MCAF2/ATF7IP2 directs meiosis-specific H3K9 methylation

H3K9 tri-methylation (H3K9me3) has emerging functions in gene regulation in addition to its accumulation on constitutive heterochromatin at pericentromeres. It remains a mystery why and how H3K9me3 is dynamically regulated in male meiosis. Here, we identify a novel and critical regulator of H3K9 methylation and spermatogenic heterochromatin organization: the germline-specific protein MCAF2 (ATF7IP2). We show that MCAF2 amasses on autosomal and X pericentric heterochromatin in male germ cells. On the sex chromosomes, which undergo meiotic sex chromosome inactivation (MSCI), the DNA damage response pathway recruits MCAF2 to X pericentric heterochromatin, where it facilitates the recruitment of SETDB1, a histone methyltransferase that catalyzes H3K9me3. In the absence of MCAF2, germ cells are arrested in meiotic prophase, and the mutant analyses revealed that MCAF2 is required for the maintenance of MSCI, and for global activation of autosomal genes and retrotransposon-derived loci in meiosis; this reveals a regulatory function for MCAF2 that is counterintuitive to its association with repressive H3K9me3. Taken together, we propose that MCAF2 is a downstream effector of the DDR pathway in meiosis that coordinates the organization of heterochromatin and gene regulation through the spatial regulation of SETDB1-mediated H3K9me3 deposition. Overall design: Whole cell lysates were collected from P14 Mcaf2ctrl or Mcaf2KO testes.