., Carnesecchi, J., 2023. Integrating transcription and splicing into cell fate: Transcription factors on the block. WIREs RNA 14, e1752. https://doi.org/10.1002/wrna.1752

Bourgeois, C.F., Mortreux, F., Auboeuf, D., 2016. The multiple functions of RNA helicases as drivers and regulators of gene expression. Nat. Rev. Mol. Cell Biol. 17, 426-438. https://doi.org/10.1038/nrm.2016.50

Boxus, M., Twizere, J.-C., Legros, S., Dewulf, J.-F., Kettmann, R., Willems, L., 2008. The HTLV-1 Tax interactome. Retrovirology 5, 76. https://doi.org/10.1186/1742-4690-5-76

Brasier, A.R., 2006. The NF-κB Regulatory Network. Cardiovasc. Toxicol. 6, 111-130. https://doi.org/10.1385/CT:6:2:111

Brasier, A.R., Tian, B., Jamaluddin, M., Kalita, M.K., Garofalo, R.P., Lu, M., 2011. RelA Ser276 phosphorylation-coupled Lys310 acetylation controls transcriptional elongation of inflammatory cytokines in respiratory syncytial virus infection. J. Virol. 85, 11752-11769. https://doi.org/10.1128/JVI.05360-11

Brodsky, A.S., Meyer, C.A., Swinburne, I.A., Hall, G., Keenan, B.J., Liu, X.S., Fox, E.A., Silver, P.A., 2005. Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biol. 6, R64. https://doi.org/10.1186/gb-2005-6-8-r64

Brown, J.M., Green, J., das Neves, R.P., Wallace, H.A.C., Smith, A.J.H., Hughes, J., Gray, N., Taylor, S., Wood, W.G., Higgs, D.R., Iborra, F.J., Buckle, V.J., 2008. Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J. Cell Biol. 182, 1083-1097. https://doi.org/10.1083/jcb.200803174

Brown, J.M., Leach, J., Reittie, J.E., Atzberger, A., Lee-Prudhoe, J., Wood, W.G., Higgs, D.R., Iborra, F.J., Buckle, V.J., 2006. Coregulated human globin genes are frequently in spatial proximity when active. J. Cell Biol. 172, 177-187. https://doi.org/10.1083/jcb.200507073

Buratti, E., Baralle, F.E., 2004. Influence of RNA Secondary Structure on the Pre-mRNA Splicing Process. Mol. Cell. Biol. 24, 10505-10514. https://doi.org/10.1128/MCB.24.24.10505-10514.2004

Busch, A., Hertel, K.J., 2012. EVOLUTION OF SR PROTEIN AND HnRNP SPLICING REGULATORY FACTORS. Wiley Interdiscip. Rev. RNA 3, 1-12. https://doi.org/10.1002/wrna.100
Caggiano, C., Pieraccioli, M., Panzeri, V., Sette, C., Bielli, P., 2019. c-MYC empowers transcription and productive splicing of the oncogenic splicing factor Sam68 in cancer. Nucleic Acids Res. 47, 6160–6171. https://doi.org/10.1093/nar/gkz344

Cai, S., Lee, C.C., Kohwi-Shigematsu, T., 2006. SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes. Nat. Genet. 38, 1278–1288. https://doi.org/10.1038/ng1913

Camats, M., Guil, S., Kokolo, M., Bach-Elias, M., 2008. P68 RNA helicase (DDX5) alters activity of cis- and trans-acting factors of the alternative splicing of H-Ras. PloS One 3, e2926. https://doi.org/10.1371/journal.pone.0002926

Carnesecchi, J., Boumpas, P., van Nierop y Sanchez, P., Domsch, K., Pinto, H.D., Borges Pinto, P., Lohmann, I., 2021. The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II. Nucleic Acids Res. 50, 763–783. https://doi.org/10.1093/nar/gkab1250

Carnesecchi, J., Sigismondo, G., Domsch, K., Baader, C.E.P., Rafiee, M.-R., Krijgsveld, J., Lohmann, I., 2020. Multi-level and lineage-specific interactomes of the Hox transcription factor Ubx contribute to its functional specificity. Nat. Commun. 11, 1388. https://doi.org/10.1038/s41467-020-15223-x

Caron, C., Rousset, R., Béraud, C., Moncollin, V., Egly, J.M., Jalinot, P., 1993. Functional and biochemical interaction of the HTLV-I Tax1 transactivator with TBP. EMBO J. 12, 4269–4278. https://doi.org/10.1002/j.1460-2075.1993.tb06111.x

Casola, A., Garofalo, R.P., Jamaluddin, M., Vlahopoulos, S., Brasier, A.R., 2000. Requirement of a novel upstream response element in respiratory syncytial virus-induced IL-8 gene expression. J. Immunol. Baltim. Md 1950 164, 5944–5951. https://doi.org/10.4049/jimmunol.164.11.5944

Caudron-Herger, M., Cook, P.R., Rippe, K., Papantonis, A., 2015. Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories. Nucleic Acids Res. 43, e95–e95. https://doi.org/10.1093/nar/gkv390

Cavrois, M., Wain-Hobson, S., Gessain, A., Plumelle, Y., Wattel, E., 1996. Adult T-cell leukemia/lymphoma on a background of clonally expanding human T-cell leukemia virus type-1-positive cells. Blood 88, 4646–4650.

Chen, Y., Bates, D.L., Dey, R., Chen, P.-H., Machado, A.C.D., Laird-Offringa, I.A., Rohs, R., Chen, L., 2012. DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation. Cell Rep. 2, 1197–1206. https://doi.org/10.1016/j CELREP.2012.10.012

Chen, Y., Zhang, Y., Wang, Y., Zhang, L., Brinkman, E.K., Adam, S.A., Goldman, R., van Steensel, B., Ma, J., Belmont, A.S., 2018. Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. J. Cell Biol. 217, 4025–4048. https://doi.org/10.1083/jcb.201807108
Chen, Y.-J., Chang, L.-S., 2015. NFκB- and AP-1-mediated DNA looping regulates matrix metalloproteinase-9 transcription in TNF-α-treated human leukemia U937 cells. *Biochim. Biophys. Acta BBA - Gene Regul. Mech.* 1849, 1248-1259.
https://doi.org/10.1016/j.bbagrm.2015.07.016

Cheng, C.S., Feldman, K.E., Lee, J., Verma, S., Huang, D.-B., Huynh, K., Chang, M., Ponomarenko, J.V., Sun, S.-C., Benedict, C.A., Ghosh, G., Hoffmann, A., 2011. The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50. *Sci. Signal.* 4, ra11. https://doi.org/10.1126/scisignal.2001501

Chiari, E., Lamsoul, I., Lodewick, J., Chopin, C., Bex, F., Pique, C., 2004. Stable ubiquitination of human T-cell leukemia virus type 1 tax is required for proteasome binding. *J. Virol.* 78, 11823-11832. https://doi.org/10.1128/JVI.78.21.11823-11832.2004

Cho, W.-K., Spille, J.-H., Hecht, M., Lee, C., Li, C., Grube, V., Cisse, I.I., 2018. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. *Science* 361, 412-415. https://doi.org/10.1126/science.aar4199

Cho, W.-K., Zhou, M., Jang, M.K., Huang, K., Jeong, S.-J., Ozato, K., Brady, J.N., 2007. Modulation of the Brd4/P-TEFb interaction by the human T-lymphotropic virus type 1 tax protein. *J. Virol.* 81, 11179-11186. https://doi.org/10.1128/JVI.00408-07

Chu, Z.L., DiDonato, J.A., Hawiger, J., Ballard, D.W., 1998. The tax oncoprotein of human T-cell leukemia virus type 1 associates with and persistently activates IkappaB kinases containing IKKalpha and IKKbeta. *J. Biol. Chem.* 273, 15891-15894.
https://doi.org/10.1074/jbc.273.26.15891

Cisse, I.I., Izeddin, I., Causse, S.Z., Boudarene, L., Senecal, A., Muresan, L., Dugast-Darzacq, C., Hajj, B., Dahan, M., Darzacq, X., 2013. Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells. *Science* 341, 664-667.
https://doi.org/10.1126/science.1239053

Clemens, K.E., Piras, G., Radonovich, M.F., Choi, K.S., Duvall, J.F., DeJong, J., Roeder, R., Brady, J.N., 1996. Interaction of the human T-cell lymphotropic virus type 1 tax transactivator with transcription factor IIA. *Mol. Cell. Biol.* 16, 4656-4664.
https://doi.org/10.1128/MCB.16.9.4656

Clowney, E.J., LeGros, M.A., Mosley, C.P., Clowney, F.G., Markenskoff-Papadimitriou, E.C., Myllys, M., Barnea, G., Larabell, C.A., Lomvardas, S., 2012. Nuclear Aggregation of Olfactory Receptor Genes Governs Their Monogenic Expression. *Cell* 151, 724-737.
https://doi.org/10.1016/j.cell.2012.09.043

Collins, N., Poot, R.A., Kukimoto, I., García-Jiménez, C., Dellaire, G., Varga-Weisz, P.D., 2002. An ACF1-ISWI chromatin-remodeling complex is required for DNA replication through heterochromatin. *Nat. Genet.* 32, 627-632. https://doi.org/10.1038/ng1046

Cook, L.B., Melamed, A., Niederer, H., Valganon, M., Laydon, D., Foroni, L., Taylor, G.P., Matsuoka, M., Bangham, C.R.M., 2014. The role of HTLV-1 clonality, proviral structure,
and genomic integration site in adult T-cell leukemia/lymphoma. Blood 123, 3925–3931. https://doi.org/10.1182/blood-2014-02-553602

Corcoran, A.E., 2010. The epigenetic role of non-coding RNA transcription and nuclear organization in immunoglobulin repertoire generation. Semin. Immunol., Epigenetic regulation of V(D)J recombination 22, 353–361. https://doi.org/10.1016/j.smim.2010.08.001

Cremer, T., Cremer, M., 2010. Chromosome Territories. Cold Spring Harb. Perspect. Biol. 2, a003889. https://doi.org/10.1101/cshperspect.a003889

Crosetto, N., Bienko, M., 2020. Radial Organization in the Mammalian Nucleus. Front. Genet. 11.

Curado, J., Iannone, C., Tilgner, H., Valcárcel, J., Guigó, R., 2015. Promoter-like epigenetic signatures in exons displaying cell type-specific splicing. Genome Biol. 16. https://doi.org/10.1186/s13059-015-0797-8

Currer, R., Van Duyne, R., Jaworski, E., Guendel, I., Sampey, G., Das, R., Narayanan, A., Kashanchi, F., 2012. HTLV Tax: A Fascinating Multifunctional Co-Regulator of Viral and Cellular Pathways. Front. Microbiol. 3, 406. https://doi.org/10.3389/fmicb.2012.00406

Dardenne, E., Polay Espinoza, M., Fattet, L., Germann, S., Lambert, M.-P., Neil, H., Zonta, E., Mortada, H., Gratadou, L., Deygas, M., Chakrama, F.Z., Samaan, S., Desmet, F.-O., Tranchevent, L.-C., Dutertre, M., Rimokh, R., Bourgeois, C.F., Auboeuf, D., 2014. RNA helicases DDX5 and DDX17 dynamically orchestrate transcription, miRNA, and splicing programs in cell differentiation. Cell Rep. 7, 1900–1913. https://doi.org/10.1016/j CELREP.2014.05.010

Das, R., Yu, J., Zhang, Z., Gygi, M.P., Krainer, A.R., Gygi, S.P., Reed, R., 2007. SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol. Cell 26, 867–881. https://doi.org/10.1016/j.molcel.2007.05.036

de la Mata, M., Alonso, C.R., Kadener, S., Fededa, J.P., Blaustein, M., Pelisch, F., Cramer, P., Bentley, D., Kornbliytt, A.R., 2003. A Slow RNA Polymerase II Affects Alternative Splicing In Vivo. Mol. Cell 12, 525–532. https://doi.org/10.1016/j.molcel.2003.08.001

de la Mata, M., Kornbliytt, A.R., 2006. RNA polymerase II C-terminal domain mediates regulation of alternative splicing by SRp20. Nat. Struct. Mol. Biol. 13, 973–980. https://doi.org/10.1038/nsmb1155

Dekker, J., Rippe, K., Dekker, M., Kleckner, N., 2002. Capturing Chromosome Conformation. Science 295, 1306–1311. https://doi.org/10.1126/science.1067799

Deng, W., Rupon, J.W., Krivega, I., Breda, L., Motta, I., Jahn, K.S., Reik, A., Gregory, P.D., Rivella, S., Dean, A., Blobel, G.A., 2014. Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping. Cell 158, 849–860. https://doi.org/10.1016/j.cell.2014.05.050
Denker, A., Laat, W. de, 2016. The second decade of 3C technologies: detailed insights into nuclear organization. *Genes Dev.* 30, 1357–1382.
https://doi.org/10.1101/gad.281964.116

Devaiah, B.N., Lewis, B.A., Cherman, N., Hewitt, M.C., Albrecht, B.K., Robey, P.G., Ozato, K., Sims, R.J., Singer, D.S., 2012. BRD4 is an atypical kinase that phosphorylates Serine2 of the RNA Polymerase II carboxy-terminal domain. *Proc. Natl. Acad. Sci.* 109, 6927–6932.
https://doi.org/10.1073/pnas.1120422109

Dittmer, J., Pise-Masison, C.A., Clemens, K.E., Choi, K.S., Brady, J.N., 1997. Interaction of human T-cell lymphotropic virus type I Tax, Ets1, and Sp1 in transactivation of the PTHrP P2 promoter. *J. Biol. Chem.* 272, 4953–4958. https://doi.org/10.1074/jbc.272.8.4953

Dixon, J.R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J.E., Lee, A.Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., Diao, Y., Liang, J., Zhao, H., Lobanenkov, V.V., Ecker, J.R., Thomson, J., Ren, B., 2015. Chromatin Architecture Reorganization during Stem Cell Differentiation. *Nature* 518, 331–336. https://doi.org/10.1038/nature14222

Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S., Ren, B., 2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions. *Nature* 485, 376–380. https://doi.org/10.1038/nature11082

Easley, R., Carpio, L., Guendel, I., Klase, Z., Choi, S., Kehn-Hall, K., Brady, J.N., Kashanchi, F., 2010. Human T-Lymphotropic Virus Type 1 Transcription and Chromatin-Remodeling Complexes. *J. Virol.* 84, 4755–4768. https://doi.org/10.1128/JVI.00851-09

Ego, T., Ariumi, Y., Shimotohno, K., 2002. The interaction of HTLV-1 Tax with HDAC1 negatively regulates the viral gene expression. *Oncogene* 21, 7241–7246.
https://doi.org/10.1038/sj.onc.1205701

Escoffier, E., Rezza, A., Roborel de Climens, A., Belleville, A., Gazzolo, L., Gilson, E., Duc Dodon, M., 2005. A balanced transcription between telomerase and the telomeric DNA-binding proteins TRF1, TRF2 and Pot1 in resting, activated, HTLV-1-transformed and Tax-expressing human T lymphocytes. *Retrovirology* 2, 77. https://doi.org/10.1186/1742-4690-2-77

Eskiw, C.H., Rapp, A., Carter, D.R.F., Cook, P.R., 2008. RNA polymerase II activity is located on the surface of protein-rich transcription factories. *J. Cell Sci.* 121, 1999–2007.
https://doi.org/10.1242/jcs.027250

Estes, P.A., Cooke, N.E., Liebhaber, S.A., 1992. A native RNA secondary structure controls alternative splice-site selection and generates two human growth hormone isoforms. *J. Biol. Chem.* 267, 14902–14908. https://doi.org/10.1016/S0021-9258(18)42125-4

Faber, G.P., Nadav-Eliyahu, S., Shav-Tal, Y., 2022. Nuclear speckles – a driving force in gene expression. *J. Cell Sci.* 135, jcs259594. https://doi.org/10.1242/jcs.259594
Fagerlund, R., Behar, M., Fortmann, K.T., Lin, Y.E., Vargas, J.D., Hoffmann, A., 2015. Anatomy of a negative feedback loop: the case of IκBα. J. R. Soc. Interface 12, 20150262. https://doi.org/10.1098/rsif.2015.0262

Fan, N., Gavalchin, J., Paul, B., Wells, K.H., Lane, M.J., Poiesz, B.J., 1992. Infection of peripheral blood mononuclear cells and cell lines by cell-free human T-cell lymphoma/leukemia virus type I. J. Clin. Microbiol. 30, 905-910.

Fanucchi, S., Shibayama, Y., Burd, S., Weinberg, M.S., Mhlanga, M.M., 2013. Chromosomal Contact Permits Transcription between Coregulated Genes. Cell 155, 606-620. https://doi.org/10.1016/j.cell.2013.09.051

Federman, N., Fuente, V. de la, Zalcman, G., Corbi, N., Onori, A., Passananti, C., Romano, A., 2013. Nuclear Factor κB-Dependent Histone Acetylation is Specifically Involved in Persistent Forms of Memory. J. Neurosci. 33, 7603-7614. https://doi.org/10.1523/JNEUROSCI.4181-12.2013

Felber, B.K., Paskalis, H., Kleinman-Ewing, C., Wong-Staal, F., Pavlakis, G.N., 1985. The pX Protein of HTLV-I Is a Transcriptional Activator of Its Long Terminal Repeats. Science 229, 675-679. https://doi.org/10.1126/science.2992082

Feldman, I., Feldman, G.M., Mobarak, C., Dunkelberg, J.C., Leslie, K.K., 2007. Identification of Proteins within the Nuclear Factor-κB Transcriptional Complex Including Estrogen Receptor-α. Am. J. Obstet. Gynecol. 196, 394.e1-394.e13. https://doi.org/10.1016/j.ajog.2006.12.033

Fiorini, F., Robin, J.-P., Kanaan, J., Borowiak, M., Croquette, V., Le Hir, H., Jalinot, P., Mocquet, V., 2018. HTLV-1 Tax plugs and freezes UPF1 helicase leading to nonsense-mediated mRNA decay inhibition. Nat. Commun. 9, 431. https://doi.org/10.1038/s41467-017-02793-6

Fong, N., Bentley, D.L., 2001. Capping, splicing, and 3' processing are independently stimulated by RNA polymerase II: different functions for different segments of the CTD. Genes Dev. 15, 1783-1795. https://doi.org/10.1101/gad.889101

Fong, N., Kim, H., Zhou, Y., Ji, X., Qiu, J., Saldi, T., Diener, K., Jones, K., Fu, X.-D., Bentley, D.L., 2014. Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev. 28, 2663-2676. https://doi.org/10.1101/gad.252106.114

Fong, Y.W., Zhou, Q., 2001. Stimulatory effect of splicing factors on transcriptional elongation. Nature 414, 929-933. https://doi.org/10.1038/414929a

Fraedrich, K., Müller, B., Grassmann, R., 2005. The HTLV-1 Tax protein binding domain of cyclin-dependent kinase 4 (CDK4) includes the regulatory PSTAIRE helix. Retrovirology 2, 54. https://doi.org/10.1186/1742-4690-2-54

Franke, M., Ibrahim, D.M., Andrey, G., Schwarzer, W., Heinrich, V., Schöpflin, R., Kraft, K., Kempfer, R., Jerković, I., Chan, W.-L., Spielmann, M., Timmermann, B., Wittler, L., Kurth, I., Cambiaso, P., Zuffardi, O., Houge, G., Lambie, L., Brancati, F., Pombo, A., Vingron, M.,
Spitz, F., Mundlos, S., 2016. Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature 538, 265–269.
https://doi.org/10.1038/nature19800

Franzoso, G., Bours, V., Park, S., Tomfta-Yamaguchi, M., Kelly, K., Siebenlist, U., 1992. The candidate oncoprotein Bcl-3 is an antagonist of pSO/NF-κB-mediated inhibition. Nature 359, 339–342. https://doi.org/10.1038/359339a0

Fujii, M., Tsuchiya, H., Chuhjo, T., Minamino, T., Miyamoto, K., Seiki, M., 1994. Serum response factor has functional roles both in indirect binding to the CAرG box and in the transcriptional activation function of human T-cell leukemia virus type I Tax. J. Virol. 68, 7275–7283. https://doi.org/10.1128/jvi.68.11.7275-7283.1994

Fujimoto, T., Hata, T., Itoyama, T., Nakamura, H., Tsukasaki, K., Yamada, Y., Ikeda, S., Sadamori, N., Tomonaga, M., 1999. High rate of chromosomal abnormalities in HTLV-I-infected T-cell colonies derived from prodromal phase of adult T-cell leukemia: a study of IL-2-stimulated colony formation in methylcellulose. Cancer Genet. Cytogenet. 109, 1–13.
https://doi.org/10.1016/s0165-4608(98)00141-1

Fullwood, M.J., Liu, M.H., Pan, Y.F., Liu, J., Xu, H., Mohamed, Y.B., Orlov, Y.L., Velkov, S., Ho, A., Mei, P.H., Chew, E.G.Y., Huang, P.Y.H., Welboren, W.-J., Han, Y., Ooi, H.S., Ariyaratne, P.N., Vega, V.B., Luo, Y., Tan, P.Y., Choy, P.Y., Wansa, K.D.S.A., Zhao, B., Lim, K.S., Leow, S.C., Yow, J.S., Joseph, R., Li, H., Desai, K.V., Thomsen, J.S., Lee, Y.K., Karuturi, R.K.M., Herve, T., Bourque, G., Stunnenberg, H.G., Ruan, X., Cacheux-Rataboul, V., Sung, W.-K., Liu, E.T., Wei, C.-L., Cheung, E., Ruan, Y., 2009. An oestrogen-receptor-α-bound human chromatin interactome. Nature 462, 58–64. https://doi.org/10.1038/nature08497

Fyodorov, D.V., Kadonaga, J.T., 2002. Dynamics of ATP-dependent chromatin assembly by ACF. Nature 418, 897–900. https://doi.org/10.1038/nature00929

Gabet, A.-S., Mortreux, F., Charneau, P., Riou, P., Duc-Dodon, M., Wu, Y., Jeang, K.-T., Wattel, E., 2003. Inactivation of hTERT transcription by Tax. Oncogene 22, 3734–3741.
https://doi.org/10.1038/sj.onc.1206468

Galganski, L., Urbanek, M.O., Krzyzosiak, W.J., 2017. Nuclear speckles: molecular organization, biological function and role in disease. Nucleic Acids Res. 45, 10350–10368.
https://doi.org/10.1093/nar/gkx759

Gates, L.A., Foulds, C.E., O'Malley, B.W., 2017. Histone Marks in the 'Driver's Seat': Functional Roles in Steering the Transcription Cycle. Trends Biochem. Sci. 42, 977–989.
https://doi.org/10.1016/j.tibs.2017.10.004

Geiger, T.R., Sharma, N., Kim, Y.-M., Nyborg, J.K., 2008. The human T-cell leukemia virus type 1 tax protein confers CBP/p300 recruitment and transcriptional activation properties to phosphorylated CREB. Mol. Cell. Biol. 28, 1383–1392.
https://doi.org/10.1128/MCB.01657-07
Gerritsen, M.E., Williams, A.J., Neish, A.S., Moore, S., Shi, Y., Collins, T., 1997. CREB-binding protein/p300 are transcriptional coactivators of p65. Proc. Natl. Acad. Sci. 94, 2927–2932. https://doi.org/10.1073/pnas.94.7.2927

Gessain, A., Gessain, A., Cassar, O., 2012. Epidemiological Aspects and World Distribution of HTLV-1 Infection. Front. Microbiol. 3.

Geuens, T., Bouhy, D., Timmerman, V., 2016. The hnRNP family: insights into their role in health and disease. Hum. Genet. 135, 851–867. https://doi.org/10.1007/s00439-016-1683-5

Ghisletti, S., Barozzi, I., Mietton, F., Polletti, S., De Santa, F., Venturini, E., Gregory, L., Lonie, L., Chew, A., Wei, C.-L., Ragoussis, J., Natoli, G., 2010. Identification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages. Immunity 32, 317–328. https://doi.org/10.1016/j.immuni.2010.02.008

Ghosh, S., Hayden, M.S., 2008. New regulators of NF-κB in inflammation. Nat. Rev. Immunol. 8, 837–848. https://doi.org/10.1038/nri2423

Gibson, B.A., Doolittle, L.K., Schneider, M.W.G., Jensen, L.E., Gamarra, N., Henry, L., Gerlich, D.W., Redding, S., Rosen, M.K., 2019. Organization of Chromatin by Intrinsic and Regulated Phase Separation. Cell 179, 470-484.e21. https://doi.org/10.1016/j.cell.2019.08.037

Gillet, N.A., Malani, N., Melamed, A., Gormley, N., Carter, R., Bentley, D., Berry, C., Bushman, F.D., Taylor, G.P., Bangham, C.R.M., 2011. The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones. Blood 117, 3113–3122. https://doi.org/10.1182/blood-2010-10-312926

Giraud, G., Terrone, S., Bourgeois, C.F., 2018. Functions of DEAD box RNA helicases DDX5 and DDX17 in chromatin organization and transcriptional regulation. BMB Rep. 51, 613–622. https://doi.org/10.5483/BMBRep.2018.51.12.234

Gohda, J., Irisawa, M., Tanaka, Y., Sato, S., Ohtani, K., Fujisawa, J., Inoue, J., 2007. HTLV-1 Tax-induced NFκB activation is independent of Lys-63-linked-type polyubiquitination. Biochem. Biophys. Res. Commun. 357, 225–230. https://doi.org/10.1016/j.bbrc.2007.03.125

Gonçalves, D.U., Proietti, F.A., Ribas, J.G.R., Araújo, M.G., Pinheiro, S.R., Guedes, A.C., Carneiro-Proietti, A.B.F., 2010. Epidemiology, Treatment, and Prevention of Human T-Cell Leukemia Virus Type 1-Associated Diseases. Clin. Microbiol. Rev. 23, 577–589. https://doi.org/10.1128/CMR.00063-09

Grinev, V.V., Barneh, F., Ilyushonak, I.M., Nakjang, S., Smink, J., van Oort, A., Clough, R., Seyani, M., McNeill, H., Reza, M., Martinez-Soria, N., Assi, S.A., Ramanouskaya, T.V., Bonifer, C., Heidenreich, O., 2021. RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia. Nat. Commun. 12, 520. https://doi.org/10.1038/s41467-020-20848-z
Gross, C., Thoma-Kress, A.K., 2016. Molecular Mechanisms of HTLV-1 Cell-to-Cell Transmission. Viruses 8, 74. https://doi.org/10.3390/v8030074

Grossman, W.J., Kimata, J.T., Wong, F.H., Zutter, M., Ley, T.J., Ratner, L., 1995. Development of leukemia in mice transgenic for the tax gene of human T-cell leukemia virus type I. Proc. Natl. Acad. Sci. U. S. A. 92, 1057-1061. https://doi.org/10.1073/pnas.92.4.1057

Groussaud, D., Khair, M., Tollenaere, A.I., Waast, L., Kuo, M.-S., Mangeney, M., Martella, C., Fardini, Y., Coste, S., Souidi, M., Benit, L., Pique, C., Issad, T., 2017. Hijacking of the O-GlcNAcZYME complex by the HTLV-1 Tax oncoprotein facilitates viral transcription. PLoS Pathog. 13, e1006518. https://doi.org/10.1371/journal.ppat.1006518

Grumont, R.J., Gerondakis, S., 1994. The subunit composition of NF-kappa B complexes changes during B-cell development. Cell Growth Differ. Mol. Biol. J. Am. Assoc. Cancer Res. 5, 1321-1331.

Gu, B., Eick, D., Bensaude, O., 2013. CTD serine-2 plays a critical role in splicing and termination factor recruitment to RNA polymerase II in vivo. Nucleic Acids Res. 41, 1591-1603. https://doi.org/10.1093/nar/gks1327

Guo, Y., Monahan, K., Wu, H., Gertz, J., Varley, K.E., Li, W., Myers, R.M., Maniatis, T., Wu, Q., 2012. CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice. Proc. Natl. Acad. Sci. 109, 21081-21086. https://doi.org/10.1073/pnas.1219280110

Guo, Y.E., Manteiga, J.C., Henninger, J.E., Sabari, B.R., Dall'Agnese, A., Hannett, N.M., Spille, J.-H., Afeyan, L.K., Zamudio, A.V., Shrinivas, K., Abraham, B.J., Boija, A., Decker, T.-M., Rimel, J.K., Fant, C.B., Lee, T.I., Cisse, I.I., Sharp, P.A., Taatjes, D.J., Young, R.A., 2019. Pol II phosphorylation regulates a switch between transcriptional and splicing condensates. Nature 572, 543-548. https://doi.org/10.1038/s41586-019-1464-0

Guo, Z., Boekhoudt, G.H., Boss, J.M., 2003. Role of the intronic enhancer in tumor necrosis factor-mediated induction of manganous superoxide dismutase. J. Biol. Chem. 278, 23570-23578. https://doi.org/10.1074/jbc.M303431200

Hakim, O., Sung, M.-H., Nakayamada, S., Voss, T.C., Baek, S., Hager, G.L., 2013. Spatial congregation of STAT binding directs selective nuclear architecture during T-cell functional differentiation. Genome Res. 23, 462-472. https://doi.org/10.1101/gr.147652.112

Han, H., Braunschweig, U., Gonatopoulos-Pournatzis, T., Weatheritt, R.J., Hirsch, C.L., Ha, K.C.H., Radovani, E., Nabeel-Shah, S., Sterne-Weiler, T., Wang, J., O'Hanlon, D., Pan, Q., Ray, D., Zheng, H., Vizeacoumar, F., Datti, A., Magomedova, L., Cummins, C.L., Hughes, T.R., Greenblatt, J.F., Wrana, J.L., Moffat, J., Blencowe, B.J., 2017. Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors. Mol. Cell 65, 539-553.e7. https://doi.org/10.1016/j.molcel.2017.01.011

Han, X., Yu, D., Gu, R., Jia, Y., Wang, Q., Jaganathan, A., Yang, X., Yu, M., Babault, N., Zhao, C., Yi, H., Zhang, Q., Zhou, M.-M., Zeng, L., 2020. Roles of the BRD4 short isoform in phase
separation and active gene transcription. Nat. Struct. Mol. Biol. 27, 333-341.
https://doi.org/10.1038/s41594-020-0394-8

Hansen, A.S., Hsieh, T.-H.S., Cattoglio, C., Pustova, I., Saldaña-Meyer, R., Reinberg, D., Darzacq, X., Tjian, R., 2019. Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. Mol. Cell 76, 395-411.e13.
https://doi.org/10.1016/j.molcel.2019.07.039

Harhaj, E.W., Good, L., Xiao, G., Sun, S.-C., 1999. Gene expression profiles in HTLV-I-immortalized T cells: deregulated expression of genes involved in apoptosis regulation. Oncogene 18, 1341-1349. https://doi.org/10.1038/sj.onc.1202405

Hasegawa, H., Sawa, H., Lewis, M.J., Orba, Y., Sheehy, N., Yamamoto, Y., Ichinohe, T., Tsunetsugu-Yokota, Y., Katano, H., Takahashi, H., Matsuda, J., Sata, T., Kurata, T., Nagashima, K., Hall, W.W., 2006. Thymus-derived leukemia-lymphoma in mice transgenic for the Tax gene of human T-lymphotropic virus type I. Nat. Med. 12, 466-472. https://doi.org/10.1038/nm1389

Hayden, M.S., Ghosh, S., 2008. Shared Principles in NF-κB Signaling. Cell 132, 344-362.
https://doi.org/10.1016/j.cell.2008.01.020

Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H., Glass, C.K., 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589. https://doi.org/10.1016/j.molcel.2010.05.004

Hemmings, B.A., Restuccia, D.F., 2012. PI3K-PKB/Akt Pathway. Cold Spring Harb. Perspect. Biol. 4, a011189. https://doi.org/10.1101/cshperspect.a011189

Henikoff, S., Smith, M.M., 2015. Histone Variants and Epigenetics. Cold Spring Harb. Perspect. Biol. 7, a019364. https://doi.org/10.1101/cshperspect.a019364

Henninger, J.E., Oksuz, O., Shrinivas, K., Sagi, I., LeRoy, G., Zheng, M.M., Andrews, J.O., Zamudio, A.V., Lazaris, C., Hannett, N.M., Lee, T.I., Sharp, P.A., Cissé, I.I., Chakraborty, A.K., Young, R.A., 2021. RNA-Mediated Feedback Control of Transcriptional Condensates. Cell 184, 207-225.e24. https://doi.org/10.1016/j.cell.2020.11.030

Higuchi, M., Tsubata, C., Kondo, R., Yoshida, S., Takahashi, M., Oie, M., Tanaka, Y., Mahieux, R., Matsuoka, M., Fujii, M., 2007. Cooperation of NF-kappaB2/p100 activation and the PDZ domain binding motif signal in human T-cell leukemia virus type 1 (HTLV-1) Tax1 but not HTLV-2 Tax2 is crucial for interleukin-2-independent growth transformation of a T-cell line. J. Virol. 81, 11900-11907. https://doi.org/10.1128/JVI.00532-07

Hnilicová, J., Hozeifi, S., Dušková, E., Icha, J., Tománková, T., Staněk, D., 2011. Histone Deacetylase Activity Modulates Alternative Splicing. PLOS ONE 6, e16727.
https://doi.org/10.1371/journal.pone.0016727
Hnisz, D., Shrinivas, K., Young, R.A., Chakraborty, A.K., Sharp, P.A., 2017. A phase separation model predicts key features of transcriptional control. Cell 169, 13–23.
https://doi.org/10.1016/j.cell.2017.02.007

Hoesel, B., Schmid, J.A., 2013. The complexity of NF-κB signaling in inflammation and cancer. Mol. Cancer 12, 86. https://doi.org/10.1186/1476-4598-12-86

Hondele, M., Sachdev, R., Heinrich, S., Wang, J., Vallotton, P., Fontoura, B.M.A., Weis, K., 2019. DEAD-box ATPases are global regulators of phase-separated organelles. Nature 573, 144–148. https://doi.org/10.1038/s41586-019-1502-y

Hong, L., Schroth, G.P., Matthews, H.R., Yau, P., Bradbury, E.M., 1993. Studies of the DNA binding properties of histone H4 amino terminus. Thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 “tail” to DNA. J. Biol. Chem. 268, 305–314.

Hong, X., Scofield, D.G., Lynch, M., 2006. Intron Size, Abundance, and Distribution within Untranslated Regions of Genes. Mol. Biol. Evol. 23, 2392–2404.
https://doi.org/10.1093/molbev/msl111

Hönig, A., Auboeuf, D., Parker, M.M., O'Malley, B.W., Berget, S.M., 2002. Regulation of Alternative Splicing by the ATP-Dependent DEAD-Box RNA Helicase p72. Mol. Cell. Biol. 22, 5698–5707. https://doi.org/10.1128/MCB.22.16.5698-5707.2002

Hozak, P., Cook, P.R., Schofer, C., Mosgoller, W., Wachtler, F., 1994. Site of transcription of ribosomal RNA and intranucleolar structure in HeLa cells. J. Cell Sci. 107, 639–648.
https://doi.org/10.1242/jcs.107.2.639

Hu, Q., Kim, E.J., Feng, J., Grant, G.R., Heller, E.A., 2017. Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain. PLOS Comput. Biol. 13, e1005602. https://doi.org/10.1371/journal.pcbi.1005602

Huang, B., Yang, X.-D., Lamb, A., Chen, L.-F., 2010. Posttranslational modifications of NF-κB: another layer of regulation for NF-κB signaling pathway. Cell. Signal. 22, 1282–1290.
https://doi.org/10.1016/j cellsig.2010.03.017

Huang, J., Ren, T., Guan, H., Jiang, Y., Cheng, H., 2009. HTLV-1 Tax is a critical lipid raft modulator that hijacks IkappaB kinases to the microdomains for persistent activation of NF-kappaB. J. Biol. Chem. 284, 6208–6217.
https://doi.org/10.1074/jbc.M806390200

Huang, Y., Li, W., Yao, X., Lin, Q., Yin, J., Liang, Y., Heiner, M., Tian, B., Hui, J., Wang, G., 2012. Mediator Complex Regulates Alternative mRNA Processing via the Med23 Subunit. Mol. Cell 45, 459–469. https://doi.org/10.1016/j.molcel.2011.12.022

Huo, X., Ji, L., Zhang, Y., Lv, P., Cao, X., Wang, Q., Yan, Z., Dong, S., Du, D., Zhang, F., Wei, G., Liu, Y., Wen, B., 2020. The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation. Mol. Cell 77, 368-383.e7. https://doi.org/10.1016/j.molcel.2019.10.001
Iborra, F.J., Pombo, A., Jackson, D.A., Cook, P.R., 1996. Active RNA polymerases are localized within discrete transcription "factories" in human nuclei. J. Cell Sci. 109, 1427-1436.
https://doi.org/10.1242/jcs.109.6.1427

Igakura, T., Stinchcombe, J.C., Goon, P.K.C., Taylor, G.P., Weber, J.N., Griffiths, G.M., Tanaka, Y., Osame, M., Bangham, C.R.M., 2003. Spread of HTLV-I between lymphocytes by virus-induced polarization of the cytoskeleton. Science 299, 1713-1716.
https://doi.org/10.1126/science.1080115

Ilik, İ.A., Malszycki, M., Lübke, A.K., Schade, C., Meierhofer, D., Aktaş, T., 2020. SON and SRRM2 are essential for nuclear speckle formation. eLife 9, e60579.
https://doi.org/10.7554/eLife.60579

Ip, J.Y., Schmidt, D., Pan, Q., Ramani, A.K., Fraser, A.G., Odom, D.T., Blencowe, B.J., 2011. Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res. 21, 390-401. https://doi.org/10.1101/gr.111070.110

Ishov, A.M., Gurumurthy, A., Bungert, J., 2020. Coordination of transcription, processing, and export of highly expressed RNAs by distinct biomolecular condensates. Emerg. Top. Life Sci. 4, 281-291. https://doi.org/10.1042/ETLS20190160

Itabashi, K., Miyazawa, T., 2021. Mother-to-Child Transmission of Human T-Cell Leukemia Virus Type 1: Mechanisms and Nutritional Strategies for Prevention. Cancers 13, 4100.
https://doi.org/10.3390/cancers13164100

Iwai, K., Mori, N., Oie, M., Yamamoto, N., Fujii, M., 2001. Human T-Cell Leukemia Virus Type 1 Tax Protein Activates Transcription through AP-1 Site by Inducing DNA Binding Activity in T Cells. Virology 279, 38-46. https://doi.org/10.1006/viro.2000.0669

Iwanaga, R., Ozono, E., Fujisawa, J., Ikeda, M.-A., Okamura, N., Huang, Y., Ohtani, K., 2008. Activation of the cyclin D2 and cdk6 genes through NF-??B is critical for cell-cycle progression induced by HTLV-I Tax. Oncogene 27, 5635-42.
https://doi.org/10.1038/onc.2008.174

Jackson, D.A., Hassan, A.B., Errington, R.J., Cook, P.R., 1993. Visualization of focal sites of transcription within human nuclei. EMBO J. 12, 1059-1065.

Jackson, D.A., Iborra, F.J., Manders, E.M.M., Cook, P.R., 1998. Numbers and Organization of RNA Polymerases, Nascent Transcripts, and Transcription Units in HeLa Nuclei. Mol. Biol. Cell 9, 1523-1536.

Jeang, K.T., Widen, S.G., Semmes, O.J., Wilson, S.H., 1990. HTLV-I trans-activator protein, tax, is a trans-repressor of the human beta-polymerase gene. Science 247, 1082-1084.
https://doi.org/10.1126/science.2309119

Jeong, S.-J., Lu, H., Cho, W.-K., Park, H.U., Pise-Masison, C., Brady, J.N., 2006. Coactivator-Associated Arginine Methyltransferase 1 Enhances Transcriptional Activity of the Human T-Cell Lymphotropic Virus Type 1 Long Terminal Repeat through Direct Interaction with Tax. J. Virol. 80, 10036-10044. https://doi.org/10.1128/JVI.00186-06
Jiang, H., Lu, H., Schiltz, R.L., Pise-Masison, C.A., Ogryzko, V.V., Nakatani, Y., Brady, J.N., 1999. PCAF interacts with tax and stimulates tax transactivation in a histone acetyltransferase-independent manner. Mol. Cell. Biol. 19, 8136-8145.
https://doi.org/10.1128/MCB.19.12.8136

Jin, D.Y., Giordano, V., Kibler, K.V., Nakano, H., Jeang, K.T., 1999. Role of adapter function in oncoprotein-mediated activation of NF-kappaB. Human T-cell leukemia virus type I Tax interacts directly with IkappaB kinase gamma. J. Biol. Chem. 274, 17402-17405.
https://doi.org/10.1074/jbc.274.25.17402

Jin, D.Y., Teramoto, H., Giam, C.Z., Chun, R.F., Gutkind, J.S., Jeang, K.T., 1997. A human suppressor of c-Jun N-terminal kinase 1 activation by tumor necrosis factor alpha. J. Biol. Chem. 272, 25816-25823. https://doi.org/10.1074/jbc.272.41.25816

Jin, F., Li, Y., Dixon, J.R., Selvaraj, S., Ye, Z., Lee, A.Y., Yen, C.-A., Schmitt, A.D., Espinoza, C.A., Ren, B., 2013. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503, 290-294. https://doi.org/10.1038/nature12644

Jones, K.S., Fugo, K., Petrow-Sadowski, C., Huang, Y., Bertolette, D.C., Lisinski, I., Cushman, S.W., Jacobson, S., Ruscetti, F.W., 2006. Human T-Cell Leukemia Virus Type 1 (HTLV-1) and HTLV-2 Use Different Receptor Complexes To Enter T Cells. J. Virol. 80, 8291-8302.
https://doi.org/10.1128/JVI.00389-06

Jones, K.S., Petrow-Sadowski, C., Bertolette, D.C., Huang, Y., Ruscetti, F.W., 2005. Heparan sulfate proteoglycans mediate attachment and entry of human T-cell leukemia virus type 1 virions into CD4+ T cells. J. Virol. 79, 12692-12702.
https://doi.org/10.1128/JVI.79.20.12692-12702.2005

Jones, P.L., Ping, D., Boss, J.M., 1997. Tumor necrosis factor alpha and interleukin-1beta regulate the murine manganese superoxide dismutase gene through a complex intronic enhancer involving C/EBP-beta and NF-kappaB. Mol. Cell. Biol. 17, 6970-6981.
https://doi.org/10.1128/MCB.17.12.6970

Journo, C., Filipe, J., About, F., Chevalier, S.A., Afonso, P.V., Brady, J.N., Flynn, D., Tangy, F., Israël, A., Vidalain, P.-O., Mahieux, R., Weil, R., 2009. NRP/Optineurin Cooperates with TAX1BP1 to Potentiate the Activation of NF-κB by Human T-Lymphotropic Virus Type 1 Tax Protein. PLoS Pathog. 5, e1000521. https://doi.org/10.1371/journal.ppat.1000521

Kamoi, K., Yamamoto, K., Misawa, A., Miyake, A., Ishida, T., Tanaka, Y., Mochizuki, M., Watanabe, T., 2006. SUV39H1 interacts with HTLV-1 Tax and abrogates Tax transactivation of HTLV-1 LTR. Retrovirology 3, 5. https://doi.org/10.1186/1742-4690-3-5

Kao, S.Y., Marriott, S.J., 1999. Disruption of nucleotide excision repair by the human T-cell leukemia virus type 1 Tax protein. J. Virol. 73, 4299-4304.
https://doi.org/10.1128/JVI.73.5.4299-4304.1999

Kar, A., Fushimi, K., Zhou, X., Ray, P., Shi, C., Chen, X., Liu, Z., Chen, S., Wu, J.Y., 2011. RNA Helicase p68 (DDX5) Regulates tau Exon 10 Splicing by Modulating a Stem-Loop
Structure at the 5' Splice Site. Mol. Cell. Biol. 31, 1812-1821.
https://doi.org/10.1128/MCB.01149-10

Karki, S., Banerjee, S., Mclean, K., Dinner, A., Clark, M.R., 2019a. Transcription factories in Igk allelic choice and diversity. Adv. Immunol. 141, 33-49.
https://doi.org/10.1016/bs.ai.2018.11.001

Karki, S., Banerjee, S., Mclean, K., Dinner, A., Clark, M.R., 2019b. Chapter Two - Transcription factories in Igk allelic choice and diversity, in: Alt, F. (Ed.), Advances in Immunology. Academic Press, pp. 33-49. https://doi.org/10.1016/bs.ai.2018.11.001

Kataoka, K., Nagata, Y., Kitanaka, A., Shiraishi, Y., Shimamura, T., Yasunaga, J., Totoki, Y., Chiba, K., Sato-Otsubo, A., Nagae, G., Ishii, R., Muto, S., Kotani, S., Watatani, Y., Takeda, J., Sanada, M., Tanaka, H., Suzuki, H., Sato, Y., Shiozawa, Y., Yoshizato, T., Yoshida, K., Makishima, H., Iwanaga, M., Ma, G., Nosaka, K., Hishizawa, M., Itonaga, H., Imaizumi, Y., Munakata, W., Ogasawara, H., Sato, T., Sasai, K., Muramoto, K., Penova, M., Kawaguchi, T., Nakamura, H., Hama, N., Shide, K., Kubuki, Y., Hidaka, T., Kameda, T., Nakamaki, T., Ishiyama, K., Miyawaki, S., Yoon, S.-S., Tobinai, K., Miyazaki, Y., Takaori-Kondo, A., Matsuda, F., Takeuchi, K., Nureki, O., Aburatani, H., Watanabe, T., Shibata, T., Matsuoka, M., Miyano, S., Shimoda, K., Ogawa, S., 2015. Integrated molecular analysis of adult T cell leukemia/lymphoma. Nat. Genet. 47, 1304-1315.
https://doi.org/10.1038/ng.3415

Khan, D.H., Gonzalez, C., Cooper, C., Sun, J.-M., Chen, H.Y., Healy, S., Xu, W., Smith, K.T., Workman, J.L., Leygue, E., Davie, J.R., 2014. RNA-dependent dynamic histone acetylation regulates MCL1 alternative splicing. Nucleic Acids Res. 42, 1656-1670.
https://doi.org/10.1093/nar/gkt1134

Khodor, Y.L., Rodriguez, J., Abruzzi, K.C., Tang, C.-H.A., Marr, M.T., Rosbash, M., 2011. Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. Genes Dev. 25, 2502-2512. https://doi.org/10.1101/gad.178962.111

Kibler, K.V., Jeang, K.T., 2001. CREB/ATF-dependent repression of cyclin a by human T-cell leukemia virus type 1 Tax protein. J. Virol. 75, 2161-2173.
https://doi.org/10.1128/JVI.75.5.2161-2173.2001

Kikutake, C., Suyama, M., 2022. Pan-cancer analysis of mutations in open chromatin regions and their possible association with cancer pathogenesis. Cancer Med. 11, 3902-3916.
https://doi.org/10.1002/cam4.4749

Kim, J., Venkata, N.C., Hernandez Gonzalez, G.A., Khanna, N., Belmont, A.S., 2019. Gene expression amplification by nuclear speckle association. J. Cell Biol. 219, e201904046.
https://doi.org/10.1083/jcb.201904046

Kim, J.-W., Jang, S.-M., Kim, C.-H., An, J.-H., Kang, E.-J., Choi, K.-H., 2012. New Molecular Bridge between RelA/p65 and NF-κB Target Genes via Histone Acetyltransferase TIP60 Cofactor. J. Biol. Chem. 287, 7780-7791. https://doi.org/10.1074/jbc.M111.278465
Kim, S., Shendure, J., 2019. Mechanisms of Interplay between Transcription Factors and the 3D Genome. Mol. Cell 76, 306-319. https://doi.org/10.1016/j.molcel.2019.08.010

Kim, S.J., Kehrl, J.H., Burton, J., Tendler, C.L., Jeang, K.T., Danielpour, D., Thevenin, C., Kim, K.Y., Sporn, M.B., Roberts, A.B., 1990. Transactivation of the transforming growth factor beta 1 (TGF-beta 1) gene by human T lymphotropic virus type 1 tax: a potential mechanism for the increased production of TGF-beta 1 in adult T cell leukemia. J. Exp. Med. 172, 121-129. https://doi.org/10.1084/jem.172.1.121

Kinjo, T., Ham-Terhune, J., Peloponese, J.-M., Jeang, K.-T., 2010. Induction of Reactive Oxygen Species by Human T-Cell Leukemia Virus Type 1 Tax Correlates with DNA Damage and Expression of Cellular Senescence Marker. J. Virol. 84, 5431-5437. https://doi.org/10.1128/JVI.02460-09

Kirk, P.D.W., Huvet, M., Melamed, A., Maertens, G.N., Bangham, C.R.M., 2016. Retroviruses integrate into a shared, non-palindromic DNA motif. Nat. Microbiol. 2, 1-6. https://doi.org/10.1038/nmicrobiol.2016.212

Kitajima, I., Shinohara, T., Bilakovics, J., Brown, D.A., Xu, X., Nerenberg, M., 1992. Ablation of Transplanted HTLV-I Tax-Transformed Tumors in Mice by Antisense Inhibition of NF-κB. Science 258, 1792-1795. https://doi.org/10.1126/science.1299224

Kogure, Y., Kataoka, K., 2017. Genetic alterations in adult T-cell leukemia/lymphoma. Cancer Sci. 108, 1719-1725. https://doi.org/10.1111/cas.13303

Kolasinska-Zwierz, P., Down, T., Latorre, I., Liu, T., Liu, X.S., Ahringer, J., 2009. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat. Genet. 41, 376-381. https://doi.org/10.1038/ng.322

Kolovos, P., Georgomanolis, T., Koeferle, A., Larkin, J.D., Brant, L., Nikolicć, M., Gusmao, E.G., Zirkel, A., Knoch, T.A., van Ijcken, W.F., Cook, P.R., Costa, I.G., Grosveld, F.G., Papantonis, A., 2016. Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response. Genome Res. 26, 1478-1489. https://doi.org/10.1101/gr.210005.116

Kornbliytt, A.R., Schor, I.E., Alló, M., Dujardin, G., Petrillo, E., Muñoz, M.J., 2013. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat. Rev. Mol. Cell Biol. 14, 153-165. https://doi.org/10.1038/nrm3525

Koyanagi, Y., Itoyama, Y., Nakamura, N., Takamatsu, K., Kira, J.-I., Iwamasa, T., Goto, I., Yamamoto, N., 1993. In Vivo Infection of Human T-Cell Leukemia Virus Type I in Non-T Cells. Virology 196, 25-33. https://doi.org/10.1006/viro.1993.1451

Kuo, L.J., Yang, L.-X., 2008. Gamma-H2AX - a novel biomarker for DNA double-strand breaks. Vivo Athens Greece 22, 305-309.

Kuo, Y.-L., Giam, C.-Z., 2006. Activation of the anaphase promoting complex by HTLV-1 tax leads to senescence. EMBO J. 25, 1741-1752. https://doi.org/10.1038/sj.emboj.7601054
Kurita, D., Yasunaga, J., Tanaka, A., Mohamed, M., Matsuoka, M., 2018. Dynamic Changes of Chromatin Structure and Transcriptome By Transient Expression of HTLV-1 Tax in ATL Cells. Blood 132, 4094. https://doi.org/10.1182/blood-2018-99-11125

Lambert, M.-P., Terrone, S., Giraud, G., Benoit-Pilven, C., Cluet, D., Combaret, V., Mortreux, F., Auboeuf, D., Bourgeois, C.F., 2018. The RNA helicase DDX17 controls the transcriptional activity of REST and the expression of proneural microRNAs in neuronal differentiation. Nucleic Acids Res. 46, 7686-7700. https://doi.org/10.1093/nar/gky545

Lambert, S., Bouttier, M., Vassy, R., Seigneuret, M., Petrow-Sadowski, C., Janvier, S., Heveker, N., Ruscetti, F.W., Perret, G., Jones, K.S., Pique, C., 2009. HTLV-1 uses HSPG and neuropilin-1 for entry by molecular mimicry of VEGF165. Blood 113, 5176-5185. https://doi.org/10.1182/blood-2008-04-150342

Lamsoul, I., Lodewick, J., Lebrun, S., Brasseur, R., Burny, A., Gaynor, R.B., Bex, F., 2005. Exclusive ubiquitination and sumoylation on overlapping lysine residues mediate NF-kappaB activation by the human T-cell leukemia virus tax oncoprotein. Mol. Cell. Biol. 25, 10391-10406. https://doi.org/10.1128/MCB.25.23.10391-10406.2005

Lanoix, J., Lacoste, J., Pepin, N., Rice, N., Hiscott, J., 1994. Overproduction of NFKB2 (lyt-10) and c-Rel: a mechanism for HTLV-I Tax-mediated trans-activation via the NF-kappa B signalling pathway. Oncogene 9, 841-852.

Larkin, J.D., Papantonis, A., Cook, P.R., Marenduzzo, D., 2013. Space exploration by the promoter of a long human gene during one transcription cycle. Nucleic Acids Res. 41, 2216-2227. https://doi.org/10.1093/nar/gks1441

Larson, A.G., Elnatan, D., Keenen, M.M., Trnka, M.J., Johnston, J.B., Burlingame, A.L., Agard, D.A., Redding, S., Narlikar, G.J., 2017. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 547, 236-240. https://doi.org/10.1038/nature22822

Lawrence, T., Bebien, M., Liu, G.Y., Nizet, V., Karin, M., 2005. IKKalpha limits macrophage NF-kappaB activation and contributes to the resolution of inflammation. Nature 434, 1138-1143. https://doi.org/10.1038/nature03491

Lee, D.K., Kim, B.-C., Brady, J.N., Jeang, K.-T., Kim, S.-J., 2002. Human T-cell lymphotropic virus type 1 tax inhibits transforming growth factor-beta signaling by blocking the association of Smad proteins with Smad-binding element. J. Biol. Chem. 277, 33766-33775. https://doi.org/10.1074/jbc.M200150200

Lee, J.-H., Wang, R., Xiong, F., Krakowiak, J., Liao, Z., Nguyen, P.T., Moroz-Omori, E.V., Shao, J., Zhu, X., Bolt, M.J., Wu, H., Singh, P.K., Bi, M., Shi, C.J., Jamal, N., Li, G., Mistry, R., Jung, S.Y., Tsai, K.-L., Ferreon, J.C., Stossi, F., Caflisch, A., Liu, Z., Mancini, M.A., Li, W., 2021. Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. Mol. Cell 81, 3368-3385.e9. https://doi.org/10.1016/j.molcel.2021.07.024
Lee, Y., Rio, D.C., 2015. Mechanisms and Regulation of Alternative Pre-mRNA Splicing. Annu. Rev. Biochem. 84, 291–323. https://doi.org/10.1146/annurev-biochem-060614-034316

Lemasson, I., Polakowski, N.J., Laybourn, P.J., Nyborg, J.K., 2006. Tax-dependent displacement of nucleosomes during transcriptional activation of human T-cell leukemia virus type 1. J. Biol. Chem. 281, 13075–13082. https://doi.org/10.1074/jbc.M512193200

Leung, T.H., Hoffmann, A., Baltimore, D., 2004. One Nucleotide in a κB Site Can Determine Cofactor Specificity for NF-κB Dimers. Cell 118, 453–464. https://doi.org/10.1016/j.cell.2004.08.007

Li, G., Ruan, X., Auerbach, R.K., Sandhu, K.S., Zheng, M., Wang, P., Poh, H.M., Goh, Y., Lim, J., Zhang, J., Sim, H.S., Peh, S.Q., Mulawadi, F.H., Ong, C.T., Orlov, Y.L., Hong, S., Zhang, Z., Landt, S., Raha, D., Euskirchen, G., Wei, C.-L., Ge, W., Wang, H., Davis, C., Fisher, K., Mortazavi, A., Gerstein, M., Gingeras, T., Wold, B., Sun, Y., Fullwood, M.J., Cheung, E., Liu, E., Sung, W.-K., Snyder, M., Ruan, Y., 2012. Extensive Promoter-centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell 148, 84–98. https://doi.org/10.1016/j.cell.2011.12.014

Li, X., Zhao, Y., Tian, B., Jamaluddin, M., Mitra, A., Yang, J., Rowicka, M., Brasier, A.R., Kudlicki, A., 2014. Modulation of Gene Expression Regulated by the Transcription Factor NF-κB/RelA. J. Biol. Chem. 289, 11927–11944. https://doi.org/10.1074/jbc.M113.539965

Liao, S.E., Regev, O., 2021. Splicing at the phase-separated nuclear speckle interface: a model. Nucleic Acids Res. 49, 636–645. https://doi.org/10.1093/nar/gkaa1209

Lieberman-Aiden, E., van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O., Sandstrom, R., Bernstein, B., Bender, M.A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J., Mirny, L.A., Lander, E.S., Dekker, J., 2009. Comprehensive mapping of long range interactions reveals folding principles of the human genome. Science 326, 289–293. https://doi.org/10.1126/science.1181369

Lim, C.-A., Yao, F., Wong, J.J.-Y., George, J., Xu, H., Chiu, K.P., Sung, W.-K., Lipovich, L., Vega, V.B., Chen, J., Shahab, A., Zhao, X.D., Hibberd, M., Wei, C.-L., Lim, B., Ng, H.-H., Ruan, Y., Chin, K.-C., 2007. Genome-wide Mapping of RELA(p65) Binding Identifies E2F1 as a Transcriptional Activator Recruited by NF-κB upon TLR4 Activation. Mol. Cell 27, 622–635. https://doi.org/10.1016/j.molcel.2007.06.038

Lin, C., Yang, L., Yang, J.J., Huang, Y., Liu, Z.-R., 2005. ATPase/Helicase Activities of p68 RNA Helicase Are Required for Pre-mRNA Splicing but Not for Assembly of the Spliceosome. Mol. Cell. Biol. 25, 7484–7493. https://doi.org/10.1128/MCB.25.17.7484-7493.2005

Lin, H.-C., Hickey, M., Hsu, L., Medina, D., Rabson, A.B., 2005. Activation of human T cell leukemia virus type 1 LTR promoter and cellular promoter elements by T cell receptor signaling and HTLV-1 Tax expression. Virology 339, 1–11. https://doi.org/10.1016/j.virol.2005.05.015
Lin, R., Gewert, D., Hiscott, J., 1995. Differential Transcriptional Activation in Vitro by NF-κB/Rel Proteins (*). J. Biol. Chem. 270, 3123–3131. https://doi.org/10.1074/jbc.270.7.3123

Lin, S., Coutinho-Mansfield, G., Wang, D., Pandit, S., Fu, X.-D., 2008. The splicing factor SC35 has an active role in transcriptional elongation. Nat. Struct. Mol. Biol. 15, 819–826. https://doi.org/10.1038/nsmb.1461

Liu, Y., Nanni, L., Sungalee, S., Zufferey, M., Tavernari, D., Mina, M., Ceri, S., Oricchio, E., Ciriello, G., 2021. Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes. Nat. Commun. 12, 2439. https://doi.org/10.1038/s41467-021-22666-3

Liu, Y., Wang, Y., Yamakuchi, M., Masuda, S., Tokioka, T., Yamaoka, S., Maruyama, I., Kitajima, I., 2001. Phosphoinositide-3 kinase-PKB/Akt pathway activation is involved in fibroblast Rat-1 transformation by human T-cell leukemia virus type I tax. Oncogene 20, 2514–2526. https://doi.org/10.1038/sj.onc.1204364

Llères, D., Moindrot, B., Pathak, R., Piras, V., Matelot, M., Pignard, B., Marchand, A., Poncelet, M., Perrin, A., Tellier, V., Feil, R., Noordermeer, D., 2019. CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains. Genome Biol. 20, 272. https://doi.org/10.1186/s13059-019-1896-8

Lodewick, J., Lamsoul, I., Polania, A., Lebrun, S., Burny, A., Ratner, L., Bex, F., 2009. Acetylation of the human T-cell leukemia virus type 1 Tax oncoprotein by p300 promotes activation of the NF-kappaB pathway. Virology 386, 68–78. https://doi.org/10.1016/j.virol.2008.12.043

Long, J.C., Caceres, J.F., 2008. The SR protein family of splicing factors: master regulators of gene expression. Biochem. J. 417, 15–27. https://doi.org/10.1042/BJ20081501

Longo, D.L., Gelmann, E.P., Cossman, J., Young, R.A., Gallo, R.C., O’Brien, S.J., Matis, L.A., 1984. Isolation of HTLV-transformed B-lymphocyte clone from a patient with HTLV-associated adult T-cell leukaemia. Nature 310, 505–506. https://doi.org/10.1038/310505a0

Loomis, R.J., Naoe, Y., Parker, J.B., Savic, V., Bozovsky, M.R., Macfarlan, T., Manley, J.L., Chakravarti, D., 2009. Chromatin Binding of SRp20 and ASF/SF2 and Dissociation from Mitotic Chromosomes Is Modulated by Histone H3 Serine 10 Phosphorylation. Mol. Cell 33, 450–461. https://doi.org/10.1016/j.molcel.2009.02.003

Lu, H., Pise-Masison, C.A., Linton, R., Park, H.U., Schiltz, R.L., Sartorelli, V., Brady, J.N., 2004. Tax relieves transcriptional repression by promoting histone deacetylase 1 release from the human T-cell leukemia virus type 1 long terminal repeat. J. Virol. 78, 6735–6743. https://doi.org/10.1128/JVI.78.13.6735-6743.2004

Lu, X., Chen, Q., Liu, H., Zhang, X., 2021. Interplay Between Non-Canonical NF-κB Signaling and Hepatitis B Virus Infection. Front. Immunol. 12.
Luco, R.F., Pan, Q., Tominaga, K., Blencowe, B.J., Pereira-Smith, O.M., Misteli, T., 2010. Regulation of Alternative Splicing by Histone Modifications. Science 327, 996–1000. https://doi.org/10.1126/science.1184208

Luger, K., Mäder, A.W., Richmond, R.K., Sargent, D.F., Richmond, T.J., 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260. https://doi.org/10.1038/38444

Lunning, M.A., Mehta-Shah, N., Horwitz, S.M., 2020. Adult T-Cell Leukemia/Lymphoma, in: Abeloff's Clinical Oncology. Elsevier, pp. 1965-1974.e3. https://doi.org/10.1016/B978-0-323-47674-4.00105-5

Lupiáñez, D.G., Kraft, K., Heinrich, V., Krawitz, P., Brancati, F., Klopocki, E., Horn, D., Kayserili, H., Opitz, J.M., Laxova, R., Santos-Simarro, F., Gilbert-Dussardier, B., Wittler, L., Borschiwer, M., Haas, S.A., Osterwalder, M., Franke, M., Timmermann, B., Hecht, J., Spielmann, M., Visel, A., Mundlos, S., 2015. Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions. Cell 161, 1012–1025. https://doi.org/10.1016/j.cell.2015.04.004

Lyngdoh, D.L., Shukla, H., Sonkar, A., Anupam, R., Tripathi, T., 2019. Portrait of the Intrinsically Disordered Side of the HTLV-1 Proteome. ACS Omega 4, 10003–10018. https://doi.org/10.1021/acsomega.9b01017

Maeda, M., Tanabe-Shibuya, J., Miyazato, P., Masutani, H., Yasunaga, J., Usami, K., Shimizu, A., Matsuoka, M., 2020. IL-2/IL-2 Receptor Pathway Plays a Crucial Role in the Growth and Malignant Transformation of HTLV-1-Infected T Cells to Develop Adult T-Cell Leukemia. Front. Microbiol. 11, 356. https://doi.org/10.3389/fmicb.2020.00356

Mahgoub, M., Yasunaga, J., Iwami, S., Nakaoka, S., Koizumi, Y., Shimura, K., Matsuoka, M., 2018. Sporadic on/off switching of HTLV-1 Tax expression is crucial to maintain the whole population of virus-induced leukemic cells. Proc. Natl. Acad. Sci. 115, E1269–E1278. https://doi.org/10.1073/pnas.1715724115

Majorovits, E., Nejmeddine, M., Tanaka, Y., Taylor, G.P., Fuller, S.D., Bangham, C.R.M., 2008. Human T-Lymphotropic Virus-1 Visualized at the Virological Synapse by Electron Tomography. PLOS ONE 3, e2251. https://doi.org/10.1371/journal.pone.0002251

Manel, N., Kim, F.J., Kinet, S., Taylor, N., Sitbon, M., Battini, J.-L., 2003. The Ubiquitous Glucose Transporter GLUT-1 Is a Receptor for HTLV. Cell 115, 449–459. https://doi.org/10.1016/S0092-8674(03)00881-X

Mao, Y.S., Zhang, B., Spector, D.L., 2011. Biogenesis and Function of Nuclear Bodies. Trends Genet. TIG 27, 295–306. https://doi.org/10.1016/j.tig.2011.05.006

Mariner, J.M., Lantz, V., Waldmann, T.A., Azimi, N., 2001. Human T Cell Lymphotropic Virus Type I Tax Activates IL-15Rα Gene Expression Through an NF-κB Site. J. Immunol. 166, 2602–2609. https://doi.org/10.4049/jimmunol.166.4.2602
Marino, M.M., Rega, C., Russo, R., Valletta, M., Gentile, M.T., Esposito, S., Baglivo, I., De Feis, I., Angelini, C., Xiao, T., Felsenfeld, G., Chambery, A., Pedone, P.V., 2019. Interactome mapping defines BRG1, a component of the SWI/SNF chromatin remodeling complex, as a new partner of the transcriptional regulator CTCF. J. Biol. Chem. 294, 861–873.
https://doi.org/10.1074/jbc.RA118.004882

Marriott, S.J., Semmes, O.J., 2005. Impact of HTLV-I Tax on cell cycle progression and the cellular DNA damage repair response. Oncogene 24, 5986–5995.
https://doi.org/10.1038/sj.onc.1208976

Martella, C., Tollenaere, A.I., Waast, L., Lacombe, B., Groussaud, D., Margottin-Goguet, F., Ramirez, B.C., Pique, C., 2020. Human T-Cell Lymphotropic Virus Type 1 Transactivator Tax Exploits the XPB Subunit of TFIIH during Viral Transcription. J. Virol. 94, e02171-19.
https://doi.org/10.1128/JVI.02171-19

Martella, C., Waast, L., Pique, C., 2022. Tax, marionnettiste de la transcription du HTLV-1. médecine/sciences 38, 359–365. https://doi.org/10.1051/medsci/2022039

Martin, E.W., Holehouse, A.S., 2020. Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof. Emerg. Top. Life Sci. 4, 307–329. https://doi.org/10.1042/ETLS20190164

Martin, J.L., Maldonado, J.O., Mueller, J.D., Zhang, W., Mansky, L.M., 2016. Molecular Studies of HTLV-1 Replication: An Update. Viruses 8, 31. https://doi.org/10.3390/v8020031

Martin, S., Pombo, A., 2003. Transcription factories: quantitative studies of nanostructures in the mammalian nucleus. Chromosome Res. Int. J. Mol. Supramol. Evol. Asp. Chromosome Biol. 11, 461–470. https://doi.org/10.1023/a:1024926710797

Martone, R., Euskirchen, G., Bertone, P., Hartman, S., Royce, T.E., Luscombe, N.M., Rinn, J.L., Nelson, F.K., Miller, P., Gerstein, M., Weissman, S., Snyder, M., 2003. Distribution of NF-B-binding sites across human chromosome 22. Proc. Natl. Acad. Sci. 100, 12247–12252.
https://doi.org/10.1073/pnas.2135255100

Matsuo, M., Ueno, T., Monde, K., Sugata, K., Tan, B.J.Y., Rahman, A., Miyazato, P., Uchiyama, K., Islam, S., Katsuya, H., Nakajima, S., Tokunaga, M., Nosaka, K., Hata, H., Utsunomiya, A., Fujisawa, J., Satou, Y., 2022. Identification and characterization of a novel enhancer in the HTLV-1 proviral genome. Nat. Commun. 13, 2405.
https://doi.org/10.1038/s41467-022-30029-9

Matsuoka, M., Jeang, K.-T., 2007. Human T-cell leukaemia virus type 1 (HTLV-1) infectivity and cellular transformation. Nat. Rev. Cancer 7, 270–280. https://doi.org/10.1038/nrc2111

McCracken, S., Fong, N., Yankulov, K., Ballantyne, S., Pan, G., Greenblatt, J., Patterson, S.D., Wickens, M., Bentley, D.L., 1997. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385, 357–361.
https://doi.org/10.1038/385357a0
McGinty, R.K., Tan, S., 2015. Nucleosome Structure and Function. Chem. Rev. 115, 2255-2273.
https://doi.org/10.1021/cr500373h

McManus, C.J., Graveley, B.R., 2011. RNA structure and the mechanisms of alternative splicing.
Curr. Opin. Genet. Dev. 21, 373-379. https://doi.org/10.1016/j.gde.2011.04.001

Melamed, A., Fitzgerald, T.W., Wang, Y., Ma, J., Birney, E., Bangham, C.R.M., 2022. Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription. Sci. Adv. 8, eabm6210.
https://doi.org/10.1126/sciadv.abm6210

Melamed, A., Laydon, D.J., Gillet, N.A., Tanaka, Y., Taylor, G.P., Bangham, C.R.M., 2013. Genome-wide Determinants of Proviral Targeting, Clonal Abundance and Expression in Natural HTLV-1 Infection. PLOS Pathog. 9, e1003271.
https://doi.org/10.1371/journal.ppat.1003271

Melnik, S., Deng, B., Papantonis, A., Baboo, S., Carr, I.M., Cook, P.R., 2011. The proteomes of transcription factories containing RNA polymerases I, II or III. Nat. Methods 8, 963-968.
https://doi.org/10.1038/nmeth.1705

Mercer, T.R., Edwards, S.L., Clark, M.B., Neph, S.J., Wang, H., Stergachis, A.B., John, S., Sandstrom, R., Li, G., Sandhu, K.S., Ruan, Y., Nielsen, L.K., Mattick, J.S., Stamatoyannopoulos, J.A., 2013. DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nat. Genet. 45, 852-859.
https://doi.org/10.1038/ng.2677

Misteli, T., Cáceres, J.F., Spector, D.L., 1997. The dynamics of a pre-mRNA splicing factor in living cells. Nature 387, 523-527. https://doi.org/10.1038/387523a0

Mitchell, J.A., Fraser, P., 2008. Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev. 22, 20-25.
https://doi.org/10.1101/gad.454008

Mizuguchi, M., Asao, H., Hara, T., Higuchi, M., Fujii, M., Nakamura, M., 2009. Transcriptional activation of the interleukin-21 gene and its receptor gene by human T-cell leukemia virus type 1 Tax in human T-cells. J. Biol. Chem. 284, 25501-25511.
https://doi.org/10.1074/jbc.M109.010959

Mocquet, V., Neusiedler, J., Rende, F., Cluet, D., Robin, J.-P., Terme, J.-M., Duc Dodon, M., Wittmann, J., Morris, C., Le Hir, H., Ciminale, V., Jalinot, P., 2012. The Human T-Lymphotropic Virus Type 1 Tax Protein Inhibits Nonsense-Mediated mRNA Decay by Interacting with INT6/EIF3E and UPF1. J. Virol. 86, 7530-7543.
https://doi.org/10.1128/JVI.07021-11

Moen, P.T., Johnson, C.V., Byron, M., Shopland, L.S., de la Serna, I.L., Imbalzano, A.N., Lawrence, J.B., 2004. Repositioning of muscle-specific genes relative to the periphery of SC-35 domains during skeletal myogenesis. Mol. Biol. Cell 15, 197-206.
https://doi.org/10.1091/mbc.e03-06-0388
Moldón, A., Malapeira, J., Gabrielli, N., Gogol, M., Gómez-Escoda, B., Ivanova, T., Seidel, C., Ayté, J., 2008. Promoter-driven splicing regulation in fission yeast. Nature 455, 997–1000. https://doi.org/10.1038/nature07325

Monahan, K., Horta, A., Lomvardas, S., 2019. LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice. Nature 565, 448–453. https://doi.org/10.1038/s41586-018-0845-0

Mori, N., Mukaida, N., Ballard, D.W., Matsushima, K., Yamamoto, N., 1998. Human T-cell leukemia virus type I Tax transactivates human interleukin 8 gene through acting concurrently on AP-1 and nuclear factor-kappaB-like sites. Cancer Res. 58, 3993–4000.

Morris, C., Wittmann, J., Jäck, H.-M., Jalinot, P., 2007. Human INT6/eIF3e is required for nonsense-mediated mRNA decay. EMBO Rep. 8, 596–602. https://doi.org/10.1038/sj.embor.7400955

Morrison, D.K., 2012. MAP Kinase Pathways. Cold Spring Harb. Perspect. Biol. 4, a011254. https://doi.org/10.1101/cshperspect.a011254

Mortillaro, M.J., Blencowe, B.J., Wei, X., Nakayasu, H., Du, L., Warren, S.L., Sharp, P.A., Berezney, R., 1996. A hyperphosphorylated form of the large subunit of RNA polymerase II is associated with splicing complexes and the nuclear matrix. Proc. Natl. Acad. Sci. 93, 8253–8257. https://doi.org/10.1073/pnas.93.16.8253

Mozzherin, D.Ju., Shibutani, S., Tan, C.-K., Downey, K.M., Fisher, P.A., 1997. Proliferating cell nuclear antigen promotes DNA synthesis past template lesions by mammalian DNA polymerase δ. Proc. Natl. Acad. Sci. U. S. A. 94, 6126–6131.

Mulloy, J.C., Kislyakova, T., Cereseto, A., Casareto, L., LoMonico, A., Fullen, J., Lorenzi, M.V., Cara, A., Nicot, C., Giam, C., Franchini, G., 1998. Human T-cell lymphotropic/leukemia virus type 1 Tax abrogates p53-induced cell cycle arrest and apoptosis through its CREB/ATF functional domain. J. Virol. 72, 8852–8860. https://doi.org/10.1128/JVI.72.11.8852-8860.1998

Muñoz, M.J., de la Mata, M., Kornbliytt, A.R., 2010. The carboxy terminal domain of RNA polymerase II and alternative splicing. Trends Biochem. Sci. 35, 497–504. https://doi.org/10.1016/j.tibs.2010.03.010

Murphy, E.L., Lee, T.-H., Chafets, D., Nass, C.C., Wang, B., Loughlin, K., Smith, D., for the HTLV Outcomes Study Investigators, 2004. Higher Human T Lymphotropic Virus (HTLV) Provirus Load Is Associated with HTLV-I versus HTLV-II, with HTLV-II Subtype A versus B, and with Male Sex and a History of Blood Transfusion. J. Infect. Dis. 190, 504–510. https://doi.org/10.1086/422398

Nadella, M.V.P., Shu, S.T., Dirksen, W.P., Thudi, N.K., Nadella, K.S., Fernandez, S.A., Lairmore, M.D., Green, P.L., Rosol, T.J., 2008. Expression of parathyroid hormone-related protein during immortalization of human peripheral blood mononuclear cells by HTLV-1: implications for transformation. Retrovirology 5, 46. https://doi.org/10.1186/1742-4690-5-46
Nakano, K., Ando, T., Yamagishi, M., Yokoyama, K., Ishida, T., Ohsugi, T., Tanaka, Y., Brighty, D.W., Watanabe, T., 2013. Viral interference with host mRNA surveillance, the nonsense-mediated mRNA decay (NMD) pathway, through a new function of HTLV-1 Rex: implications for retroviral replication. Microbes Infect. 15, 491–505. https://doi.org/10.1016/j.micinf.2013.03.006

Natoli, G., Chiocca, S., 2008. Nuclear ubiquitin ligases, NF-kappaB degradation, and the control of inflammation. Sci. Signal. 1, pe1. https://doi.org/10.1126/stke.11pe1

Nogues, G., Kadener, S., Cramer, P., Bentley, D., Kornbliytt, A.R., 2002. Transcriptional activators differ in their abilities to control alternative splicing. J. Biol. Chem. 277, 43110–43114. https://doi.org/10.1074/jbc.M208418200

Nojima, T., Rebelo, K., Gomes, T., Grosso, A.R., Proudfoot, N.J., Carmo-Fonseca, M., 2018. RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing. Mol. Cell 72, 369-379.e4. https://doi.org/10.1016/j.molcel.2018.09.004

Nott, T.J., Petsalaki, E., Farber, P., Jervis, D., Fussner, E., Plochowietz, A., Craggs, T.D., Bazett-Jones, D.P., Pawson, T., Forman-Kay, J.D., Baldwin, A.J., 2015. Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol. Cell 57, 936–947. https://doi.org/10.1016/j.molcel.2015.01.013

Nowak, D.E., Tian, B., Jamaluddin, M., Boldogh, I., Vergara, L.A., Choudhary, S., Brasier, A.R., 2008. RelA Ser276 phosphorylation is required for activation of a subset of NF-kappaB-dependent genes by recruiting cyclin-dependent kinase 9/cyclin T1 complexes. Mol. Cell. Biol. 28, 3623–3638. https://doi.org/10.1128/MCB.01152-07

Ooi, S.L., Priess, J.R., Henikoff, S., 2006. Histone H3.3 Variant Dynamics in the Germline of Caenorhabditis elegans. PLOS Genet. 2, e97. https://doi.org/10.1371/journal.pgen.0020097

Osborne, C.S., Chakalova, L., Brown, K.E., Carter, D., Horton, A., Debrand, E., Goyenechea, B., Mitchell, J.A., Lopes, S., Reik, W., Fraser, P., 2004. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat. Genet. 36, 1065–1071. https://doi.org/10.1038/ng1423

O'Sullivan, J.M., Tan-Wong, S.M., Morillon, A., Lee, B., Coles, J., Mellor, J., Proudfoot, N.J., 2004. Gene loops juxtapose promoters and terminators in yeast. Nat. Genet. 36, 1014–1018. https://doi.org/10.1038/ng1411

Pahl, H.L., 1999. Activators and target genes of Rel/NF-kappaB transcription factors. Oncogene 18, 6853–6866. https://doi.org/10.1038/sj.onc.1203239

Pan, W., Meshcheryakov, V.A., Li, T., Wang, Y., Ghosh, G., Wang, V.Y.-F., 2023. Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation. eLife 12, e86258. https://doi.org/10.7554/eLife.86258
Panfil, A.R., Martinez, M.P., Ratner, L., Green, P.L., 2016. Human T-cell Leukemia Virus-associated Malignancy. Curr. Opin. Virol. 20, 40–46. https://doi.org/10.1016/j.coviro.2016.08.009

Papantonis, A., Cook, P.R., 2013. Transcription Factories: Genome Organization and Gene Regulation. Chem. Rev. 113, 8683–8705. https://doi.org/10.1021/cr300513p

Papantonis, A., Kohro, T., Baboo, S., Larkin, J.D., Deng, B., Short, P., Tsutsumi, S., Taylor, S., Kanki, Y., Kobayashi, M., Li, G., Poh, H.-M., Ruan, X., Aburatani, H., Ruan, Y., Kodama, T., Wada, Y., Cook, P.R., 2012. TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed: Specialized transcription factories. EMBO J. 31, 4404–4414. https://doi.org/10.1038/emboj.2012.288

Papantonis, A., Larkin, J.D., Wada, Y., Ohta, Y., Ihara, S., Kodama, T., Cook, P.R., 2010. Active RNA Polymerases: Mobile or Immobile Molecular Machines? PLOS Biol. 8, e1000419. https://doi.org/10.1371/journal.pbio.1000419

Park, S.-K., Xiang, Y., Feng, X., Garrard, W.T., 2014. Pronounced cohabitation of active immunoglobulin genes from three different chromosomes in transcription factories during maximal antibody synthesis. Genes Dev. 28, 1159–1164. https://doi.org/10.1101/gad.237479.114

Peloponese, J.-M., Iha, H., Yedavalli, V.R.K., Miyazato, A., Li, Y., Haller, K., Benkirane, M., Jeang, K.-T., 2004. Ubiquitination of human T-cell leukemia virus type 1 tax modulates its activity. J. Virol. 78, 11686–11695. https://doi.org/10.1128/JVI.78.21.11686-11695.2004

Peloponese, J.-M., Jeang, K.-T., 2006. Role for Akt/protein kinase B and activator protein-1 in cellular proliferation induced by the human T-cell leukemia virus type 1 tax oncoprotein. J. Biol. Chem. 281, 8927–8938. https://doi.org/10.1074/jbc.M510598200

Pène, S., Waast, L., Bonnet, A., Bénit, L., Pique, C., 2014. A non-SUMOylated tax protein is still functional for NF-κB pathway activation. J. Virol. 88, 10655–10661. https://doi.org/10.1128/JVI.01827-14

Peng, Q., Wang, L., Wang, J., Liu, C., Zheng, X., Zhang, X., Wei, L., Li, Z., Wu, Y., Wen, Y., Cao, P., Liao, Q., Yan, Q., Ma, J., 2021. Epstein–Barr virus EBNA2 phase separation regulates cancer-associated alternative RNA splicing patterns. Clin. Transl. Med. 11, e504. https://doi.org/10.1002/ctm2.504

Pessina, F., Giavazzi, F., Yin, Y., Gioia, U., Vitelli, V., Galbiati, A., Barozzi, S., Garre, M., Oldani, A., Flaus, A., Cerbino, R., Parazzoli, D., Rothenberg, E., d'Adda di Fagagna, F., 2019. Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors. Nat. Cell Biol. 21, 1286–1299. https://doi.org/10.1038/s41556-019-0392-4

Petropoulos, L., Lin, R., Hiscott, J., 1996. Human T Cell Leukemia Virus Type 1 Tax Protein Increases NF-κB Dimer Formation and Antagonizes the Inhibitory Activity of the IκBα Regulatory Protein. Virology 225, 52–64. https://doi.org/10.1006/viro.1996.0574
Phatnani, H.P., Greenleaf, A.L., 2006. Phosphorylation and functions of the RNA polymerase II CTD. *Genes Dev.* 20, 2922–2936. https://doi.org/10.1101/gad.1477006

Phillips, D.M.P., 1963. The presence of acetyl groups in histones. *Biochem. J.* 87, 258–263.

Phillips-Cremins, J.E., Sauria, M.E.G., Sanyal, A., Gerasimova, T.I., Lajoie, B.R., Bell, J.S.K., Ong, C.-T., Hookway, T.A., Guo, C., Sun, Y., Bland, M.J., Wagstaff, W., Dalton, S., McDevitt, T.C., Sen, R., Dekker, J., Taylor, J., Corces, V.G., 2013. Architectural protein subclasses shape 3-D organization of genomes during lineage commitment. *Cell* 153, 1281–1295. https://doi.org/10.1016/j.cell.2013.04.053

Philpott, S.M., Buehring, G.C., 1999. Defective DNA repair in cells with human T-cell leukemia/bovine leukemia viruses: role of tax gene. *J. Natl. Cancer Inst.* 91, 933–942. https://doi.org/10.1093/jnci/91.11.933

Pise-Masison, C.A., Dittmer, J., Clemens, K.E., Brady, J.N., 1997. Physical and functional interaction between the human T-cell lymphotropic virus type 1 Tax1 protein and the CCAAT binding protein NF-Y. *Mol. Cell. Biol.* 17, 1236–1243. https://doi.org/10.1128/MCB.17.3.1236

Pise-Masison, C.A., Mahieux, R., Jiang, H., Ashcroft, M., Radonovich, M., Duvall, J., Guillerm, C., Brady, J.N., 2000. Inactivation of p53 by human T-cell lymphotropic virus type 1 Tax requires activation of the NF-kappaB pathway and is dependent on p53 phosphorylation. *Mol. Cell. Biol.* 20, 3377–3386.

Pise-Masison, C.A., Radonovich, M., Mahieux, R., Chatterjee, P., Whiteford, C., Duvall, J., Guillerm, C., Gessain, A., Brady, J.N., 2002. Transcription Profile of Cells Infected with Human T-cell Leukemia Virus Type I Compared with Activated Lymphocytes1. *Cancer Res.* 62, 3562–3571.

Plancoulaine, S., Gessain, A., Joubert, M., Tortevoye, P., Jeanne, I., Talarmin, A., de Thé, G., Abel, L., 2000. Detection of a Major Gene Predisposing to Human T Lymphotropic Virus Type I Infection in Children among an Endemic Population of African Origin. *J. Infect. Dis.* 182, 405–412. https://doi.org/10.1086/315741

Poiesz, B.J., Ruscetti, F.W., Gazdar, A.F., Bunn, P.A., Minna, J.D., Gallo, R.C., 1980. Detection and isolation of type C retrovirus particles from fresh and cultured lymphocytes of a patient with cutaneous T-cell lymphoma. *Proc. Natl. Acad. Sci.* 77, 7415–7419. https://doi.org/10.1073/pnas.77.12.7415

Portis, T., Harding, J.C., Ratner, L., 2001. The contribution of NF-κB activity to spontaneous proliferation and resistance to apoptosis in human T-cell leukemia virus type 1 Tax-induced tumors. *Blood* 98, 1200–1208. https://doi.org/10.1182/blood.V98.4.1200

Pradhan, B., Barth, R., Kim, E., Davidson, I.F., Bauer, B., van Laar, T., Yang, W., Ryu, J.-K., van der Torre, J., Peters, J.-M., Dekker, C., 2022. SMC complexes can traverse physical roadblocks bigger than their ring size. *Cell Rep.* 41, 111491. https://doi.org/10.1016/j.celrep.2022.111491
Qin, W., Cho, K.F., Cavanagh, P.E., Ting, A.Y., 2021. Deciphering molecular interactions by proximity labeling. Nat. Methods 18, 133–143. https://doi.org/10.1038/s41592-020-01010-5

Quinodoz, S.A., Ollikainen, N., Tabak, B., Palla, A., Schmidt, J.M., Detmar, E., Lai, M.M., Shishkin, A.A., Bhat, P., Takei, Y., Trinh, V., Aznauryan, E., Russell, P., Cheng, C., Jovanovic, M., Chow, A., Cai, L., McDonel, P., Garber, M., Guttman, M., 2018. Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus. Cell 174, 744-757.e24. https://doi.org/10.1016/j.cell.2018.05.024

Ramanouskaya, T.V., Grinev, V.V., 2017. The determinants of alternative RNA splicing in human cells. Mol. Genet. Genomics 292, 1175–1195. https://doi.org/10.1007/s00438-017-1350-0

Rao, S.S.P., Huntley, M.H., Durand, N.C., Stamenova, E.K., Bochkov, I.D., Robinson, J.T., Sanborn, A., Machol, I., Omer, A.D., Lander, E.S., Aiden, E.L., 2014a. A three-dimensional map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680. https://doi.org/10.1016/j.cell.2014.11.021

Rao, S.S.P., Huntley, M.H., Durand, N.C., Stamenova, E.K., Bochkov, I.D., Robinson, J.T., Sanborn, A., Machol, I., Omer, A.D., Lander, E.S., Aiden, E.L., 2014b. A three-dimensional map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680. https://doi.org/10.1016/j.cell.2014.11.021

Reber, L., Vermeulen, L., Haegeman, G., Frossard, N., 2009. Ser276 phosphorylation of NF-kB p65 by MSK1 controls SCF expression in inflammation. PloS One 4, e4393. https://doi.org/10.1371/journal.pone.0004393

Reddy, T.R., Tang, H., Li, X., Wong-Staal, F., 1997. Functional interaction of the HTLV-1 transactivator Tax with activating transcription factor-4 (ATF4). Oncogene 14, 2785–2792. https://doi.org/10.1038/sj.onc.1201119

Rickman, D.S., Soong, T.D., Moss, B., Mosquera, J.M., Dlabal, J., Terry, S., MacDonald, T.Y., Tripodi, J., Bunting, K., Najfeld, V., Demichelis, F., Melnick, A.M., Elemento, O., Rubin, M.A., 2012. Oncogene-mediated alterations in chromatin conformation. Proc. Natl. Acad. Sci. 109, 9083–9088. https://doi.org/10.1073/pnas.1112570109

Riedlinger, T., Liefke, R., Meier-Soelch, J., Jurida, L., Nist, A., Stiewe, T., Kracht, M., Schmitz, M.L., 2019. NF-κB p65 dimerization and DNA-binding is important for inflammatory gene expression. FASEB J. 33, 4188–4202. https://doi.org/10.1096/fj.201801638R

Rizkallah, G., Mahieux, R., Dutartre, H., 2015. Transmission intercellulaire de HTLV-1 - Des mécanismes loin d'être complètement élucidés. médecine/sciences 31, 629–637. https://doi.org/10.1051/medsci/20153106016

Robek, M.D., Ratner, L., 1999. Immortalization of CD4(+) and CD8(+) T lymphocytes by human T-cell leukemia virus type 1 Tax mutants expressed in a functional molecular clone. J. Virol. 73, 4856–4865. https://doi.org/10.1128/JVI.73.6.4856-4865.1999
Romanelli, M., Diani, E., Bergamo, E., Casoli, C., Ciminale, V., Bex, F., Bertazzoni, U., 2013. Highlights on distinctive structural and functional properties of HTLV Tax proteins. Front. Microbiol. 4.

Rossow, K.L., Janknecht, R., 2003. Synergism between p68 RNA helicase and the transcriptional coactivators CBP and p300. Oncogene 22, 151-156. https://doi.org/10.1038/sj.onc.1206067

Rowley, M.J., Corces, V.G., 2018. Organizational principles of 3D genome architecture. Nat. Rev. Genet. 19, 789-800. https://doi.org/10.1038/s41576-018-0060-8

Ruben, S., Poteat, H., Tan, T.-H., Kawakami, K., Roeder, R., Haseltine, W., Rosen, C.A., 1988. Cellular Transcription Factors and Regulation of IL-2 Receptor Gene Expression by HTLV-I tax Gene Product. Science 241, 89-92. https://doi.org/10.1126/science.2838905

Ruiz-Velasco, M., Kumar, M., Lai, M.C., Bhat, P., Solis-Pinson, A.B., Reyes, A., Kleinsorg, S., Noh, K.-M., Gibson, T.J., Zaugg, J.B., 2017. CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals. Cell Syst. 5, 628-637.e6. https://doi.org/10.1016/j.cels.2017.10.018

Sabari, B.R., Dall'Agnese, A., Boija, A., Klein, I.A., Coffey, E.L., Shrinivas, K., Abraham, B.J., Hannett, N.M., Zamudio, A.V., Manteiga, J.C., Li, C.H., Guo, Y.E., Day, D.S., Schuijers, J., Vasile, E., Malik, S., Hnisz, D., Lee, T.I., Cisse, I.I., Roeder, R.G., Sharp, P.A., Chakraborty, A.K., Young, R.A., 2018. Coactivator condensation at super-enhancers links phase separation and gene control. Science 361, eaar3958. https://doi.org/10.1126/science.aar3958

Saccani, S., Marazzi, I., Beg, A.A., Natoli, G., 2004. Degradation of promoter-bound p65/RelA is essential for the prompt termination of the nuclear factor kappaB response. J. Exp. Med. 200, 107-113. https://doi.org/10.1084/jem.20040196

Saccani, S., Pantano, S., Natoli, G., 2003. Modulation of NF-κB Activity by Exchange of Dimers. Mol. Cell 11, 1563-1574. https://doi.org/10.1016/S1097-2765(03)00227-2

Saccani, S., Pantano, S., Natoli, G., 2002. p38-dependent marking of inflammatory genes for increased NF-κB recruitment. Nat. Immunol. 3, 69-75. https://doi.org/10.1038/ni748

Saha, A., Wittmeyer, J., Cairns, B.R., 2006. Chromatin remodelling: the industrial revolution of DNA around histones. Nat. Rev. Mol. Cell Biol. 7, 437-447. https://doi.org/10.1038/nrm1945

Saint-André, V., Batsché, E., Rachez, C., Muchardt, C., 2011. Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons. Nat. Struct. Mol. Biol. 18, 337-344. https://doi.org/10.1038/nsmb.1995

Saldaña-Meyer, R., Rodriguez-Hernaez, J., Escobar, T., Nishana, M., Jácome-López, K., Nora, E.P., Bruneau, B.G., Tsirigos, A., Furlan-Magaril, M., Skok, J., Reinberg, D., 2019. RNA
Interactions Are Essential for CTCF-Mediated Genome Organization. Mol. Cell 76, 412-422.e5. https://doi.org/10.1016/j.molcel.2019.08.015

Sallam, T., Jones, M., Thomas, B.J., Wu, X., Gilliland, T., Qian, K., Eskin, A., Casero, D., Zhang, Z., Sandhu, J., Salisbury, D., Rajbhandari, P., Civelek, M., Hong, C., Ito, A., Liu, X., Daniel, B., Lusis, A.J., Whitelegge, J., Nagy, L., Castrillo, A., Smale, S., Tontonoz, P., 2018. Transcriptional regulation of macrophage cholesterol efflux and atherogenesis by a long noncoding RNA. Nat. Med. 24, 304-312. https://doi.org/10.1038/nm.4479

Satou, Y., Miyazato, P., Ishihara, K., Yaguchi, H., Melamed, A., Miura, M., Fukuda, A., Nosaka, K., Watanabe, T., Rowan, A.G., Nakao, M., Bangham, C.R.M., 2016. The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome. Proc. Natl. Acad. Sci. U. S. A. 113, 3054-3059. https://doi.org/10.1073/pnas.1423199113

Schoenfelder, S., Sexton, T., Chakalova, L., Cope, N.F., Horton, A., Andrews, S., Kurukuti, S., Mitchell, J.A., Umlauf, D., Dimitrova, D.S., Eskiw, C.H., Luo, Y., Wei, C.-L., Ruan, Y., Bieker, J.J., Fraser, P., 2010. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat. Genet. 42, 53-61. https://doi.org/10.1038/ng.496

Schor, I.E., Rascovan, N., Pelisch, F., Alló, M., Kornbliytt, A.R., 2009. Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc. Natl. Acad. Sci. U. S. A. 106, 4325-4330. https://doi.org/10.1073/pnas.0810666106

Schwartz, S., Meshorer, E., Ast, G., 2009. Chromatin organization marks exon-intron structure. Nat. Struct. Mol. Biol. 16, 990-995. https://doi.org/10.1038/nsmb.1659

Segelle, A., Núñez-Álvarez, Y., Oldfield, A.J., Webb, K.M., Voigt, P., Luco, R.F., 2022. Histone marks regulate the epithelial-to-mesenchymal transition via alternative splicing. Cell Rep. 38, 110357. https://doi.org/10.1016/j.celrep.2022.110357

Semmes, O.J., Barret, J.F., Dang, C.V., Jeang, K.T., 1996. Human T-cell leukemia virus type I tax masks c-Myc function through a cAMP-dependent pathway. J. Biol. Chem. 271, 9730-9738. https://doi.org/10.1074/jbc.271.16.9730

Semmes, O.J., Jeang, K.T., 1996. Localization of human T-cell leukemia virus type 1 tax to subnuclear compartments that overlap with interchromatin speckles. J. Virol. 70, 6347-6357. https://doi.org/10.1128/jvi.70.9.6347-6357.1996

Sharma, N., Nyborg, J.K., 2008. The coactivators CBP/p300 and the histone chaperone NAP1 promote transcription-independent nucleosome eviction at the HTLV-1 promoter. Proc. Natl. Acad. Sci. U.S.A. 105, 7959-7963. https://doi.org/10.1073/pnas.0800534105

Shembade, N., Harhaj, N.S., Yamamoto, M., Akira, S., Harhaj, E.W., 2007. The human T-cell leukemia virus type 1 Tax oncoprotein requires the ubiquitin-conjugating enzyme Ubc13 for NF-kappaB activation. J. Virol. 81, 13735-13742. https://doi.org/10.1128/JVI.01790-07
Shen, H., Kan, J.L.C., Green, M.R., 2004. Arginine-Serine-Rich Domains Bound at Splicing Enhancers Contact the Branchpoint to Promote Prespliceosome Assembly. Mol. Cell 13, 367-376. https://doi.org/10.1016/S1097-2765(04)00025-5

Sheppard, K.A., Phelps, K.M., Williams, A.J., Thanos, D., Glass, C.K., Rosenfeld, M.G., Gerritsen, M.E., Collins, T., 1998. Nuclear integration of glucocorticoid receptor and nuclear factor-kappaB signaling by CREB-binding protein and steroid receptor coactivator-1. J. Biol. Chem. 273, 29291-29294. https://doi.org/10.1074/jbc.273.45.29291

Shiama, N., 1997. The p300/CBP family: integrating signals with transcription factors and chromatin. Trends Cell Biol. 7, 230-236. https://doi.org/10.1016/S0962-8924(97)01048-9

Shih, V.F.-S., Kearns, J.D., Basak, S., Savinova, O.V., Ghosh, G., Hoffmann, A., 2009. Kinetic control of negative feedback regulators of NF-κB/RelA determines their pathogen- and cytokine-receptor signaling specificity. Proc. Natl. Acad. Sci. 106, 9619-9624. https://doi.org/10.1073/pnas.0812367106

Shih, V.F.-S., Tsui, R., Caldwell, A., Hoffmann, A., 2011. A single NFκB system for both canonical and non-canonical signaling. Cell Res. 21, 86-102. https://doi.org/10.1038/cr.2010.161

Shirinian, M., Kfoury, Y., Dassouki, Z., El-Hajj, H., Bazarbachi, A., 2013. Tax-1 and Tax-2 similarities and differences: focus on post-translational modifications and NF-κB activation. Front. Microbiol. 4, 231. https://doi.org/10.3389/fmicb.2013.00231

Shopland, L.S., Johnson, C.V., Byron, M., McNeil, J., Lawrence, J.B., 2003. Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods. J. Cell Biol. 162, 981-990. https://doi.org/10.1083/jcb.200303131

Showpnil, I.A., Selich-Anderson, J., Taslim, C., Boone, M.A., Crow, J.C., Theisen, E.R., Lessnick, S.L., 2022. EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma. Nucleic Acids Res. 50, 9814-9837. https://doi.org/10.1093/nar/gkac747

Shukla, S., Kavak, E., Gregory, M., Imashimizu, M., Shutinoski, B., Kashlev, M., Oberdoerffer, P., Sandberg, R., Oberdoerffer, S., 2011. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479, 74-79. https://doi.org/10.1038/nature10442

Sibon, D., Gabet, A.-S., Zandecki, M., Pinatel, C., Thête, J., Delfau-Larue, M.-H., Rabaaoui, S., Gessain, A., Gout, O., Jacobson, S., Mortreux, F., Wattel, E., 2006. HTLV-1 propels untransformed CD4⁺ lymphocytes into the cell cycle while protecting CD8⁺ cells from death. J. Clin. Invest. 116, 974-983. https://doi.org/10.1172/JCI27198

Silbermann, K., Schneider, G., Grassmann, R., 2008. Stimulation of interleukin-13 expression by human T-cell leukemia virus type 1 oncoprotein Tax via a dually active promoter element responsive to NF-κB and NFAT. J. Gen. Virol. 89, 2788-2798. https://doi.org/10.1099/vir.0.2008/003699-0
Sims, R.J., Millhouse, S., Chen, C.-F., Lewis, B.A., Erdjument-Bromage, H., Tempst, P., Manley, J.L., Reinberg, D., 2007. Recognition of Trimethylated Histone H3 Lysine 4 Facilitates the Recruitment of Transcription Postinitiation Factors and Pre-mRNA Splicing. Mol. Cell 28, 665-676. https://doi.org/10.1016/j.molcel.2007.11.010

Singh, M., Popowicz, G.M., Krajewski, M., Holak, T.A., 2007. Structural Ramification for Acetyl-Lysine Recognition by the Bromodomain of Human BRG1 Protein, a Central ATPase of the SWI/SNF Remodeling Complex. ChemBioChem 8, 1308-1316. https://doi.org/10.1002/cbic.200600562

Smith, K.P., Moen, P.T., Wydner, K.L., Coleman, J.R., Lawrence, J.B., 1999. Processing of endogenous pre-mRNAs in association with SC-35 domains is gene specific. J. Cell Biol. 144, 617-629. https://doi.org/10.1083/jcb.144.4.617

Sofiadis, K., Papantonis, A., 2018. Transcription Factories as Spatial and Functional Organization Nodes, in: Nuclear Architecture and Dynamics. Elsevier, pp. 283-296. https://doi.org/10.1016/B978-0-12-803480-4.00012-0

Somasundaram, K., Gupta, B., Jain, N., Jana, S., 2022. LncRNAs divide and rule: The master regulators of phase separation. Front. Genet. 13, 930792. https://doi.org/10.3389/fgene.2022.930792

Spector, D. I., Fu, X. d., Maniatis, T., 1991. Associations between distinct pre-mRNA splicing components and the cell nucleus. EMBO J. 10, 3467-3481. https://doi.org/10.1002/j.1460-2075.1991.tb04911.x

Spector, D.L., Lamond, A.I., 2011. Nuclear Speckles. Cold Spring Harb. Perspect. Biol. 3, a000646. https://doi.org/10.1101/cshperspect.a000646

Spector, D.L., Schrier, W.H., Busch, H., 1983. Immunoelectron microscopic localization of snRNPs. Biol. Cell 49, 1-10. https://doi.org/10.1111/j.1768-322x.1984.tb00215.x

Spielmann, M., Lupiáñez, D.G., Mundlos, S., 2018. Structural variation in the 3D genome. Nat. Rev. Genet. 19, 453-467. https://doi.org/10.1038/s41576-018-0007-0

Spies, N., Nielsen, C.B., Padgett, R.A., Burge, C.B., 2009. Biased Chromatin Signatures Around Polyadenylation Sites and Exons. Mol. Cell 36, 245-254. https://doi.org/10.1016/j.molcel.2009.10.008

Strahl, B.D., Allis, C.D., 2000. The language of covalent histone modifications. Nature 403, 41-45. https://doi.org/10.1038/47412

Strom, A.R., Emelyanov, A.V., Mir, M., Fyodorov, D.V., Darzacq, X., Karpen, G.H., 2017. Phase separation drives heterochromatin domain formation. Nature 547, 241-245. https://doi.org/10.1038/nature22989

Sullivan, D.E., Ferris, M., Nguyen, H., Abboud, E., Brody, A.R., 2009. TNF-alpha induces TGF-beta1 expression in lung fibroblasts at the transcriptional level via AP-1 activation. J. Cell. Mol. Med. 13, 1866-1876. https://doi.org/10.1111/j.1582-4934.2009.00647.x
Sun, S.C., Ballard, D.W., 1999. Persistent activation of NF-kappaB by the tax transforming protein of HTLV-1: hijacking cellular IkappaB kinases. Oncogene 18, 6948-6958.
https://doi.org/10.1038/sj.onc.1203220

Suzuki, S., Singhirunnusorn, P., Mori, A., Yamaoka, S., Kitajima, I., Saiki, I., Sakurai, H., 2007. Constitutive Activation of TAK1 by HTLV-1 Tax-dependent Overexpression of TAB2 Induces Activation of JNK-ATF2 but Not IKK-NF-κB*. J. Biol. Chem. 282, 25177-25181.
https://doi.org/10.1074/jbc.C700065200

Suzuki, T., Hirai, H., Murakami, T., Yoshida, M., 1995. Tax protein of HTLV-1 destabilizes the complexes of NF-kappa B and I kappa B-alpha and induces nuclear translocation of NF-kappa B for transcriptional activation. Oncogene 10, 1199-1207.

Suzuki, T., Hirai, H., Yoshida, M., 1994. Tax protein of HTLV-1 interacts with the Rel homology domain of NF-kappa B p65 and c-Rel proteins bound to the NF-kappa B binding site and activates transcription. Oncogene 9, 3099-3105.

Takeda, S., Maeda, M., Morikawa, S., Taniguchi, Y., Yasunaga, J.-I., Nosaka, K., Tanaka, Y., Matsuoka, M., 2004. Genetic and epigenetic inactivation of tax gene in adult T-cell leukemia cells. Int. J. Cancer 109, 559-567. https://doi.org/10.1002/ijc.20007

Takenouchi, N., Yamano, Y., Usuku, K., Osame, M., Izumo, S., 2003. Usefulness of proviral load measurement for monitoring of disease activity in individual patients with human T-lymphotropic virus type I-associated myelopathy/tropical spastic paraparesis. J. Neurovirol. 9, 29-35. https://doi.org/10.1080/13550280390173418

Tammer, L., Hameiri, O., Keydar, I., Roy, V.R., Ashkenazy-Titelman, A., Custódio, N., Sason, I., Shayevitch, R., Rodríguez-Vaello, V., Rino, J., Lev Maor, G., Leader, Y., Khair, D., Aiden, E.L., Elkon, R., Irimia, M., Sharan, R., Shav-Tal, Y., Carmo-Fonseca, M., Ast, G., 2022. Gene architecture directs splicing outcome in separate nuclear spatial regions. Mol. Cell 82, 1021-1034.e8. https://doi.org/10.1016/j.molcel.2022.02.001

Tan-Wong, S.M., Zaugg, J.B., Camblong, J., Xu, Z., Zhang, D.W., Mischo, H.E., Ansari, A.Z., Luscombe, N.M., Steinmetz, L.M., Proudfoot, N.J., 2012. Gene loops enhance transcriptional directionality. Science 338, 671-675.
https://doi.org/10.1126/science.1224350

Tattermusch, S., Skinner, J.A., Chaussabel, D., Banchereau, J., Berry, M.P., McNab, F.W., O'Garra, A., Taylor, G.P., Bangham, C.R.M., 2012. Systems biology approaches reveal a specific interferon-inducible signature in HTLV-1 associated myelopathy. PLoS Pathog. 8, e1002480. https://doi.org/10.1371/journal.ppat.1002480

Terrone, S., Valat, J., Fontrodona, N., Giraud, G., Claude, J.-B., Combe, E., Lapendry, A., Polvèche, H., Ameur, L.B., Duvermy, A., Modolo, L., Bernard, P., Mortreux, F., Auboeuf, D., Bourgeois, C.F., 2022. RNA helicase-dependent gene looping impacts messenger RNA processing. Nucleic Acids Res. 50, 9226-9246.
https://doi.org/10.1093/nar/gkac717
Tezuka, K., Fuchi, N., Okuma, K., Tsukiyama, T., Miura, S., Hasegawa, Y., Nagata, A., Komatsu, N., Hasegawa, H., Sasaki, D., Sasaki, E., Mizukami, T., Kuramitsu, M., Matsuoka, S., Yanagihara, K., Miura, K., Hamaguchi, I., 2020. HTLV-1 targets human placental trophoblasts in seropositive pregnant women. J. Clin. Invest. 130, 6171–6186.
https://doi.org/10.1172/JCI135525

Thénoz, M., Vernin, C., Mortada, H., Karam, M., Pinatel, C., Gessain, A., Webb, T.R., Auboeuf, D., Wattel, E., Mortreux, F., 2014. HTLV-1-infected CD4+ T-cells display alternative exon usages that culminate in adult T-cell leukemia. Retrovirology 11, 119.
https://doi.org/10.1186/s12977-014-0119-3

Tilgner, H., Nikolaou, C., Althammer, S., Sammeth, M., Beato, M., Valcárcel, J., Guigó, R., 2009. Nucleosome positioning as a determinant of exon recognition. Nat. Struct. Mol. Biol. 16, 996–1001. https://doi.org/10.1038/nsmb.1658

Ting, A.Y., Endy, D., 2002. Decoding NF-κB Signaling. Science 298, 1189–1190.
https://doi.org/10.1126/science.1079331

Tong, A.-J., Liu, X., Thomas, B.J., Lissner, M.M., Baker, M.R., Senagolage, M.D., Allred, A.L., Barish, G.D., Smale, S.T., 2016. A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation. Cell 165, 165–179.
https://doi.org/10.1016/j.cell.2016.01.020

Tsukada, J., Misago, M., Serino, Y., Ogawa, R., Murakami, S., Nakanishi, M., Tonai, S., Kominato, Y., Morimoto, I., Auron, P.E., Eto, S., 1997. Human T-cell leukemia virus type I Tax transactivates the promoter of human prointerleukin-1beta gene through association with two transcription factors, nuclear factor-interleukin-6 and Spi-1. Blood 90, 3142–3153.

Tzavlaki, K., Moustakas, A., 2020. TGF-β Signaling. Biomolecules 10, 487.
https://doi.org/10.3390/biom10030487

Uchiyama, T., Yodoi, J., Sagawa, K., Takatsuki, K., Uchino, H., 1977. Adult T-cell leukemia: clinical and hematologic features of 16 cases. Blood 50, 481–492.

Ueki, K., Fruman, D.A., Brachmann, S.M., Tseng, Y.-H., Cantley, L.C., Kahn, C.R., 2002. Molecular balance between the regulatory and catalytic subunits of phosphoinositide 3-kinase regulates cell signaling and survival. Mol. Cell. Biol. 22, 965–977.
https://doi.org/10.1128/MCB.22.3.965-977.2002

Van Prooyen, N., Gold, H., Andresen, V., Schwartz, O., Jones, K., Ruscetti, F., Lockett, S., Gudla, P., Venzon, D., Franchini, G., 2010. Human T-cell leukemia virus type 1 p8 protein increases cellular conduits and virus transmission. Proc. Natl. Acad. Sci. U. S. A. 107, 20738–20743. https://doi.org/10.1073/pnas.1009635107

Vandermeulen, C., O'Grady, T., Wayet, J., Galvan, B., Maseko, S., Cherkaoui, M., Desbuleux, A., Coppin, G., Olivet, J., Ben Ameur, L., Kataoka, K., Ogawa, S., Hermine, O., Marcais, A., Thiry, M., Mortreux, F., Calderwood, M.A., Van Weyenbergh, J., Peloponese, J.-M., Charloteaux, B., Van den Broeke, A., Hill, D.E., Vidal, M., Dequiedt, F., Twizere, J.-C.,
2021. The HTLV-1 viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape. PLoS Pathog. 17, e1009919. https://doi.org/10.1371/journal.ppat.1009919

Vargas, D.Y., Shah, K., Batish, M., Levandoski, M., Sinha, S., Marras, S.A.E., Schedl, P., Tyagi, S., 2011. Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell 147, 1054–1065. https://doi.org/10.1016/j.cell.2011.10.024

Vendel, A.C., McBryant, S.J., Lumb, K.J., 2003. KIX-mediated assembly of the CBP-CREB-HTLV-1 tax coactivator-activator complex. Biochemistry 42, 12481–12487. https://doi.org/10.1021/bi0353023

Verdonck, K., González, E., Van Dooren, S., Vandamme, A.-M., Vanham, G., Gotuzzo, E., 2007. Human T-lymphotropic virus 1: recent knowledge about an ancient infection. Lancet Infect. Dis. 7, 266–281. https://doi.org/10.1016/S1473-3099(07)70081-6

Vlahopoulos, S., Boldogh, I., Casola, A., Brasier, A.R., 1999. Nuclear factor-kappaB-dependent induction of interleukin-8 gene expression by tumor necrosis factor alpha: evidence for an antioxidant sensitive activating pathway distinct from nuclear translocation. Blood 94, 1878–1889.

Wäldele, K., Schneider, G., Ruckes, T., Grassmann, R., 2004. Interleukin-13 Overexpression by Tax Transactivation: a Potential Autocrine Stimulus in Human T-Cell Leukemia Virus-Infected Lymphocytes. J. Virol. 78, 6081–6090. https://doi.org/10.1128/JVI.78.12.6081-6090.2004

Wang, V.Y.-F., Huang, W., Asagiri, M., Spann, N., Hoffmann, A., Glass, C., Ghosh, G., 2012. The Transcriptional Specificity of NF-κB Dimers Is Coded within the κB DNA Response Elements. Cell Rep. 2, 824–839. https://doi.org/10.1016/j.celrep.2012.08.042

Wansink, D., Schul, W., van der Kraan, I., van Steensel, B., van Driel, R., de Jong, L., 1993. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J. Cell Biol. 122, 283–293. https://doi.org/10.1083/jcb.122.2.283

Warf, M.B., Berglund, J.A., 2010. The role of RNA structure in regulating pre-mRNA splicing. Trends Biochem. Sci. 35, 169–178. https://doi.org/10.1016/j.tibs.2009.10.004

Watanabe, T., 2011. Current status of HTLV-1 infection. Int. J. Hematol. 94, 430–434. https://doi.org/10.1007/s12185-011-0934-4

Wattel, E., Cavrois, M., Gessain, A., Wain-Hobson, S., 1996. Clonal expansion of infected cells: a way of life for HTLV-I. J. Acquir. Immune Defic. Syndr. Hum. Retrovirology Off. Publ. Int. Retrovirology Assoc. 13 Suppl 1, S92-99. https://doi.org/10.1097/00042560-199600001-00016

Winter, H.Y., Marriott, S.J., 2007. Human T-Cell Leukemia Virus Type 1 Tax Enhances Serum Response Factor DNA Binding and Alters Site Selection. J. Virol. 81, 6089–6098. https://doi.org/10.1128/JVI.02179-06
Wongtrakoongate, P., Riddick, G., Fucharoen, S., Felsenfeld, G., 2015. Association of the Long Non-coding RNA Steroid Receptor RNA Activator (SRA) with TrxG and PRC2 Complexes. PLoS Genet. 11, e1005615. https://doi.org/10.1371/journal.pgen.1005615

Wu, K., Bottazzi, M.E., de la Fuente, C., Deng, L., Gitlin, S.D., Maddukuri, A., Dadgar, S., Li, H., Vertes, A., Pumfery, A., Kashanchi, F., 2004. Protein profile of tax-associated complexes. J. Biol. Chem. 279, 495-508. https://doi.org/10.1074/jbc.M310069200

Wu, X., Sun, S.-C., 2007. Retroviral oncoprotein Tax deregulates NF-kappaB by activating Tak1 and mediating the physical association of Tak1-IKK. EMBO Rep. 8, 510-515. https://doi.org/10.1038/sj.embor.7400931

Xiao, G., Cvijic, M.E., Fong, A., Harhaj, E.W., Uhlik, M.T., Waterfield, M., Sun, S.C., 2001. Retroviral oncoprotein Tax induces processing of NF-kappaB2/p100 in T cells: evidence for the involvement of IKKalpha. EMBO J. 20, 6805-6815. https://doi.org/10.1093/emboj/20.23.6805

Xing, Y., Johnson, C.V., Moen, P.T., McNeil, J.A., Lawrence, J., 1995. Nonrandom gene organization: structural arrangements of specific pre-mRNA transcription and splicing with SC-35 domains. J. Cell Biol. 131, 1635-1647. https://doi.org/10.1083/jcb.131.6.1635

Xu, S., Lai, S.-K., Sim, D.Y., Ang, W.S.L., Li, H.Y., Roca, X., 2022. SRRM2 organizes splicing condensates to regulate alternative splicing. Nucleic Acids Res. 50, 8599-8614. https://doi.org/10.1093/nar/gkac669

Xu, S.-J., Lombroso, S.I., Fischer, D.K., Carpenter, M.D., Marchione, D.M., Hamilton, P.J., Lim, C.J., Neve, R.L., Garcia, B.A., Wimmer, M.E., Pierce, R.C., Heller, E.A., 2021. Chromatin-mediated alternative splicing regulates cocaine-reward behavior. Neuron 109, 2943-2966.e8. https://doi.org/10.1016/j.neuron.2021.08.008

Xu, X., Heidenreich, O., Kitajima, I., McGuire, K., Li, Q., Su, B., Nerenberg, M., 1996. Constitutively activated JNK is associated with HTLV-1 mediated tumorigenesis. Oncogene 13, 135-142.

Yamaguchi, K., Watanabe, T., 2002. Human T lymphotropic virus type-I and adult T-cell leukemia in Japan. Int. J. Hematol. 76, 240-245. https://doi.org/10.1007/BF03165123

Yamaoka, S., Inoue, H., Sakurai, M., Sugiyama, T., Hazama, M., Yamada, T., Hatanaka, M., 1996. Constitutive activation of NF-kappa B is essential for transformation of rat fibroblasts by the human T-cell leukemia virus type I Tax protein. EMBO J. 15, 873-887. https://doi.org/10.1002/j.1460-2075.1996.tb00422.x

Yang, J., Mitra, A., Dojer, N., Fu, S., Rowicka, M., Brasier, A.R., 2013. A probabilistic approach to learn chromatin architecture and accurate inference of the NF-κB/RelA regulatory network using ChIP-Seq. Nucleic Acids Res. 41, 7240-7259. https://doi.org/10.1093/nar/gkt493
Yao, H., Brick, K., Evrard, Y., Xiao, T., Camerini-Otero, R.D., Felsenfeld, G., 2010. Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. *Genes Dev.* 24, 2543–2555.
https://doi.org/10.1101/gad.1967810

Yashiki, S., Fujiyoshi, T., Arima, N., Osame, M., Yoshinaga, M., Nagata, Y., Tara, M., Nomura, K., Utsunomiya, A., Hanada, S., Tajima, K., Sonoda, S., 2001. HLA-A*26, HLA-B*4002, HLA-B*4006, and HLA-B*4801 alleles predispose to adult T cell leukemia: the limited recognition of HTLV type 1 tax peptide anchor motifs and epitopes to generate anti-HTLV type 1 tax CD8(+) cytotoxic T lymphocytes. *AIDS Res. Hum. Retroviruses* 17, 1047–1061. https://doi.org/10.1089/088922201300343735

Yin, M.J., Christerson, L.B., Yamamoto, Y., Kwak, Y.T., Xu, S., Mercurio, F., Barbosa, M., Cobb, M.H., Gaynor, R.B., 1998. HTLV-I Tax protein binds to MEKK1 to stimulate IkappaB kinase activity and NF-kappaB activation. *Cell* 93, 875–884.
https://doi.org/10.1016/s0092-8674(00)81447-6

Ying, Y., Wang, X.-J., Vuong, C.K., Lin, C.-H., Damianov, A., Black, D.L., 2017. Splicing activation by Rbfox requires self-aggregation through its tyrosine-rich domain. *Cell* 170, 312–323.e10. https://doi.org/10.1016/j.cell.2017.06.022

Zentner, G.E., Henikoff, S., 2013. Regulation of nucleosome dynamics by histone modifications. *Nat. Struct. Mol. Biol.* 20, 259–266. https://doi.org/10.1038/nsmb.2470

Zhang, L., Liu, M., Merling, R., Giam, C.-Z., 2006. Versatile reporter systems show that transactivation by human T-cell leukemia virus type 1 Tax occurs independently of chromatin remodeling factor BRG1. *J. Virol.* 80, 7459–7468.
https://doi.org/10.1128/JVI.00130-06

Zhang, Y., Qian, J., Gu, C., Yang, Y., 2021. Alternative splicing and cancer: a systematic review. *Signal Transduct. Target. Ther.* 6, 1–14. https://doi.org/10.1038/s41392-021-00486-7

Zhao, B., Barrera, L.A., Ersing, I., Willox, B., Schmidt, S.C.S., Greenfeld, H., Zhou, H., Mollo, S.B., Shi, T.T., Takasaki, K., Jiang, S., Cahir-McFarland, E., Kellis, M., Bulyk, M.L., Kieff, E., Gewurz, B.E., 2014. The NF-κB Genomic Landscape in Lymphoblastoid B-cells. *Cell Rep.* 8, 1595–1606. https://doi.org/10.1016/j.celrep.2014.07.037

Zhao, M., Joy, J., Zhou, W., De, S., Iii, W.H.W., Becker, K.G., Ji, H., Sen, R., 2018. Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation. *PLOS Biol.* 16, e2006347. https://doi.org/10.1371/journal.pbio.2006347

Zhao, T., 2016. The Role of HBZ in HTLV-1-Induced Oncogenesis. *Viruses* 8, 34.
https://doi.org/10.3390/v8020034

Zhao, W., Wang, L., Zhang, M., Wang, P., Zhang, L., Yuan, C., Qi, J., Qiao, Y., Kuo, P.C., Gao, C., 2011. NF-κB- and AP-1-Mediated DNA Looping Regulates Osteopontin Transcription in Endotoxin-Stimulated Murine Macrophages. *J. Immunol.* 186, 3173–3179.
https://doi.org/10.4049/jimmunol.1003626
Zhao, Y.-Q., Jordan, I.K., Lunyak, V.V., 2013. Epigenetics Components of Aging in the Central Nervous System. Neurotherapeutics 10, 647–663. https://doi.org/10.1007/s13311-013-0229-y

Zhong, H., May, M.J., Jimi, E., Ghosh, S., 2002. The Phosphorylation Status of Nuclear NF-KB Determines Its Association with CBP/p300 or HDAC-1. Mol. Cell 9, 625–636. https://doi.org/10.1016/S1097-2765(02)00477-X

Zhong, H., Voll, R.E., Ghosh, S., 1998. Phosphorylation of NF-kappa B p65 by PKA stimulates transcriptional activity by promoting a novel bivalent interaction with the coactivator CBP/p300. Mol. Cell 1, 661–671. https://doi.org/10.1016/s1097-2765(00)80066-0

Zhou, M., Lu, H., Park, H., Wilson-Chiru, J., Linton, R., Brady, J.N., 2006. Tax interacts with P-TEFb in a novel manner to stimulate human T-lymphotropic virus type 1 transcription. J. Virol. 80, 4781–4791. https://doi.org/10.1128/JVI.80.10.4781-4791.2006
Résumé

L'activation de la voie NF-κB contrôle la transcription de nombreux gènes engagés dans des processus physiologiques majeurs tels que l'inflammation et la réponse immune. Néanmoins, son activation chronique est fréquemment associée dans des maladies tels que les cancers. L'organisation tridimensionnelle de la chromatine joue un rôle dans la coordination des régulations transcriptionnelles mise en place lors de l'activation de la voie NF-κB. Mes travaux montrent dans un contexte d'activation de la voie NF-κB par l'oncogène Tax du rétrovirus HTLV-1 que de nombreuses dérégulations d'épissage alternatif sont médiées par le recrutement intragénique du facteur NF-κB p65/RelA à proximité des exons régulés via ses capacité d'interaction avec des facteurs d'épissage, dont l'hélicase à ARN DDX17. Par des approches de Hi-C, 4C et 3C, mes données montrent que les régulations transcriptionnelles et co-transcriptionnelles engendrées par Tax, notamment via l'activation de la voie NF-κB, s'accompagnent d'une réorganisation de l'architecture tridimensionnelle du génome, induisant la formation de complexes multigéniques composés de gènes régulés par Tax dans leur niveau transcriptionnel ou leur épissage alternatif. Les analyses de l'enrichissement à la chromatine de p65/RelA, ainsi que des approches moléculaires permettant de moduler expérimentalement le recrutement de p65/RelA à la chromatine, ont permis d'identifier que la fixation intragénique de p65/RelA participe à la formation de contacts entre gènes et à leurs régulations au niveau de la transcription et de l'épissage alternatif. Ces données apportent de nouvelles connaissances dans les mécanismes de régulation lors de l'infection par HTLV-1 mais également dans les pathologies associées à l'activation de la voie NF-κB.