DNA methylation status determines the sensitivity of repeats to restriction by the HUSH-MORC2 complex [CUT&RUN]

The human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. However, how HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains poorly understood. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1. Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding. Simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric α-satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the independent epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development. Comparative H3K9me3 and H3K4me3 enrichment analysis of CUT&RUN-seq data for human neuroepithelial like stem cells (hNSCs). The comparison was done between hNSCs lacking MORC2, TASOR, DNMT1 and their respective controls to investigate the changes induced by the removal of the forementioned epigenetic repressors. Additionally, CUT&RUNseq was also employed to explore the occupancy of MORC2. Comparative H3K4me3 enrichment analysis of CUT&RUN-seq data for human neuroepithelial like stem cells (hNSCs). The comparison was done between hNSCs lacking DNMT1 and DNMT1+MORC2 and their respective controls to investigate the changes induced by the removal of the forementioned epigenetic repressors.