Two repeated motifs enriched within some enhancers and origins of replication are bound by SETMAR isoforms in human colon cells

Aymeric Antoine-Lorquin; Peter Arensburger; Ahmed Arnaoty; Sassan Asgari; Martine Batailler; Linda Beauclair; Catherine Belleannée; Nicolas Buisine; Vincent Coustham; Serge Guyetant; Laura Helou; Thierry Lecomte; Bruno Pitard; Isabelle Stévant; Yves Bigot

doi:10.1016/j.ygeno.2021.03.032

Two repeated motifs enriched within some enhancers and origins of replication are bound by SETMAR isoforms in human colon cells

Aymeric Antoine-Lorquin, Peter Arensburger, Ahmed Arnaoty, Sassan Asgari, Martine Batailler, Linda Beauclair, Catherine Belleannée, Nicolas Buisine, Vincent Coustham, Serge Guyetant, Laura Helou, Thierry Lecomte, Bruno Pitard, Isabelle Stévant, Yves Bigot

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

Abstract

Setmar is a gene specific to simian genomes. The function(s) of its isoforms are poorly understood and their existence in healthy tissues remains to be validated. Here we profiled SETMAR expression and its genome-wide binding landscape in colon tissue. We found isoforms V3 and V6 in healthy and tumour colon tissues as well as incell lines. In two colorectal cell lines SETMAR binds to several thousand Hsmar1 and MADE1 terminal ends, transposons mostly located in non-genic regions of active chromatin including in enhancers. It also binds to a 12-bp motifs similar to an inner motif in Hsmar1 and MADE1 terminal ends. This motif is interspersed throughout the genome and is enriched in GC-rich regions as well as in CpG islands that contain constitutive replication origins. It is also found in enhancers other than those associated with Hsmar1 and MADE1. The role of SETMAR in the expression of genes, DNA replication and in DNA repair are discussed.

Original language	English
Pages (from-to)	1589-1604
Number of pages	16
Journal	Genomics
Volume	113
Issue number	3
DOIs	https://doi.org/10.1016/j.ygeno.2021.03.032
State	Published - May 2021
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2021 Elsevier Inc.

Funding

This work was funded by the C.N.R.S., the I.N.R.A., and the GDR CNRS 2157. It also received funds from a research program grant from the Cancéropôle Grand-Ouest, the Ligue Nationale Contre le Cancer and grants from Amgen and the French National Society of Gastroenterology. Laura Helou holds a PhD fellowship from the Région Centre Val de Loire. The funders have had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

Funders	Funder number
C.N.R.S.	GDR CNRS 2157
Région Centre Val de Loire
Amgen
Ligue Contre le Cancer
Société Nationale Française de Gastro-Entérologie

Keywords

Coevolution
DNA binding
DNA replication
Domestication
Expression enhancer
MITE
Transposon

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10.1016/j.ygeno.2021.03.032

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Antoine-Lorquin, A., Arensburger, P., Arnaoty, A., Asgari, S., Batailler, M., Beauclair, L., Belleannée, C., Buisine, N., Coustham, V., Guyetant, S., Helou, L., Lecomte, T., Pitard, B., Stévant, I., & Bigot, Y. (2021). Two repeated motifs enriched within some enhancers and origins of replication are bound by SETMAR isoforms in human colon cells. Genomics, 113(3), 1589-1604. https://doi.org/10.1016/j.ygeno.2021.03.032

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Antoine-Lorquin, A, Arensburger, P, Arnaoty, A, Asgari, S, Batailler, M, Beauclair, L, Belleannée, C, Buisine, N, Coustham, V, Guyetant, S, Helou, L, Lecomte, T, Pitard, B, Stévant, I & Bigot, Y 2021, 'Two repeated motifs enriched within some enhancers and origins of replication are bound by SETMAR isoforms in human colon cells', Genomics, vol. 113, no. 3, pp. 1589-1604. https://doi.org/10.1016/j.ygeno.2021.03.032

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AU - Antoine-Lorquin, Aymeric

AU - Arensburger, Peter

AU - Arnaoty, Ahmed

AU - Asgari, Sassan

AU - Batailler, Martine

AU - Beauclair, Linda

AU - Belleannée, Catherine

AU - Buisine, Nicolas

AU - Coustham, Vincent

AU - Guyetant, Serge

AU - Helou, Laura

AU - Lecomte, Thierry

AU - Pitard, Bruno

AU - Stévant, Isabelle

AU - Bigot, Yves

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Two repeated motifs enriched within some enhancers and origins of replication are bound by SETMAR isoforms in human colon cells

Abstract

Bibliographical note

Funding

Keywords

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