Unique regions flanking IAPEz but not MERVL elements are highly enriched in KAP1. (A) Profiling of KAP1 in the flanking sequence of all full-length IAPEz, MERVL and MMERVK10C ERVs. KAP1 ChIP-seq reads  from wt mESCs were aligned to the mouse genome (mm9), and the density profile of unique reads mapping to the 6 kb regions flanking all annotated intact MERVL (656), MMERVK10C (298) and IAPEz (599) elements, was plotted as shown. (B-C) Heat maps of KAP1 enrichment in the genomic regions flanking 599 IAPEz and 656 MERVL elements in wt mESCs. KAP1 ChIP-seq reads  were aligned to the mouse genome (mm9), and the density of uniquely aligned reads, mapping to the 6 kb regions flanking all intact ERVs of the specified families, was plotted. Reads extending into the ERV are due to in silico extension of aligned reads by 300 bp. (D) ChIP and qPCR analysis of KAP1 in TT2 wt mESCs at the LTRs of IAPEz, MMERVK10C and MERVL, as well as the MERVL pol internal region. IgG, negative control IP. Data are mean enrichment from three technical replicates as a percentage of the input chromatin and error bars represent SD. IgG, immunoglobulin G; IP, immunoprecipitation; SD, standard deviation.