Complete loss of H3K9 methylation dissolves mouse heterochromatin organization

AbstractHistone H3 lysine 9 (H3K9) methylation is a central epigenetic modification that defines heterochromatin from unicellular to multicellular organisms. In mammalian cells, H3K9 methylation can be catalyzed by at least six distinct SET domain enzymes: Suv39h1/Suv39h2, Eset1/Eset2 and G9a/Glp. We used mouse embryonic fibroblasts (MEFs) with a conditional mutation for Eset1 and introduced progressive deletions for the other SET domain genes by CRISPR/Cas9 technology. Compound mutant MEFs for all six SET domain lysine methyltransferase (KMT) genes lack all H3K9 methylation states, derepress nearly all families of repeat elements and display genomic instabilities. Strikingly, the 6KO H3K9 KMT MEF cells no longer maintain heterochromatin organization and have lost electron-dense heterochromatin. This is a compelling analysis of H3K9 methylation-deficient mammalian chromatin and reveals a definitive function for H3K9 methylation in protecting heterochromatin organization and genome integrity.

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The H3K9 Methylation Writer SETDB1 and its Reader MPP8 Cooperate to Silence Satellite DNA Repeats in Mouse Embryonic Stem Cells

Genes ◽

10.3390/genes10100750 ◽

2019 ◽

Vol 10 (10) ◽

pp. 750 ◽

Cited By ~ 1

Author(s):

Cruz-Tapias ◽

Robin ◽

Pontis ◽

Maestro ◽

Ait-Si-Ali

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Embryonic Stem ◽

Dna Repeats ◽

H3k9 Methylation ◽

Set Domain ◽

Histone Lysine Methyltransferase ◽

Satellite Repeats ◽

M Phase ◽

Lysine Methyltransferase

SETDB1 (SET Domain Bifurcated histone lysine methyltransferase 1) is a key lysine methyltransferase (KMT) required in embryonic stem cells (ESCs), where it silences transposable elements and DNA repeats via histone H3 lysine 9 tri-methylation (H3K9me3), independently of DNA methylation. The H3K9 methylation reader M-Phase Phosphoprotein 8 (MPP8) is highly expressed in ESCs and germline cells. Although evidence of a cooperation between H3K9 KMTs and MPP8 in committed cells has emerged, the interplay between H3K9 methylation writers and MPP8 in ESCs remains elusive. Here, we show that MPP8 interacts physically and functionally with SETDB1 in ESCs. Indeed, combining biochemical, transcriptomic and genomic analyses, we found that MPP8 and SETDB1 co-regulate a significant number of common genomic targets, especially the DNA satellite repeats. Together, our data point to a model in which the silencing of a class of repeated sequences in ESCs involves the cooperation between the H3K9 methylation writer SETDB1 and its reader MPP8.

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Separate Domains of Rev1 Mediate Two Modes of DNA Damage Bypass in Mammalian Cells

Molecular and Cellular Biology ◽

10.1128/mcb.00071-09 ◽

2009 ◽

Vol 29 (11) ◽

pp. 3113-3123 ◽

Cited By ~ 73

Author(s):

Jacob G. Jansen ◽

Anastasia Tsaalbi-Shtylik ◽

Giel Hendriks ◽

Himabindu Gali ◽

Ayal Hendel ◽

...

Keyword(s):

Dna Damage ◽

Mammalian Cells ◽

Uv Light ◽

Brct Domain ◽

Mouse Embryonic Fibroblasts ◽

Embryonic Fibroblasts ◽

Dna Damage Signaling ◽

Dna Damage Responses ◽

Y Family

ABSTRACT The Y family DNA polymerase Rev1 has been proposed to play a regulatory role in the replication of damaged templates. To elucidate the mechanism by which Rev1 promotes DNA damage bypass, we have analyzed the progression of replication on UV light-damaged DNA in mouse embryonic fibroblasts that contain a defined deletion in the N-terminal BRCT domain of Rev1 or that are deficient for Rev1. We provide evidence that Rev1 plays a coordinating role in two modes of DNA damage bypass, i.e., an early and a late pathway. The cells carrying the deletion in the BRCT domain are deficient for the early pathway, reflecting a role of the BRCT domain of Rev1 in mutagenic translesion synthesis. Rev1-deficient cells display a defect in both modes of DNA damage bypass. Despite the persistent defect in the late replicational bypass of fork-blocking (6-4)pyrimidine-pyrimidone photoproducts, overall replication is not strongly affected by Rev1 deficiency. This results in almost completely replicated templates that contain gaps encompassing the photoproducts. These gaps are inducers of DNA damage signaling leading to an irreversible G2 arrest. Our results corroborate a model in which Rev1-mediated DNA damage bypass at postreplicative gaps quenches irreversible DNA damage responses.

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SETDB1-Mediated Silencing of Retroelements

Viruses ◽

10.3390/v12060596 ◽

2020 ◽

Vol 12 (6) ◽

pp. 596 ◽

Cited By ~ 3

Author(s):

Kei Fukuda ◽

Yoichi Shinkai

Keyword(s):

Genome Stability ◽

Histone H3 ◽

Endogenous Retroviruses ◽

H3k9 Methylation ◽

Epigenetic Factors ◽

Set Domain ◽

H3k9 Trimethylation ◽

Histone Lysine ◽

Histone Lysine Methyltransferase ◽

Lysine Methyltransferase

SETDB1 (SET domain bifurcated histone lysine methyltransferase 1) is a protein lysine methyltransferase and methylates histone H3 at lysine 9 (H3K9). Among other H3K9 methyltransferases, SETDB1 and SETDB1-mediated H3K9 trimethylation (H3K9me3) play pivotal roles for silencing of endogenous and exogenous retroelements, thus contributing to genome stability against retroelement transposition. Furthermore, SETDB1 is highly upregulated in various tumor cells. In this article, we describe recent advances about how SETDB1 activity is regulated, how SETDB1 represses various types of retroelements such as L1 and class I, II, and III endogenous retroviruses (ERVs) in concert with other epigenetic factors such as KAP1 and the HUSH complex and how SETDB1-mediated H3K9 methylation can be maintained during replication.

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Silica–PEG gel immobilization of mammalian cells

Journal of Materials Chemistry B ◽

10.1039/c4tb00812j ◽

2014 ◽

Vol 2 (42) ◽

pp. 7440-7448 ◽

Cited By ~ 5

Author(s):

Eduardo Reátegui ◽

Lisa Kasinkas ◽

Katrina Kniesz ◽

Molly A. Lefebvre ◽

Alptekin Aksan

Keyword(s):

Mammalian Cells ◽

Mouse Embryonic Fibroblasts ◽

Embryonic Fibroblasts ◽

Human Foreskin Fibroblasts

In this study, human foreskin fibroblasts and mouse embryonic fibroblasts were encapsulated in mechanically reversible, THEOS and THEOS–PEG gels that completely immobilized them restricting their motility, growth and proliferation.

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Apoptosis and development

Essays in Biochemistry ◽

10.1042/bse0390011 ◽

2003 ◽

Vol 39 ◽

pp. 11-24 ◽

Cited By ~ 6

Author(s):

Justin V McCarthy

Keyword(s):

Drosophila Melanogaster ◽

Mammalian Cells ◽

Cell Number ◽

Model Organisms ◽

Biological Processes ◽

Nematode Caenorhabditis Elegans ◽

Apoptotic Pathway ◽

Genetic Pathways ◽

Evolutionarily Conserved ◽

Multicellular Organisms

Apoptosis is an evolutionarily conserved process used by multicellular organisms to developmentally regulate cell number or to eliminate cells that are potentially detrimental to the organism. The large diversity of regulators of apoptosis in mammalian cells and their numerous interactions complicate the analysis of their individual functions, particularly in development. The remarkable conservation of apoptotic mechanisms across species has allowed the genetic pathways of apoptosis determined in lower species, such as the nematode Caenorhabditis elegans and the fruitfly Drosophila melanogaster, to act as models for understanding the biology of apoptosis in mammalian cells. Though many components of the apoptotic pathway are conserved between species, the use of additional model organisms has revealed several important differences and supports the use of model organisms in deciphering complex biological processes such as apoptosis.

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Analysis of the Myod1 cistrome in mouse embryonic fibroblasts

Signaling Pathways Project Datasets ◽

10.1621/l8ubydcl99 ◽

2019 ◽

Author(s):

ML Conerly

Keyword(s):

Mouse Embryonic Fibroblasts ◽

Embryonic Fibroblasts

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Regulation of c-Fos Gene Expression by NF-κB: A p65 Homodimer Binding Site in Mouse Embryonic Fibroblasts but Not Human HEK293 Cells

PLoS ONE ◽

10.1371/journal.pone.0084062 ◽

2013 ◽

Vol 8 (12) ◽

pp. e84062 ◽

Cited By ~ 10

Author(s):

Yu-Cheng Tu ◽

Duen-Yi Huang ◽

Shine-Gwo Shiah ◽

Jang-Shiun Wang ◽

Wan-Wan Lin

Keyword(s):

Gene Expression ◽

Binding Site ◽

Hek293 Cells ◽

Mouse Embryonic Fibroblasts ◽

Embryonic Fibroblasts

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Introduction of Mouse Embryonic Fibroblasts into Early Embryos: From Confusion to Constructive Discussion. Comment on Savatier, P. Introduction of Mouse Embryonic Fibroblasts into Early Embryos Causes Reprogramming and (Con)fusion. Cells 2021, 10, 772

Cells ◽

10.3390/cells10061534 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1534

Author(s):

Krystyna Żyżyńska-Galeńska ◽

Jolanta Karasiewicz ◽

Agnieszka Bernat

Keyword(s):

Mouse Embryonic Fibroblasts ◽

Embryonic Fibroblasts ◽

Early Embryos ◽

Constructive Discussion

We would like to address the issues raised by Pierre Savatier in “Introduction of Mouse Embryonic Fibroblasts into Early Embryos Causes Reprogramming and (Con)Fusion” [...]

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