RESF1 regulates imprinting genes and ERVs. (A) Expression change of repetitive elements repressed by SETDB1 and/or RESF1 in Setdb1 and Resf1 KO mESCs. All repetitive elements repressed by both SETDB1 and RESF1 were ERV retrotransposons. Previously reported RNA-seq data from Setdb1 KO mESC (Karimi et al. 2011) was used for the analysis. (B) Length distribution of repeat class in entire genome (left) and RESF1 binding sites (right). ERV retrotransposon (LTR) was enriched in RESF1 binding sites. (C) List of imprinting genes dysregulated in Resf1 KO cells. Direction of expression change of these genes was almost same those in Setdb1 KO mESCs. Six out of 10 dysregulated imprinting genes were located near RESF1 binding sites (<500 kb), and these RESF1 binding sites were occupied by SETDB1. Publicly available RNA-seq data in Setdb1 KO mESCs (GSE29413) (Karimi et al. 2011) and SETDB1 ChIP-seq data in mESCs (GSE17642) (Yuan et al. 2009) were used. (D) Representative view of RESF1 binding site around imprinting genes. Regions in red or blue boxes represent RESF1 binding sites or dysregulated gene in Resf1 KO cells, respectively. See also Supplemental Figure S6.