title: Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells.
abstract: Heterochromatin is required to restrict aberrant expression of retrotransposons, but it remains poorly defined due to the underlying repeat-rich sequences. We dissected Suv39h-dependent histone H3 lysine 9 trimethylation (H3K9me3) by genome-wide ChIP sequencing in mouse embryonic stem cells (ESCs). Refined bioinformatic analyses of repeat subfamilies indicated selective accumulation of Suv39h-dependent H3K9me3 at interspersed repetitive elements that cover ∼5% of the ESC epigenome. The majority of the ∼8,150 intact long interspersed nuclear elements (LINEs) and endogenous retroviruses (ERVs), but only a minor fraction of the >1.8 million degenerate and truncated LINEs/ERVs, are enriched for Suv39h-dependent H3K9me3. Transcriptional repression of intact LINEs and ERVs is differentially regulated by Suv39h and other chromatin modifiers in ESCs but governed by DNA methylation in committed cells. These data provide a function for Suv39h-dependent H3K9me3 chromatin to specifically repress intact LINE elements in the ESC epigenome.
authors: Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
authors: Aydan
authors: A
authors: Bulut-Karslioglu
authors: Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
authors: Inti A
authors: IA
authors: De La Rosa-Velázquez
authors: Bioinformatics Unit, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
authors: Fidel
authors: F
authors: Ramirez
authors: Bioinformatics Unit, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
authors: Maxim
authors: M
authors: Barenboim
authors: Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
authors: Megumi
authors: M
authors: Onishi-Seebacher
authors: Department of Genetics/Epigenetics, Saarland University, 66123 Saarbrücken, Germany.
authors: Julia
authors: J
authors: Arand
authors: Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
authors: Carmen
authors: C
authors: Galán
authors: Georg E
authors: GE
authors: Winter
authors: Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
authors: Bettina
authors: B
authors: Engist
authors: Borbala
authors: B
authors: Gerle
authors: Roderick J
authors: RJ
authors: O'Sullivan
authors: Joost H A
authors: JH
authors: Martens
authors: Department of Genetics/Epigenetics, Saarland University, 66123 Saarbrücken, Germany.
authors: Jörn
authors: J
authors: Walter
authors: Bioinformatics Unit, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
authors: Thomas
authors: T
authors: Manke
authors: Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
authors: Monika
authors: M
authors: Lachner
authors: Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany. Electronic address: jenuwein@ie-freiburg.mpg.de.
authors: Thomas
authors: T
authors: Jenuwein
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D019175:DNA Methylation; D053595:Embryonic Stem Cells / Q000201:enzymology*; D020077:Endogenous Retroviruses / Q000235:genetics*; D020868:Gene Silencing; D011495:Histone-Lysine N-Methyltransferase / Q000502:physiology*; D006657:Histones / Q000378:metabolism*; D020084:Long Interspersed Nucleotide Elements; D008780:Methyltransferases / Q000502:physiology*; D051379:Mice; D011499:Protein Processing, Post-Translational; D012097:Repressor Proteins / Q000502:physiology*
chemical_list: D006657:Histones; D012097:Repressor Proteins; C498700:Suv39h1 protein, mouse; D008780:Methyltransferases; D011495:Histone-Lysine N-Methyltransferase; C000592056:Suv39h2 protein, mouse