title: Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells.
abstract: Transcription of endogenous retroviruses (ERVs) is inhibited by de novo DNA methylation during gametogenesis, a process initiated after birth in oocytes and at approximately embryonic day 15.5 (E15.5) in prospermatogonia. Earlier in germline development, the genome, including most retrotransposons, is progressively demethylated. Young ERVK and ERV1 elements, however, retain intermediate methylation levels. As DNA methylation reaches a low point in E13.5 primordial germ cells (PGCs) of both sexes, we determined whether retrotransposons are marked by H3K9me3 and H3K27me3 using a recently developed low-input ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing) method. Although these repressive histone modifications are found predominantly on distinct genomic regions in E13.5 PGCs, they concurrently mark partially methylated long terminal repeats (LTRs) and LINE1 elements. Germline-specific conditional knockout of the H3K9 methyltransferase SETDB1 yields a decrease of both marks and DNA methylation at H3K9me3-enriched retrotransposon families. Strikingly, Setdb1 knockout E13.5 PGCs show concomitant derepression of many marked ERVs, including intracisternal A particle (IAP), ETn, and ERVK10C elements, and ERV-proximal genes, a subset in a sex-dependent manner. Furthermore, Setdb1 deficiency is associated with a reduced number of male E13.5 PGCs and postnatal hypogonadism in both sexes. Taken together, these observations reveal that SETDB1 is an essential guardian against proviral expression prior to the onset of de novo DNA methylation in the germline.
authors.affiliation: Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan;
authors.forename: Sheng
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan;
authors.forename: Julie
authors.initials: J
authors.lastname: Brind'Amour
authors.affiliation: Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan; Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada;
authors.forename: Mohammad M
authors.initials: MM
authors.lastname: Karimi
authors.affiliation: Division of Epigenomics and Development, Department of Molecular Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
authors.forename: Kenjiro
authors.initials: K
authors.lastname: Shirane
authors.affiliation: Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan;
authors.forename: Aaron
authors.initials: A
authors.lastname: Bogutz
authors.affiliation: Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan;
authors.forename: Louis
authors.initials: L
authors.lastname: Lefebvre
authors.affiliation: Division of Epigenomics and Development, Department of Molecular Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan; Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan;
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Sasaki
authors.affiliation: Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan; Cellular Memory Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan.
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Shinkai
authors.affiliation: Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan; mlorincz@mail.ubc.ca.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Lorincz
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D019175:DNA Methylation; D020077:Endogenous Retroviruses / Q000235:genetics / Q000378:metabolism*; D005260:Female; D005718:Gametogenesis / Q000235:genetics; D017353:Gene Deletion; D055786:Gene Knockout Techniques; D020868:Gene Silencing; D005854:Germ Cells / Q000378:metabolism* / Q000821:virology; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics / Q000378:metabolism*; D006657:Histones / Q000378:metabolism*; D008297:Male; D051379:Mice; D014158:Transcription, Genetic; D014775:Virus Activation / Q000235:genetics
chemical_list: D006657:Histones; D011495:Histone-Lysine N-Methyltransferase; C516239:SETDB1 protein, mouse
keywords: DNA methylation; H3K27me3; H3K9me3; Setdb1; endogenous retroviruses; germ cell development