Figure 5

Chromatin environment of intervening regions of methylated copies. (A) The average H3K4me3 and CTCF profiles of the intervening regions between ERV and gene are shown. Gene regions represented on the left part of panel A show only H3K4me3 enrichment while regions represented on the right harbor both H3K4me3 and CTCF. The genes included in the data set are Eef1e1, Gng10, Hus1 and Pnpt1 for the left panel and Mthfd2l and Atxn1l for the right panel. The four genes not included in this analysis but in Table 2 are either absent from Encode strains or not studied in tissues available at Encode. (B) Average profiles of intervening regions adjacent to unmethylated copies (associated genes transcribed). The regions included in this analysis are from the following genes: Lair, Cyb5r1, Bola1, Cdgap and Cml2 which constitute all the unmethylated copies available. (C) Average profile of intervening regions harboring a tissue-specific methylated epiallele. The regions included in this analysis harbor the following genes : Lair, Cdgap and Cml2, which constitutes the only cases where the associated ERV copy is found methylated in one tissue (associated genes silent) and unmethylated in another (associated genes transcribed). The flanking regions chosen for this analysis (400 bp and 200 bp) correspond to a minimum length common for all regions analyzed (with the exception of Cml2 which is 68 bp from its ERV copy). (D) Cdgap chromatin immunoprecipitation-qPCR in ES cells (top) and lung (bottom). We assayed for permissive marks (H3K4me3, H3 acetylation) and repressive marks (H3K27me3) along with a mock control (IgG) in the intervening region between Cdgap and the ERV copy. Numbers in the cartoon show the localization of the quantitative PCR primer pairs. H3K27me3 enrichment is shown in opposite direction of H3K4me3. bp: base pairs; CGI: CpG Island; CTCF: CCCTC-binding factor; ERV: endogenous retrovirus; ES: embryonic stem; IgG: immunoglobulin G; LTR: long terminal repeat.