RT Journal
A1 Papin, Christophe
A1 Ibrahim, Abdulkhaleg
A1 Gras, Stéphanie Le
A1 Velt, Amandine
A1 Stoll, Isabelle
A1 Jost, Bernard
A1 Menoni, Hervé
A1 Bronner, Christian
A1 Dimitrov, Stefan
A1 Hamiche, Ali
T1 Combinatorial DNA methylation codes at repetitive elements
JF Genome Research 
JO Genome Research 
YR 2017 
FD June 01 
VO 27 
IS 6 
SP 934 
OP 946 
DO 10.1101/gr.213983.116 
UL http://genome.cshlp.org/content/27/6/934.abstract 
AB DNA methylation is an essential epigenetic modification, present in both unique DNA sequences and repetitive elements, but its exact function in repetitive elements remains obscure. Here, we describe the genome-wide comparative analysis of the 5mC, 5hmC, 5fC, and 5caC profiles of repetitive elements in mouse embryonic fibroblasts and mouse embryonic stem cells. We provide evidence for distinct and highly specific DNA methylation/oxidation patterns of the repetitive elements in both cell types, which mainly affect CA repeats and evolutionarily conserved mouse-specific transposable elements including IAP-LTRs, SINEs B1m/B2m, and L1Md-LINEs. DNA methylation controls the expression of these retroelements, which are clustered at specific locations in the mouse genome. We show that TDG is implicated in the regulation of their unique DNA methylation/oxidation signatures and their dynamics. Our data suggest the existence of a novel epigenetic code for the most recently acquired evolutionarily conserved repeats that could play a major role in cell differentiation.