Coevolution; DNA binding; DNA replication; Domestication; Expression enhancer; MITE; Transposon; Protein Isoforms; Histone-Lysine N-Methyltransferase; SETMAR protein, human; Colon/metabolism; Enhancer Elements, Genetic; Humans; Protein Isoforms/genetics; DNA Repair; Histone-Lysine N-Methyltransferase/genetics; Regulatory Sequences, Nucleic Acid; Colon; Genetics
Abstract :
[en] 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.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Antoine-Lorquin, Aymeric; IRISA, 263 avenue du Général Leclerc, 35042 Rennes, France
Arensburger, Peter; Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, - United States
Arnaoty, Ahmed; EA GICC, 7501, CHRU de Tours, 37044 TOURS, Cedex 09, France
Asgari, Sassan; School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
Batailler, Martine; PRC, UMR INRA 0085, CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly, France
Beauclair, Linda; PRC, UMR INRA 0085, CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly, France
Belleannée, Catherine; IRISA, 263 avenue du Général Leclerc, 35042 Rennes, France
Buisine, Nicolas; UMR CNRS 7221, Muséum National d'Histoire Naturelle, 75005 Paris, France
Coustham, Vincent; BOA, INRAE, Université de Tours, 37380 Nouzilly, France
Guyetant, Serge; Tumorothèque du CHRU de Tours, 37044 Tours, Cedex, France
Helou, Laura ; Université de Liège - ULiège > Département des sciences cliniques ; PRC, UMR INRA 0085, CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly, France
Lecomte, Thierry; EA GICC, 7501, CHRU de Tours, 37044 TOURS, Cedex 09, France
Pitard, Bruno; Université de Nantes, CNRS ERL6001, Inserm 1232, CRCINA, F-44000 Nantes, France
Stévant, Isabelle; Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon, 1, 46 allée d'Italie, 69364 Lyon, France
Bigot, Yves; PRC, UMR INRA 0085, CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly, France. Electronic address: yves.bigot@inrae.fr
National Cancer Association SNFGE - French National Society of Gastroenterology Cancéropôle du Grand Ouest
Funding text :
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.
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