# The lncRNA ANRIL-induced gene modulation depends on its Exon21 enriched in Transposable Elements

Aymeric Sanchez, Charbel Alfeghaly, Lilia Ayadi, Wassim Rhalloussi, Quentin Thuillier, Valérie Bourguignon-Igel, V. Marchand, Isabelle Behm-Ansmant, Yuri Motorin, Sylvain Maenner

► To cite this version:

Aymeric Sanchez, Charbel Alfeghaly, Lilia Ayadi, Wassim Rhalloussi, Quentin Thuillier, et al. The lncRNA ANRIL-induced gene modulation depends on its Exon21 enriched in Transposable Elements. 12th SifrARN, Oct 2022, Bordeaux, France. hal-04577641

HAL Id: hal-04577641

https://hal.univ-lorraine.fr/hal-04577641

Submitted on 16 May 2024

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# The IncRNA ANRIL-induced gene modulation depends on its Exon21 enriched in Transposable Elements

Aymeric Sanchez¹, Charbel Alfeghaly¹, Lilia Ayadi¹, Wassim Rhalloussi², Quentin Thuillier², Valérie Igel-Bourguignon², Virginie Marchand², Isabelle Behm-Ansmant¹, Yuri Motorin¹, Sylvain Maëner¹

¹ Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France

² Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, F-54000 Nancy, France

**Abstract:** Long non-coding RNAs (longer than 200nts, IncRNAs) are critical regulators of gene expression. LncRNAs regulatory activities rely on functional domains within their sequences often including Transposable Elements (TE) derived sequences. Due to their important regulatory function, IncRNAs are consequently linked to various pathologies (cancers, cardiovascular diseases...). ANRIL (Antisense non-coding RNA in the INK4 locus), one of the disease-associated IncRNA is well described for its association with pathologies. However, the underlying molecular aspects of its function as well as the diseases association are not fully understood. We identified several exonic sequences noticeably enriched in TE within ANRIL, among which Exon 21 contains 67% of TE-derived sequences. The generation of the Exon 21 depleted HEK293 cell line allowed to investigate its function revealing its importance for the deposition of H3K27me3 at promoter level of a subset of genes. In parallel, the purification of Exon 21 associated proteins allowed to identify a promising protein partners named hnRNPK and SUZ12 presumably important for ANRIL functions.

<figure><img src="image_2.png" /></figure>

**References:** Alfeghaly C, Sanchez A, Rouget R, Thuillier Q, Igel-Bourguignon V, Marchand V, Branlant C, Motorin Y, Behm-Ansmant I, Maëner S. Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL. Nucleic Acids Res. 2021 May 21:49(9):4954-4970.
Holdt, L.M., Hoffmann, S., Sass, K., Langenberger, D., Scholz, M., Krohn, K., Finstermeier, K., Stahringer, A., Wilfert, W., Beutner, F., et al. (2013). Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet. 9, e1003588.
Johnson R, Guigó R. The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs. RNA. 2014 Jul;20(7):959-76.
Kotake, Y., Nakagawa, T., Kitagawa, K., Suzuki, S., Liu, N., Kitagawa, M., and Xiong, Y. (2011). Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene. Oncogene 30, 1956-1962.
Lo Sardo, V., Chubukov, P., Ferguson, W., Kumar, A., Teng, E.L., Duran, M., Zhang, L., Cost, G., Engler, A.J., Urnov, F., et al. (2018). Unveiling the Role of the Most Impactful Cardiovascular Risk Locus through Haplotype Editing. Cell 175, 1796-1810.e20.
Yap, K. L., Li, S., Muñoz-Cabello, A. M., Raguz, S., Zeng, L., Mujtaba, S., ... & Zhou, M. M. (2010). Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Molecular cell, 38(5), 662-674.
<figure><img src="image_1.png" /></figure>

# The IncRNA ANRIL-induced gene modulation depends on its Exon21 enriched in Transposable Elements

Aymeric Sanchez¹, Charbel Alfeghaly¹, Lilia Ayadi¹, Wassim Rhaloussi², Quentin Thuillier², Valérie Igel-Bourguignon², Virginie Marchand², Isabelle Behm-Ansmant¹, Yuri Motorin¹, Sylvain Maenner¹

¹ Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France

² Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, F-54000 Nancy, France

**Abstract:** Long non-coding RNAs (longer than 200nts, IncRNAs) are critical regulators of gene expression. LncRNAs regulatory activities rely on functional domains within their sequences often including Transposable Elements (TE) derived sequences. Due to their important regulatory function, IncRNAs are consequently linked to various pathologies (cancers, cardiovascular diseases...). ANRIL (Antisense non-coding RNA in the INK4 locus), one of the disease-associated IncRNA is well described for its association with pathologies. However, the underlying molecular aspects of its function as well as the diseases association are not fully understood. We identified several exonic sequences noticeably enriched in TE within ANRIL, among which Exon 21 contains 67% of TE-derived sequences. The generation of the Exon 21 depleted HEK293 cell line allowed to investigate its function revealing its importance for the deposition of H3K27me3 at promoter level of a subset of genes. In parallel, the purification of Exon 21 associated proteins allowed to identify a promising protein partners named hnRNPK and SUZ12 presumably important for ANRIL functions.

<figure><img src="image_2.png" /></figure>

**References:** Alfeghaly C, Sanchez A, Rouget R, Thuillier Q, Igel-Bourguignon V, Marchand V, Branlant C, Motorin Y, Behm-Ansmant I, Maenner S. Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL. Nucleic Acids Res. 2021 May 21:49(9):4954-4970.
Holdt, L.M., Hoffmann, S., Sass, K., Langenberger, D., Scholz, M., Krohn, K., Finstermeier, K., Stahringer, A., Wilfert, W., Beutner, F., et al. (2013). Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet. 9, e1003588.
Johnson R, Guigó R. The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs. RNA. 2014 Jul;20(7):959-76.
Kotake, Y., Nakagawa, T., Kitagawa, K., Suzuki, S., Liu, N., Kitagawa, M., and Xiong, Y. (2011). Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene. Oncogene 30, 1956-1962.
Lo Sardo, V., Chubukov, P., Ferguson, W., Kumar, A., Teng, E.L., Duran, M., Zhang, L., Cost, G., Engler, A.J., Urnov, F., et al. (2018). Unveiling the Role of the Most Impactful Cardiovascular Risk Locus through Haplotype Editing. Cell 175, 1796-1810.e20.
Yap, K. L., Li, S., Muñoz-Cabello, A. M., Raguz, S., Zeng, L., Mujtaba, S., ... & Zhou, M. M. (2010). Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Molecular cell, 38(5), 662-674.