Fig. 1

LINEs are predominantly epigenetically repressed, but a subset also exhibit enhancer-associated epigenetics. A A heatmap shows enrichment (red) and depletion (blue) of LINE families for the histone modifications H3K9me3 (top) and H3K27ac (bottom) in 16 publicly available human primary blood cell types obtained through the Blueprint Database [28]. Enrichment of ChIP signal at LINEs was quantified using Giggle [38]. Columns represent annotated LINE families with enrichment scores of more than 100 or depletion scores of less than -100 for either histone mark in any of the datasets shown. Unfiltered heatmaps of all LINE families, as well as SINE, ERV and DNA transposon families are available in (Additional file 1: Fig. S1). Most LINE families, especially younger L1M and L1P families are strongly enriched for repressive H3K9me3 and strongly depleted for activating H3K27ac, as expected. B Heatmaps and metaplots show ChIP signal of repressive H3K9me3 and enhancer associated H3K4me1 and H3K27ac at individual LINE-1s of lengths > 500 bp, in both primary naive B cells [28], and in the lymphoblastoid cell line GM12878 [29]. 10 kb windows were set around the 5’ end of the LINE-1 to cover the entire length of LINEs. Many LINE-1s are silenced by H3K9me3 as expected (navy), and some have enhancer associated epigenetic modifications (yellow). A subset, labeled as “bivalent” exhibit both repressive and enhancer associated signals (cyan)