L1 retrotransposons were repressed by MORC2A. (A) Expression change of repetitive elements repressed by SETDB1 and/or MORC2A in Setdb1 and Morc2a KO mESCs. Previously reported RNA-seq data from Setdb1 KO mESC (Karimi et al. 2011) was used for the analysis. (B) Occupancy of repeat class in entire genome (left) or MORC2A binding sites (right). (C) Fraction of MORC2A binding sites overlapping with L1Md_Gf (L1MdTf_II), L1MdA (L1MdA_I), or L1Md_T in all MORC2A binding sites. (D) Enrichment of MORC2A along L1Md_T. MORC2A ChIP-seq reads were aligned to the L1Md_T consensus sequence, and enrichment of MORC2A relative to input for each 100-bp bin was plotted. (E) ChIP-qPCR confirmation of MORC2A binding to 5′ UTR of L1Md_T. MORC2A ChIPs were performed Morc2a KO mESCs stably expressing V5-tagged WT MORC2A. Anti-V5 Ab was used. (F) ChIP-qPCR analysis of H3K9me3 at L1Md_T in Morc2a KO cells. (G) Repression of L1P4a, L1PA2, L1M3a (L1M3B), and L1HS by human MORC2 in HeLa cells. Publicly available RNA-seq data in Morc2 knockout HeLa cells (GSE95452) were used for the analysis. Human MORC2 also repressed L1. (H) Enrichment of human MORC2 in 5′ UTR of L1HS. Publicly available human MORC2 ChIP-seq data (GSE95456) was used for the analysis. Data represent mean ± SE (n = 3). (*) P-value <0.01 (t-test). See also Supplemental Figure S4.