Kris G. Alavattam1,2,8, Jasmine M. Esparza3,8, Mengwen Hu1,3,8, Ryuki Shimada4,8, Anna R. Kohrs1, Hironori Abe1,3,4, Yasuhisa Munakata1,3, Kai Otsuka3, Saori Yoshimura4, Yuka Kitamura3, Yu-Han Yeh1,3, Yueh-Chiang Hu1,5, Jihye Kim6, Paul R. Andreassen5,7, Kei-ichiro Ishiguro4 and Satoshi H. Namekawa1,3,5 1Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA; 2Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA; 3Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA; 4Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto 860-0811, Japan; 5Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA; 6Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan; 7Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA Corresponding authors: snamekawaucdavis.edu, ishigurokumamoto-u.ac.jp

↵8 These authors contributed equally to this work.

Abstract

H3K9 trimethylation (H3K9me3) plays emerging roles in gene regulation, beyond its accumulation on pericentric constitutive heterochromatin. It remains a mystery why and how H3K9me3 undergoes dynamic regulation in male meiosis. Here, we identify a novel, critical regulator of H3K9 methylation and spermatogenic heterochromatin organization: the germline-specific protein ATF7IP2 (MCAF2). We show that in male meiosis, ATF7IP2 amasses on autosomal and X-pericentric heterochromatin, spreads through the entirety of the sex chromosomes, and accumulates on thousands of autosomal promoters and retrotransposon loci. On the sex chromosomes, which undergo meiotic sex chromosome inactivation (MSCI), the DNA damage response pathway recruits ATF7IP2 to X-pericentric heterochromatin, where it facilitates the recruitment of SETDB1, a histone methyltransferase that catalyzes H3K9me3. In the absence of ATF7IP2, male germ cells are arrested in meiotic prophase I. Analyses of ATF7IP2-deficient meiosis reveal the protein's essential roles in the maintenance of MSCI, suppression of retrotransposons, and global up-regulation of autosomal genes. We propose that ATF7IP2 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.

Received September 30, 2023. Accepted January 31, 2024.