53. Ramirez, F., Dundar, F., Diehl, S., Gruning, B. A. & Manke, T. deep-Tools: a flexible platform for exploring deep-sequencing data. *Nucleic Acids Res.* **42**, W187–W191 (2014).

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

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

56. Li, Q. H., Brown, J. B., Huang, H. Y. & Bickel, P. J. Measuring Reproducibility of High-Throughput Experiments. *Ann. Appl Stat.* **5**, 1752–1779 (2011).

57. Lun, A. T. & Smyth, G. K. csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows. *Nucleic Acids Res.* **44**, e45 (2016).

58. R Core Team. *R: A language and environment for statistical computing* (R Core Team, 2014).

59. Li, H. et al. The Sequence Alignment/Map format and SAMtools. *Bioinformatics* **25**, 2078–2079 (2009).

60. Taboada, B., Estrada, K., Ciria, R. & Merino, E. Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes. *Bioinformatics* **34**, 4118–4120 (2018).

61. 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).

62. Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. *EMBnet.journal*. **17**, https://doi.org/10.14806/ej.17.1.200 (2011).

63. Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. *Bioinformatics* **30**, 923–930 (2014).

64. Gu, Z., Gu, L., Eils, R., Schlesner, M. & Brors, B. circleize Implements and enhances circular visualization in R. *Bioinformatics* **30**, 2811–2812, (2014).

65. Brugger, K. et al. Mobile elements in archaeal genomes. *FEMS Microbiol. Lett.* **206**, 131–141 (2002).

66. Siguier, P., Perochon, J., Lestrade, L., Mahillon, J. & Chandler, M. ISfinder: the reference centre for bacterial insertion sequences. *Nucleic Acids Res.* **34**, D32–D36 (2006).

67. Madeira, F. et al. Search and sequence analysis tools services from EMBL-EBI in 2022. *Nucleic Acids Res.* **50**, W276–W279 (2022).

68. Ofer, S. et al. DNA-bridging by an archaeal histone variant via a unique tetramerisation interface. *Commun. Biol.* **6**, 968 (2023).

## Acknowledgements

We thank Malcolm White (University of St Andrews, UK), Remus Dame (Leiden University, NL), Michael Terns (University of Georgia, GA) and Roger Garrett (University of Copenhagen, DK) for valuable advice on the project and Stephen Bell (Indiana University Bloomington, USA) for sharing the CID coordinates. Research in the RNAP laboratory at UCL is

funded by a Wellcome Investigator Award in Science ‘Mechanisms and Regulation of RNAP transcription’ to FW (WT 207446/Z/17/Z).

## Author contributions

F.B., M.S., J.C., X.F., D.Baq., T.F., D.K.P., D.Bar., M.K., Q.S. and F.W. F.B., M.S., J.C., X.F., D.Baq., T.F., D.K.P., D.Bar. designed and performed experimental work. F.B. performed computational data analyses. M.K., Q.S. and F.W. acquired funding and supervised the work. F.B. and F.W. coordinated the project and wrote the manuscript with input from all authors.

## Competing interests

The authors declare no competing interests.

## Additional information

**Supplementary information** The online version contains supplementary material available at https://doi.org/10.1038/s41467-024-45728-8.

**Correspondence** and requests for materials should be addressed to Fabian Blombach or Finn Werner.

**Peer review information** *Nature Communications* thanks the anonymous reviewers for their contribution to the peer review of this work. A peer review file is available.

**Reprints and permissions information** is available at http://www.nature.com/reprints

**Publisher’s note** Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

**Open Access** This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

© The Author(s) 2024
53. Ramirez, F., Dundar, F., Diehl, S., Gruning, B. A. & Manke, T. deep-Tools: a flexible platform for exploring deep-sequencing data. *Nucleic Acids Res.* **42**, W187–W191 (2014).

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

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

56. Li, Q. H., Brown, J. B., Huang, H. Y. & Bickel, P. J. Measuring Reproducibility of High-Throughput Experiments. *Ann. Appl Stat.* **5**, 1752–1779 (2011).

57. Lun, A. T. & Smyth, G. K. csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows. *Nucleic Acids Res.* **44**, e45 (2016).

58. R Core Team. *R: A language and environment for statistical computing* (R Core Team, 2014).

59. Li, H. et al. The Sequence Alignment/Map format and SAMtools. *Bioinformatics* **25**, 2078–2079 (2009).

60. Taboada, B., Estrada, K., Ciria, R. & Merino, E. Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes. *Bioinformatics* **34**, 4118–4120 (2018).

61. 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).

62. Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. *EMBnet.journal*. **17**, https://doi.org/10.14806/ej.17.1.200 (2011).

63. Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. *Bioinformatics* **30**, 923–930 (2014).

64. Gu, Z., Gu, L., Eils, R., Schlesner, M. & Brors, B. circleize Implements and enhances circular visualization in R. *Bioinformatics* **30**, 2811–2812, (2014).

65. Brugger, K. et al. Mobile elements in archaeal genomes. *FEMS Microbiol. Lett.* **206**, 131–141 (2002).

66. Siguier, P., Perochon, J., Lestrade, L., Mahillon, J. & Chandler, M. ISfinder: the reference centre for bacterial insertion sequences. *Nucleic Acids Res.* **34**, D32–D36 (2006).

67. Madeira, F. et al. Search and sequence analysis tools services from EMBL-EBI in 2022. *Nucleic Acids Res.* **50**, W276–W279 (2022).

68. Ofer, S. et al. DNA-bridging by an archaeal histone variant via a unique tetramerisation interface. *Commun. Biol.* **6**, 968 (2023).

## Acknowledgements

We thank Malcolm White (University of St Andrews, UK), Remus Dame (Leiden University, NL), Michael Terns (University of Georgia, GA) and Roger Garrett (University of Copenhagen, DK) for valuable advice on the project and Stephen Bell (Indiana University Bloomington, USA) for sharing the CID coordinates. Research in the RNAP laboratory at UCL is

funded by a Wellcome Investigator Award in Science 'Mechanisms and Regulation of RNAP transcription' to FW (WT 207446/Z/17/Z).

## Author contributions

F.B., M.S., J.C., X.F., D.Baq., T.F., D.K.P., D.Bar., M.K., Q.S. and F.W. F.B., M.S., J.C., X.F., D.Baq., T.F., D.K.P., D.Bar. designed and performed experimental work. F.B. performed computational data analyses. M.K., Q.S. and F.W. acquired funding and supervised the work. F.B. and F.W. coordinated the project and wrote the manuscript with input from all authors.

## Competing interests

The authors declare no competing interests.

## Additional information

**Supplementary information** The online version contains supplementary material available at https://doi.org/10.1038/s41467-024-45728-8.

**Correspondence** and requests for materials should be addressed to Fabian Blombach or Finn Werner.

**Peer review information** *Nature Communications* thanks the anonymous reviewers for their contribution to the peer review of this work. A peer review file is available.

**Reprints and permissions information** is available at http://www.nature.com/reprints

**Publisher's note** Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

**Open Access** This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

© The Author(s) 2024