scholarly journals DNA Methylation Is Linked to Deacetylation of Histone H3, but Not H4, on the Imprinted Genes Snrpnand U2af1-rs1

2001 ◽  
Vol 21 (16) ◽  
pp. 5426-5436 ◽  
Author(s):  
Richard I. Gregory ◽  
Tamzin E. Randall ◽  
Colin A. Johnson ◽  
Sanjeev Khosla ◽  
Izuho Hatada ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Es Cells ◽  
Histone H3 ◽  
Embryonic Stem ◽  
Histone Deacetylation ◽  
Differentially Methylated Region ◽  
Paternal Allele ◽  
Maternal Allele ◽  
Control Center ◽  
Mbd Protein

ABSTRACT The relationship between DNA methylation and histone acetylation at the imprinted mouse genes U2af1-rs1 and Snrpnis explored by chromatin immunoprecipitation (ChIP) and resolution of parental alleles using single-strand conformational polymorphisms. TheU2af1-rs1 gene lies within a differentially methylated region (DMR), while Snrpn has a 5′ DMR (DMR1) with sequences homologous to the imprinting control center of the Prader-Willi/Angelman region. For both DMR1 of Snrpn and the 5′ untranslated region (5′-UTR) and 3′-UTR ofU2af1-rs1, the methylated and nonexpressed maternal allele was underacetylated, relative to the paternal allele, at all H3 lysines tested (K14, K9, and K18). For H4, underacetylation of the maternal allele was exclusively (U2af1-rs1) or predominantly (Snrpn) at lysine 5. Essentially the same patterns of differential acetylation were found in embryonic stem (ES) cells, embryo fibroblasts, and adult liver from F1 mice and in ES cells from mice that were dipaternal or dimaternal for U2af1-rs1. In contrast, in a region within Snrpn that has biallelic methylation in the cells and tissues analyzed, the paternal (expressed) allele showed relatively increased acetylation of H4 but not of H3. The methyl-CpG-binding-domain (MBD) protein MeCP2 was found, by ChIP, to be associated exclusively with the maternal U2af1-rs1 allele. To ask whether DNA methylation is associated with histone deacetylation, we produced mice with transgene-induced methylation at the paternal allele of U2af1-rs1. In these mice, H3 was underacetylated across both the parental U2af1-rs1 alleles whereas H4 acetylation was unaltered. Collectively, these data are consistent with the hypothesis that CpG methylation leads to deacetylation of histone H3, but not H4, through a process that involves selective binding of MBD proteins.

scholarly journals Allelic H3K27me3 to allelic DNA methylation switch maintains noncanonical imprinting in extraembryonic cells

2019 ◽  
Vol 5 (12) ◽  
pp. eaay7246 ◽  
Author(s):  
Zhiyuan Chen ◽  
Qiangzong Yin ◽  
Azusa Inoue ◽  
Chunxia Zhang ◽  
Yi Zhang
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Genetic Manipulation ◽  
Paternal Allele ◽  
Gene Promoters ◽  
Maternal Allele ◽  
Mammalian Development ◽  
Placental Development ◽  
Early Embryos ◽  
Allele Specific

Faithful maintenance of genomic imprinting is essential for mammalian development. While germline DNA methylation–dependent (canonical) imprinting is relatively stable during development, the recently found oocyte-derived H3K27me3-mediated noncanonical imprinting is mostly transient in early embryos, with some genes important for placental development maintaining imprinted expression in the extraembryonic lineage. How these noncanonical imprinted genes maintain their extraembryonic-specific imprinting is unknown. Here, we report that maintenance of noncanonical imprinting requires maternal allele–specific de novo DNA methylation [i.e., somatic differentially methylated regions (DMRs)] at implantation. The somatic DMRs are located at the gene promoters, with paternal allele–specific H3K4me3 established during preimplantation development. Genetic manipulation revealed that both maternal EED and zygotic DNMT3A/3B are required for establishing somatic DMRs and maintaining noncanonical imprinting. Thus, our study not only reveals the mechanism underlying noncanonical imprinting maintenance but also sheds light on how histone modifications in oocytes may shape somatic DMRs in postimplantation embryos.

scholarly journals LSD1 prevents aberrant heterochromatin formation in Neurospora crassa

2020 ◽  
Vol 48 (18) ◽  
pp. 10199-10210
Author(s):  
William K Storck ◽  
Vincent T Bicocca ◽  
Michael R Rountree ◽  
Shinji Honda ◽  
Tereza Ormsby ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Neurospora Crassa ◽  
Constitutive Heterochromatin ◽  
Histone H3 ◽  
Feedback Mechanism ◽  
Histone Demethylase ◽  
Histone Deacetylation ◽  
Heterochromatin Formation ◽  
Lysine Specific Demethylase ◽  
Specialized Form

Abstract Heterochromatin is a specialized form of chromatin that restricts access to DNA and inhibits genetic processes, including transcription and recombination. In Neurospora crassa, constitutive heterochromatin is characterized by trimethylation of lysine 9 on histone H3, hypoacetylation of histones, and DNA methylation. We explored whether the conserved histone demethylase, lysine-specific demethylase 1 (LSD1), regulates heterochromatin in Neurospora, and if so, how. Though LSD1 is implicated in heterochromatin regulation, its function is inconsistent across different systems; orthologs of LSD1 have been shown to either promote or antagonize heterochromatin expansion by removing H3K4me or H3K9me respectively. We identify three members of the Neurospora LSD complex (LSDC): LSD1, PHF1, and BDP-1. Strains deficient for any of these proteins exhibit variable spreading of heterochromatin and establishment of new heterochromatin domains throughout the genome. Although establishment of H3K9me3 is typically independent of DNA methylation in Neurospora, instances of DNA methylation-dependent H3K9me3 have been found outside regions of canonical heterochromatin. Consistent with this, the hyper-H3K9me3 phenotype of Δlsd1 strains is dependent on the presence of DNA methylation, as well as HCHC-mediated histone deacetylation, suggesting that spreading is dependent on some feedback mechanism. Altogether, our results suggest LSD1 works in opposition to HCHC to maintain proper heterochromatin boundaries.

scholarly journals Establishment and Maintenance of Genomic Methylation Patterns in Mouse Embryonic Stem Cells by Dnmt3a and Dnmt3b

2003 ◽  
Vol 23 (16) ◽  
pp. 5594-5605 ◽  
Author(s):  
Taiping Chen ◽  
Yoshihide Ueda ◽  
Jonathan E. Dodge ◽  
Zhenjuan Wang ◽  
En Li
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Es Cells ◽  
Embryonic Stem ◽  
Single Copy ◽  
Dna Methyltransferases ◽  
Methylation Patterns ◽  
Genomic Methylation ◽  
De Novo Methylation

ABSTRACT We have previously shown that the DNA methyltransferases Dnmt3a and Dnmt3b carry out de novo methylation of the mouse genome during early postimplantation development and of maternally imprinted genes in the oocyte. In the present study, we demonstrate that Dnmt3a and Dnmt3b are also essential for the stable inheritance, or “maintenance,” of DNA methylation patterns. Inactivation of both Dnmt3a and Dnmt3b in embryonic stem (ES) cells results in progressive loss of methylation in various repeats and single-copy genes. Interestingly, introduction of the Dnmt3a, Dnmt3a2, and Dnmt3b1 isoforms back into highly demethylated mutant ES cells restores genomic methylation patterns; these isoforms appear to have both common and distinct DNA targets, but they all fail to restore the maternal methylation imprints. In contrast, overexpression of Dnmt1 and Dnmt3b3 failed to restore DNA methylation patterns due to their inability to catalyze de novo methylation in vivo. We also show that hypermethylation of genomic DNA by Dnmt3a and Dnmt3b is necessary for ES cells to form teratomas in nude mice. These results indicate that genomic methylation patterns are determined partly through differential expression of different Dnmt3a and Dnmt3b isoforms.

scholarly journals Characterization of Novel Parent-Specific Epigenetic Modifications Upstream of the Imprinted Mouse H19Gene

1998 ◽  
Vol 18 (11) ◽  
pp. 6767-6776 ◽  
Author(s):  
Piroska E. Szabó ◽  
Gerd P. Pfeifer ◽  
Jeffrey R. Mann
Keyword(s):  
Dna Methylation ◽  
Embryonic Stem ◽  
Dnase I ◽  
Epigenetic Modifications ◽  
Monoallelic Expression ◽  
Maternal Allele ◽  
Dnase I Footprinting ◽  
Allele Specific ◽  
Ccaat Box

ABSTRACT Genomic imprinting results in parent-specific monoallelic expression of a small number of genes in mammals. The identity of imprints is unknown, but much evidence points to a role for DNA methylation. The maternal alleles of the imprinted H19 gene are active and hypomethylated; the paternal alleles are inactive and hypermethylated. Roles for other epigenetic modifications are suggested by allele-specific differences in nuclease hypersensitivity at particular sites. To further analyze the possible epigenetic mechanisms determining monoallelic expression of H19, we have conducted in vivo dimethylsulfate and DNase I footprinting of regions upstream of the coding sequence in parthenogenetic and androgenetic embryonic stem cells. These cells carry only maternally and paternally derived alleles, respectively. We observed the presence of maternal-allele-specific dimethylsulfate and DNase I footprints at the promoter indicative of protein-DNA interactions at a CCAAT box and at binding sites for transcription factors Sp1 and AP-2. Also, at the boundary of a region further upstream for which existent differential methylation has been suggested to constitute an imprint, we observed a number of strand-specific dimethylsulfate reactivity differences specific to the maternal allele, along with an unusual chromatin structure in that both strands of maternally derived DNA were strongly hypersensitive to DNase I cutting over a distance of 100 nucleotides. We therefore reveal the existence of novel parent-specific epigenetic modifications, which in addition to DNA methylation, could constitute imprints or maintain monoallelic expression of H19.

scholarly journals Reduced Rates of Gene Loss, Gene Silencing, and Gene Mutation in Dnmt1-Deficient Embryonic Stem Cells

2001 ◽  
Vol 21 (22) ◽  
pp. 7587-7600 ◽  
Author(s):  
Matilda F. Chan ◽  
Renée van Amerongen ◽  
Tarlochan Nijjar ◽  
Edwin Cuppen ◽  
Peter A. Jones ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Tumor Suppressor ◽  
Gene Silencing ◽  
Missense Mutation ◽  
Gene Loss ◽  
Es Cells ◽  
Embryonic Stem ◽  
Gene Inactivation ◽  
Mutation Rates ◽  
Integration Sites

ABSTRACT Tumor suppressor gene inactivation is a crucial event in oncogenesis. Gene inactivation mechanisms include events resulting in loss of heterozygosity (LOH), gene mutation, and transcriptional silencing. The contribution of each of these different pathways varies among tumor suppressor genes and by cancer type. The factors that influence the relative utilization of gene inactivation pathways are poorly understood. In this study, we describe a detailed quantitative analysis of the three major gene inactivation mechanisms for a model gene at two different genomic integration sites in mouse embryonic stem (ES) cells. In addition, we targeted the major DNA methyltransferase gene, Dnmt1, to investigate the relative contribution of DNA methylation to these various competing gene inactivation pathways. Our data show that gene loss is the predominant mode of inactivation of a herpes simplex virus thymidine kinase neomycin phosphotransferase reporter gene (HSV-TKNeo) at the two integration sites tested and that this event is significantly reduced in Dnmt1-deficient cells. Gene silencing by promoter methylation requires Dnmt1, suggesting that the expression of Dnmt3a and Dnmt3b alone in ES cells is insufficient to achieve effective gene silencing. We used a novel assay to show that missense mutation rates are also substantially reduced in Dnmt1-deficient cells. This is the first direct demonstration that DNA methylation affects point mutation rates in mammalian cells. Surprisingly, the fraction of CpG transition mutations was not reduced in Dnmt1-deficient cells. Finally, we show that methyl group-deficient growth conditions do not cause an increase in missense mutation rates in Dnmt1-proficient cells, as predicted by methyltransferase-mediated mutagenesis models. We conclude that Dnmt1 deficiency and the accompanying genomic DNA hypomethylation result in a reduction of three major pathways of gene inactivation in our model system.

scholarly journals CTCF controls imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains by modulating allele-specific sub-TAD structure

2019 ◽  
Author(s):  
David Llères ◽  
Benoît Moindrot ◽  
Rakesh Pathak ◽  
Vincent Piras ◽  
Mélody Matelot ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genomic Imprinting ◽  
Chromatin Structure ◽  
Ctcf Binding ◽  
Differentially Methylated Region ◽  
Maternal Allele ◽  
Paternal Chromosome ◽  
Topologically Associating Domain ◽  
Allele Specific ◽  
Chromatin Configuration

SUMMARYMammalian genomic imprinting is essential for development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. Here, we compared chromatin structure of the two conserved imprinted domains controlled by paternal DNA methylation imprints—the Igf2-H19 and the Dlk1-Dio3 domains—and assessed the involvement of the insulator protein CTCF. At both domains, CTCF binds the maternal allele of a differentially-methylated region (DMR), in addition to multiple instances of bi-allelic CTCF binding in their surrounding TAD (Topologically Associating Domain). On the paternal chromosome, bi-allelic CTCF binding alone is sufficient to structure a first level of sub-TAD organization. Maternal-specific CTCF binding at the DMRs adds a further layer of sub-TAD organization, which essentially hijacks the existing paternal sub-TAD organisation. Genome-editing experiments at the Dlk1-Dio3 locus confirm that the maternal sub-TADs are essential during development to maintain the imprinted Dlk1 gene in an inactive state on the maternal chromosome.

scholarly journals Conserved and divergent features of DNA methylation in embryonic stem cell-derived neurons

2020 ◽  
Author(s):  
Sally Martin ◽  
Daniel Poppe ◽  
Nelly Olova ◽  
Conor O’Leary ◽  
Elena Ivanova ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Es Cells ◽  
Embryonic Stem ◽  
Nuclear Lamina ◽  
Neuronal Maturation ◽  
Neuronal Marker ◽  
Mouse Es Cells ◽  
Primary Mouse

AbstractDNA methylation functions in genome regulation and is implicated in neuronal maturation. Early post-natal accumulation of atypical non-CG methylation (mCH) occurs in neurons of mice and humans, but its precise function remains unknown. Here we investigate mCH deposition in neurons derived from mouse ES-cells in vitro and in cultured primary mouse neurons. We find that both acquire comparable levels of mCH over a similar period as in vivo. In vitro mCH deposition occurs concurrently with a transient increase in Dnmt3a expression, is preceded by expression of the post-mitotic neuronal marker Rbfox3 (NeuN) and is enriched at the nuclear lamina. Despite these similarities, whole genome bisulfite sequencing reveals that mCH patterning in mESC-derived neurons partially differs from in vivo. mESC-derived neurons therefore represent a valuable model system for analyzing the mechanisms and functional consequences of correct and aberrantly deposited CG and non-CG methylation in neuronal maturation.

scholarly journals Retroviral Expression in Embryonic Stem Cells and Hematopoietic Stem Cells

2000 ◽  
Vol 20 (20) ◽  
pp. 7419-7426 ◽  
Author(s):  
Sara R. Cherry ◽  
D. Biniszkiewicz ◽  
L. van Parijs ◽  
D. Baltimore ◽  
R. Jaenisch
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
Transcriptional Repression ◽  
Fluorescent Protein ◽  
De Novo ◽  
Es Cells ◽  
Embryonic Stem ◽  
Hematopoietic Stem

ABSTRACT Achieving long-term retroviral expression in primary cells has been problematic. De novo DNA methylation of infecting proviruses has been proposed as a major cause of this transcriptional repression. Here we report the development of a mouse stem cell virus (MSCV) long terminal repeat-based retroviral vector that is expressed in both embryonic stem (ES) cells and hematopoietic stem (HS) cells. Infected HS cells and their differentiated descendants maintained long-term and stable retroviral expression after serial adoptive transfers. In addition, retrovirally infected ES cells showed detectable expression level of the green fluorescent protein (GFP). Moreover, GFP expression of integrated proviruses was maintained after in vitro differentiation of infected ES cells. Long-term passage of infected ES cells resulted in methylation-mediated silencing, while short-term expression was methylation independent. Tissues of transgenic animals, which we derived from ES cells carrying the MSCV-based provirus, did not express GFP. However, treatment with the demethylating agent 5-azadeoxycytidine reactivated the silent provirus, demonstrating that DNA methylation is involved in the maintenance of retroviral repression. Our results indicate that retroviral expression in ES cells is repressed by methylation-dependent as well as methylation-independent mechanisms.

scholarly journals BRG1 GovernsNanogTranscription in Early Mouse Embryos and Embryonic Stem Cells via Antagonism of Histone H3 Lysine 9/14 Acetylation

2015 ◽  
Vol 35 (24) ◽  
pp. 4158-4169 ◽  
Author(s):  
Timothy S. Carey ◽  
Zubing Cao ◽  
Inchul Choi ◽  
Avishek Ganguly ◽  
Catherine A. Wilson ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Histone H3 ◽  
Embryonic Stem ◽  
Histone Deacetylation ◽  
Preimplantation Embryos ◽  
Nucleosome Remodeling ◽  
Histone Deacetylase 1

During mouse preimplantation development, the generation of the inner cell mass (ICM) and trophoblast lineages comprises upregulation ofNanogexpression in the ICM and its silencing in the trophoblast. However, the underlying epigenetic mechanisms that differentially regulateNanogin the first cell lineages are poorly understood. Here, we report that BRG1 (Brahma-related gene 1) cooperates with histone deacetylase 1 (HDAC1) to regulateNanogexpression. BRG1 depletion in preimplantation embryos andCdx2-inducible embryonic stem cells (ESCs) revealed that BRG1 is necessary forNanogsilencing in the trophoblast lineage. Conversely, in undifferentiated ESCs, loss of BRG1 augmentedNanogexpression. Analysis of histone H3 within theNanogproximal enhancer revealed that H3 lysine 9/14 (H3K9/14) acetylation increased in BRG1-depleted embryos and ESCs. Biochemical studies demonstrated that HDAC1 was present in BRG1-BAF155 complexes and BRG1-HDAC1 interactions were enriched in the trophoblast lineage. HDAC1 inhibition triggered an increase in H3K9/14 acetylation and a corresponding rise inNanogmRNA and protein, phenocopying BRG1 knockdown embryos and ESCs. Lastly, nucleosome-mapping experiments revealed that BRG1 is indispensable for nucleosome remodeling at theNanogenhancer during trophoblast development. In summary, our data suggest that BRG1 governsNanogexpression via a dual mechanism involving histone deacetylation and nucleosome remodeling.

scholarly journals Polycomb Complex 2 Is Required for E-cadherin Repression by the Snail1 Transcription Factor

2008 ◽  
Vol 28 (15) ◽  
pp. 4772-4781 ◽  
Author(s):  
Nicolás Herranz ◽  
Diego Pasini ◽  
Víctor M. Díaz ◽  
Clara Francí ◽  
Arantxa Gutierrez ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Epithelial Mesenchymal Transition ◽  
Es Cells ◽  
Histone H3 ◽  
Embryonic Stem ◽  
Cdh1 Gene ◽  
Mesenchymal Transition ◽  
Polycomb Repressive Complex 2 ◽  
Polycomb Complex ◽  
E Cadherin

ABSTRACT The transcriptional factor Snail1 is a repressor of E-cadherin (CDH1) gene expression essential for triggering epithelial-mesenchymal transition. Snail1 represses CDH1, directly binding its promoter and inducing the synthesis of the Zeb1 repressor. In this article, we show that repression of CDH1 by Snail1, but not by Zeb1, is dependent on the activity of Polycomb repressive complex 2 (PRC2). Embryonic stem (ES) cells null for Suz12, one of the components of PRC2, show higher levels of Cdh1 mRNA than control ES cells. In tumor cells, interference of PRC2 activity prevents the ability of Snail1 to downregulate CDH1 and partially derepresses CDH1. Chromatin immunoprecipitation assays demonstrated that Snail1 increases the binding of Suz12 to the CDH1 promoter and the trimethylation of lysine 27 in histone H3. Moreover, Snail1 interacts with Suz12 and Ezh2, as shown by coimmunoprecipitation experiments. In conclusion, these results demonstrate that Snail1 recruits PRC2 to the CDH1 promoter and requires the activity of this complex to repress E-cadherin expression.

Sign in / Sign up

Export Citation Format

Share Document