title: Ectopic DNMT3L triggers assembly of a repressive complex for retroviral silencing in somatic cells.
abstract: Mammalian genomes are replete with retrotransposable elements, including endogenous retroviruses. DNA methyltransferase 3-like (DNMT3L) is an epigenetic regulator expressed in prospermatogonia, growing oocytes, and embryonic stem (ES) cells. Here, we demonstrate that DNMT3L enhances the interaction of repressive epigenetic modifiers, including histone deacetylase 1 (HDAC1), SET domain, bifurcated 1 (SETDB1), DNA methyltransferase 3A (DNMT3A), and tripartite motif-containing protein 28 (TRIM28; also known as TIF1β and KAP1) in ES cells and orchestrates retroviral silencing activity with TRIM28 through mechanisms including, but not limited to, de novo DNA methylation. Ectopic expression of DNMT3L in somatic cells causes methylation-independent retroviral silencing activity by recruitment of the TRIM28/HDAC1/SETDB1/DNMT3A/DNMT3L complex to newly integrated Moloney murine leukemia virus (Mo-MuLV) proviral DNA. Concurrent with this recruitment, we also observed the accumulation of histone H3 lysine 9 trimethylation (H3K9me3) and heterochromatin protein 1 gamma (HP1γ), as well as reduced H3K9 and H3K27 acetylation at Mo-MuLV proviral sequences. Ectopic expression of DNMT3L in late-passage mouse embryonic fibroblasts (MEFs) recruited cytoplasmically localized HDAC1 to the nucleus. The formation of this epigenetic modifying complex requires interaction of DNMT3L with DNMT3A as well as with histone H3. In fetal testes at embryonic day 17.5, endogenous DNMT3L also enhanced the binding among TRIM28, DNMT3A, SETDB1, and HDAC1. We propose that DNMT3L may be involved in initiating a cascade of repressive epigenetic modifications by assisting in the preparation of a chromatin context that further attracts DNMT3A-DNMT3L binding and installs longer-term DNA methylation marks at newly integrated retroviruses.
  
  
  OBJECTIVE
  Almost half of the mammalian genome is composed of endogenous retroviruses and other retrotransposable elements that threaten genomic integrity. These elements are usually subject to epigenetic silencing. We discovered that two epigenetic regulators that lack enzymatic activity, DNA methyltransferase 3-like (DNMT3L) and tripartite motif-containing protein 28 (TRIM28), collaborate with each other to impose retroviral silencing. In addition to modulating de novo DNA methylation, we found that by interacting with TRIM28, DNMT3L can attract various enzymes to form a DNMT3L-induced repressive complex to remove active marks and add repressive marks to histone proteins. Collectively, these results reveal a novel and pivotal function of DNMT3L in shaping the chromatin modifications necessary for retroviral and retrotransposon silencing.
authors.affiliation: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.
authors.forename: Tzu-Hao
authors.initials: TH
authors.lastname: Kao
authors.affiliation: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.
authors.forename: Hung-Fu
authors.initials: HF
authors.lastname: Liao
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, College of Physicians and Surgeons, Columbia University, New York, New York, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Wolf
authors.affiliation: Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.
authors.forename: Kang-Yu
authors.initials: KY
authors.lastname: Tai
authors.affiliation: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan Genomics Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Ching-Yu
authors.initials: CY
authors.lastname: Chuang
authors.affiliation: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.
authors.forename: Hsuan-Shu
authors.initials: HS
authors.lastname: Lee
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei, Taiwan Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Hung-Chih
authors.initials: HC
authors.lastname: Kuo
authors.affiliation: Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya, Tokyo, Japan.
authors.forename: Kenichiro
authors.initials: K
authors.lastname: Hata
authors.affiliation: Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.
authors.forename: Xing
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Cheng
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, College of Physicians and Surgeons, Columbia University, New York, New York, USA.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Goff
authors.affiliation: UCL Cancer Institute, Department of Cancer Biology, University College London, London, United Kingdom.
authors.forename: Steen K T
authors.initials: SK
authors.lastname: Ooi
authors.affiliation: Department of Genetics and Development, Columbia University, New York, New York, USA.
authors.forename: Timothy H
authors.initials: TH
authors.lastname: Bestor
authors.affiliation: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan Research Centre for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan Centre for Systems Biology, National Taiwan University, Taipei, Taiwan shaupinglin@ntu.edu.tw.
authors.forename: Shau-Ping
authors.initials: SP
authors.lastname: Lin
mesh_terms: D000818:Animals; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000378:metabolism*; D000090205:DNA Methyltransferase 3A; D053595:Embryonic Stem Cells / Q000201:enzymology / Q000378:metabolism; D015870:Gene Expression; D020868:Gene Silencing; D056284:Histone Deacetylase 1 / Q000235:genetics / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D006801:Humans; D007942:Leukemia, Experimental / Q000201:enzymology* / Q000235:genetics* / Q000378:metabolism; D051379:Mice; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D008979:Moloney murine leukemia virus / Q000235:genetics / Q000502:physiology*; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D000076183:Tripartite Motif-Containing Protein 28
chemical_list: C000717967:DNMT3A protein, human; C000715535:Dnmt3a protein, mouse; D006657:Histones; D009687:Nuclear Proteins; D012097:Repressor Proteins; C498796:Dnmt3l protein, mouse; D004248:DNA (Cytosine-5-)-Methyltransferases; D000090205:DNA Methyltransferase 3A; C103190:Trim28 protein, mouse; D000076183:Tripartite Motif-Containing Protein 28; C484389:Hdac1 protein, mouse; D056284:Histone Deacetylase 1