title: Systematic identification of factors for provirus silencing in embryonic stem cells.
abstract: Embryonic stem cells (ESCs) repress the expression of exogenous proviruses and endogenous retroviruses (ERVs). Here, we systematically dissected the cellular factors involved in provirus repression in embryonic carcinomas (ECs) and ESCs by a genome-wide siRNA screen. Histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/Ube2i/Sae1/Uba2/Senp6), and chromatin modifiers (Trim28/Eset/Atf7ip) are key determinants that establish provirus silencing. RNA-seq analysis uncovered the roles of Chaf1a/b and sumoylation modifiers in the repression of ERVs. ChIP-seq analysis demonstrates direct recruitment of Chaf1a and Sumo2 to ERVs. Chaf1a reinforces transcriptional repression via its interaction with members of the NuRD complex (Kdm1a, Hdac1/2) and Eset, while Sumo2 orchestrates the provirus repressive function of the canonical Zfp809/Trim28/Eset machinery by sumoylation of Trim28. Our study reports a genome-wide atlas of functional nodes that mediate proviral silencing in ESCs and illuminates the comprehensive, interconnected, and multi-layered genetic and epigenetic mechanisms by which ESCs repress retroviruses within the genome.
authors.affiliation: Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore.
authors.forename: Bin Xia
authors.initials: BX
authors.lastname: Yang
authors.affiliation: Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
authors.forename: Chadi A
authors.initials: CA
authors.lastname: El Farran
authors.affiliation: College of Life Sciences, Nankai University, Tianjin 300071, China.
authors.forename: Hong Chao
authors.initials: HC
authors.lastname: Guo
authors.affiliation: Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
authors.forename: Tao
authors.initials: T
authors.lastname: Yu
authors.affiliation: Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore.
authors.forename: Hai Tong
authors.initials: HT
authors.lastname: Fang
authors.affiliation: Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
authors.forename: Hao Fei
authors.initials: HF
authors.lastname: Wang
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA.
authors.forename: Sharon
authors.initials: S
authors.lastname: Schlesinger
authors.affiliation: Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore.
authors.forename: Yu Fen Samantha
authors.initials: YF
authors.lastname: Seah
authors.affiliation: Membrane Traffic Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore.
authors.forename: Germaine Yen Lin
authors.initials: GY
authors.lastname: Goh
authors.affiliation: Quantitative Proteomics Group, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore.
authors.forename: Suat Peng
authors.initials: SP
authors.lastname: Neo
authors.affiliation: Division of Cancer Genetics and Therapeutics, Laboratory of NF-κB Signaling, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore.
authors.forename: Yinghui
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Lorincz
authors.affiliation: Division of Cancer Genetics and Therapeutics, Laboratory of NF-κB Signaling, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.
authors.forename: Vinay
authors.initials: V
authors.lastname: Tergaonkar
authors.affiliation: Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
authors.forename: Tit-Meng
authors.initials: TM
authors.lastname: Lim
authors.affiliation: College of Life Sciences, Nankai University, Tianjin 300071, China.
authors.forename: Lingyi
authors.initials: L
authors.lastname: Chen
authors.affiliation: Quantitative Proteomics Group, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
authors.forename: Jayantha
authors.initials: J
authors.lastname: Gunaratne
authors.affiliation: Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
authors.forename: James J
authors.initials: JJ
authors.lastname: Collins
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, New York, NY 10032, USA.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Goff
authors.affiliation: Howard Hughes Medical Institute, Boston, MA 02115, USA; Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston, MA 02115, USA.
authors.forename: George Q
authors.initials: GQ
authors.lastname: Daley
authors.affiliation: Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.
authors.forename: Hu
authors.initials: H
authors.lastname: Li
authors.affiliation: Membrane Traffic Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.
authors.forename: Frederic A
authors.initials: FA
authors.lastname: Bard
authors.affiliation: Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore. Electronic address: yhloh@imcb.a-star.edu.sg.
authors.forename: Yuin-Han
authors.initials: YH
authors.lastname: Loh
mesh_terms: D000818:Animals; D056504:Chromatin Assembly Factor-1 / Q000235:genetics / Q000378:metabolism; D054278:Embryonal Carcinoma Stem Cells / Q000821:virology; D053595:Embryonic Stem Cells / Q000821:virology*; D020077:Endogenous Retroviruses / Q000235:genetics*; D044127:Epigenesis, Genetic; D051379:Mice; D011533:Proviruses / Q000235:genetics*; D025841:Small Ubiquitin-Related Modifier Proteins / Q000378:metabolism
chemical_list: C533592:Chaf1a protein, mouse; C533594:Chaf1b protein, mouse; D056504:Chromatin Assembly Factor-1; D025841:Small Ubiquitin-Related Modifier Proteins