ChAHP and ChAHP2 control diverse retrotransposons by complementary activities [ATAC-seq]

Retrotransposon control in mammals is an intricate process that is effectuated by a broad network of chromatin regulatory pathways. We previously discovered ChAHP, a protein complex with repressive activity against SINE retrotransposons, composed of the transcription factor ADNP, chromatin remodeler CHD4, and HP1 proteins. Here we identify ChAHP2, a protein complex homologous to ChAHP, wherein ADNP is replaced by ADNP2. ChAHP2 is predominantly targeted to ERVs and LINEs, via HP1b-mediated binding of H3K9 trimethylated histones. We further demonstrate that ChAHP also binds these elements in a mechanistically equivalent manner to ChAHP2, and distinct from DNA sequence-specific recruitment at SINEs. Genetic ablation of ADNP2 alleviates ERV and LINE1 repression, which is synthetically exacerbated by additional depletion of ADNP. Together, our results reveal that the ChAHP and ChAHP2 complexes function to control both non-autonomous and autonomous retrotransposons by complementary activities, further adding to the complexity of mammalian transposon control. All experiments were performed with 2-4 biological replicates in mouse ES cells grown in media containing serum, LIF, GSK3b inhibitor and MEK inhibitor (2i). ChIP samples were produced under a variety of conditions (wild type controls, point mutations in ADNP or ADNP2, SETDB1 depletion) to assay the levels and distribution of ADNP2, ADNP and H3K9me3. Total RNAseq was performed upon individual and combined removal of ADNP and ADNP2 (genetic KO for ADNP2, protein depletion for ADNP) to test function in transcription regulation.