Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation.

Abstract:

:Methylation of DNA at the dinucleotide CpG is essential for mammalian development and is correlated with stable transcriptional silencing. This transcriptional silencing has recently been linked at a molecular level to histone deacetylation through the demonstration of a physical association between histone deacetylases and the methyl CpG-binding protein MeCP2 (refs 4,5). We previously purified a histone deacetylase complex from Xenopus laevis egg extracts that consists of six subunits, including an Rpd3-like deacetylase, the RbA p48/p46 histone-binding protein and the nucleosome-stimulated ATPase Mi-2 (ref. 6). Similar species were subsequently isolated from human cell lines, implying functional conservation across evolution. This complex represents the most abundant form of deacetylase in amphibian eggs and cultured mammalian cells. Here we identify the remaining three subunits of this enzyme complex. One of them binds specifically to methylated DNA in vitro and molecular cloning reveals a similarity to a known methyl CpG-binding protein. Our data substantiate the mechanistic link between DNA methylation, histone deacetylation and transcriptional silencing.

journal_name

Nat Genet

journal_title

Nature genetics

authors

Wade PA,Gegonne A,Jones PL,Ballestar E,Aubry F,Wolffe AP

doi

10.1038/12664

keywords:

subject

Has Abstract

pub_date

1999-09-01 00:00:00

pages

62-6

issue

1

eissn

1061-4036

issn

1546-1718

journal_volume

23

pub_type

杂志文章
  • Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability.

    abstract::Overgrowth disorders are a heterogeneous group of conditions characterized by increased growth parameters and other variable clinical features such as intellectual disability and facial dysmorphism. To identify new causes of human overgrowth, we performed exome sequencing in ten proband-parent trios and detected two d...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.2917

    authors: Tatton-Brown K,Seal S,Ruark E,Harmer J,Ramsay E,Del Vecchio Duarte S,Zachariou A,Hanks S,O'Brien E,Aksglaede L,Baralle D,Dabir T,Gener B,Goudie D,Homfray T,Kumar A,Pilz DT,Selicorni A,Temple IK,Van Maldergem L,Yac

    更新日期:2014-04-01 00:00:00

  • Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals.

    abstract::The mRNA for the Duffy blood group antigen, the erythrocyte receptor for the Plasmodium vivax malaria parasite, has recently been cloned and shown to encode a widely expressed chemokine receptor. Here, we show that the Duffy antigen/chemokine receptor gene (DARC) is composed of a single exon and that most Duffy-negati...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0695-224

    authors: Tournamille C,Colin Y,Cartron JP,Le Van Kim C

    更新日期:1995-06-01 00:00:00

  • Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.

    abstract::Measurements of erythrocytes within the blood are important clinical traits and can indicate various hematological disorders. We report here genome-wide association studies (GWAS) for six erythrocyte traits, including hemoglobin concentration (Hb), hematocrit (Hct), mean corpuscular volume (MCV), mean corpuscular hemo...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.466

    authors: Ganesh SK,Zakai NA,van Rooij FJ,Soranzo N,Smith AV,Nalls MA,Chen MH,Kottgen A,Glazer NL,Dehghan A,Kuhnel B,Aspelund T,Yang Q,Tanaka T,Jaffe A,Bis JC,Verwoert GC,Teumer A,Fox CS,Guralnik JM,Ehret GB,Rice K,Feli

    更新日期:2009-11-01 00:00:00

  • Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1.

    abstract::Genomic imprinting is an epigenetic modification that results in expression from only one of the two parental copies of a gene. Differences in methylation between the two parental chromosomes are often observed at or near imprinted genes. Beckwith-Wiedemann syndrome (BWS), which predisposes to cancer and excessive gro...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng988

    authors: Fitzpatrick GV,Soloway PD,Higgins MJ

    更新日期:2002-11-01 00:00:00

  • MPV17 encodes an inner mitochondrial membrane protein and is mutated in infantile hepatic mitochondrial DNA depletion.

    abstract::The mitochondrial (mt) DNA depletion syndromes (MDDS) are genetic disorders characterized by a severe, tissue-specific decrease of mtDNA copy number, leading to organ failure. There are two main clinical presentations: myopathic (OMIM 609560) and hepatocerebral (OMIM 251880). Known mutant genes, including TK2, SUCLA2,...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1765

    authors: Spinazzola A,Viscomi C,Fernandez-Vizarra E,Carrara F,D'Adamo P,Calvo S,Marsano RM,Donnini C,Weiher H,Strisciuglio P,Parini R,Sarzi E,Chan A,DiMauro S,Rötig A,Gasparini P,Ferrero I,Mootha VK,Tiranti V,Zeviani M

    更新日期:2006-05-01 00:00:00

  • Activating SRC mutation in a subset of advanced human colon cancers.

    abstract::The discovery of Rous sarcoma virus (RSV) led to the identification of cellular Src (c-Src), a non-receptor tyrosine kinase, which has since been implicated in the development of numerous human cancers. c-Src has been found to be highly activated in colon cancers, particularly in those metastatic to the liver. Studies...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/5971

    authors: Irby RB,Mao W,Coppola D,Kang J,Loubeau JM,Trudeau W,Karl R,Fujita DJ,Jove R,Yeatman TJ

    更新日期:1999-02-01 00:00:00

  • Mutations in CAV3 cause mechanical hyperirritability of skeletal muscle in rippling muscle disease.

    abstract::Hereditary rippling muscle disease (RMD) is an autosomal dominant human disorder characterized by mechanically triggered contractions of skeletal muscle. Genome-wide linkage analysis has identified an RMD locus on chromosome 3p25. We found missense mutations in positional candidate CAV3 (encoding caveolin 3; ref. 5) i...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/90050

    authors: Betz RC,Schoser BG,Kasper D,Ricker K,Ramírez A,Stein V,Torbergsen T,Lee YA,Nöthen MM,Wienker TF,Malin JP,Propping P,Reis A,Mortier W,Jentsch TJ,Vorgerd M,Kubisch C

    更新日期:2001-07-01 00:00:00

  • Estimating the proportion of variation in susceptibility to schizophrenia captured by common SNPs.

    abstract::Schizophrenia is a complex disorder caused by both genetic and environmental factors. Using 9,087 affected individuals, 12,171 controls and 915,354 imputed SNPs from the Schizophrenia Psychiatric Genome-Wide Association Study (GWAS) Consortium (PGC-SCZ), we estimate that 23% (s.e. = 1%) of variation in liability to sc...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.1108

    authors: Lee SH,DeCandia TR,Ripke S,Yang J,Schizophrenia Psychiatric Genome-Wide Association Study Consortium (PGC-SCZ).,International Schizophrenia Consortium (ISC).,Molecular Genetics of Schizophrenia Collaboration (MGS).,Sullivan PF,Goddard ME

    更新日期:2012-02-19 00:00:00

  • A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase.

    abstract::The development of a quantitative understanding of viral evolution and the fitness landscape in HIV-1 drug resistance is a formidable challenge given the large number of available drugs and drug resistance mutations. We analyzed a dataset measuring the in vitro fitness of 70,081 virus samples isolated from HIV-1 subty...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.795

    authors: Hinkley T,Martins J,Chappey C,Haddad M,Stawiski E,Whitcomb JM,Petropoulos CJ,Bonhoeffer S

    更新日期:2011-05-01 00:00:00

  • Mutations in X-linked PORCN, a putative regulator of Wnt signaling, cause focal dermal hypoplasia.

    abstract::Focal dermal hypoplasia is an X-linked dominant disorder characterized by patchy hypoplastic skin and digital, ocular and dental malformations. We used array comparative genomic hybridization to identify a 219-kb deletion in Xp11.23 in two affected females. We sequenced genes in this region and found heterozygous and ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng2057

    authors: Wang X,Reid Sutton V,Omar Peraza-Llanes J,Yu Z,Rosetta R,Kou YC,Eble TN,Patel A,Thaller C,Fang P,Van den Veyver IB

    更新日期:2007-07-01 00:00:00

  • Analysis of the coding genome of diffuse large B-cell lymphoma.

    abstract::Diffuse large B-cell lymphoma (DLBCL) is the most common form of human lymphoma. Although a number of structural alterations have been associated with the pathogenesis of this malignancy, the full spectrum of genetic lesions that are present in the DLBCL genome, and therefore the identity of dysregulated cellular path...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.892

    authors: Pasqualucci L,Trifonov V,Fabbri G,Ma J,Rossi D,Chiarenza A,Wells VA,Grunn A,Messina M,Elliot O,Chan J,Bhagat G,Chadburn A,Gaidano G,Mullighan CG,Rabadan R,Dalla-Favera R

    更新日期:2011-07-31 00:00:00

  • Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions.

    abstract::The importance of commensal microbes for human health is increasingly recognized, yet the impacts of evolutionary changes in human diet and culture on commensal microbiota remain almost unknown. Two of the greatest dietary shifts in human evolution involved the adoption of carbohydrate-rich Neolithic (farming) diets (...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.2536

    authors: Adler CJ,Dobney K,Weyrich LS,Kaidonis J,Walker AW,Haak W,Bradshaw CJ,Townsend G,Sołtysiak A,Alt KW,Parkhill J,Cooper A

    更新日期:2013-04-01 00:00:00

  • Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.

    abstract::The Wellcome Trust Case Control Consortium (WTCCC) primary genome-wide association (GWA) scan on seven diseases, including the multifactorial autoimmune disease type 1 diabetes (T1D), shows associations at P < 5 x 10(-7) between T1D and six chromosome regions: 12q24, 12q13, 16p13, 18p11, 12p13 and 4q27. Here, we attem...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng2068

    authors: Todd JA,Walker NM,Cooper JD,Smyth DJ,Downes K,Plagnol V,Bailey R,Nejentsev S,Field SF,Payne F,Lowe CE,Szeszko JS,Hafler JP,Zeitels L,Yang JH,Vella A,Nutland S,Stevens HE,Schuilenburg H,Coleman G,Maisuria M,Meado

    更新日期:2007-07-01 00:00:00

  • Integrated human genome-wide maps constructed using the CEPH reference panel.

    abstract::High resolution linkage maps have proven to be invaluable tools in genetic investigations. We have assembled a collection of genetic maps constructed from primary data collected from investigators performing genotyping using the Centre Etude Polymorphism Humain (CEPH) reference pedigree panel. These maps were construc...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0494-391

    authors: Buetow KH,Weber JL,Ludwigsen S,Scherpbier-Heddema T,Duyk GM,Sheffield VC,Wang Z,Murray JC

    更新日期:1994-04-01 00:00:00

  • An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma.

    abstract::Translocation events are frequent in cancer and may create chimeric fusions or 'regulatory rearrangements' that drive oncogene overexpression. Here we identify super-enhancer translocations that drive overexpression of the oncogenic transcription factor MYB as a recurrent theme in adenoid cystic carcinoma (ACC). Whole...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3502

    authors: Drier Y,Cotton MJ,Williamson KE,Gillespie SM,Ryan RJ,Kluk MJ,Carey CD,Rodig SJ,Sholl LM,Afrogheh AH,Faquin WC,Queimado L,Qi J,Wick MJ,El-Naggar AK,Bradner JE,Moskaluk CA,Aster JC,Knoechel B,Bernstein BE

    更新日期:2016-03-01 00:00:00

  • Promoter bivalency favors an open chromatin architecture in embryonic stem cells.

    abstract::In embryonic stem cells (ESCs), developmental gene promoters are characterized by their bivalent chromatin state, with simultaneous modification by MLL2 and Polycomb complexes. Although essential for embryogenesis, bivalency is functionally not well understood. Here, we show that MLL2 plays a central role in ESC genom...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-018-0218-5

    authors: Mas G,Blanco E,Ballaré C,Sansó M,Spill YG,Hu D,Aoi Y,Le Dily F,Shilatifard A,Marti-Renom MA,Di Croce L

    更新日期:2018-10-01 00:00:00

  • Finding host targets for HIV therapy.

    abstract::A CRISPR screen conducted in a CD4+ T cell leukemia line has identified host factors required for HIV infection but dispensable for cellular survival. The results highlight sulfation on the HIV co-receptor CCR5 and cellular aggregation as potential targets for therapeutic intervention. ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3777

    authors: Tsui CK,Gupta A,Bassik MC

    更新日期:2017-01-31 00:00:00

  • Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits.

    abstract::We present an approximate conditional and joint association analysis that can use summary-level statistics from a meta-analysis of genome-wide association studies (GWAS) and estimated linkage disequilibrium (LD) from a reference sample with individual-level genotype data. Using this method, we analyzed meta-analysis s...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.2213

    authors: Yang J,Ferreira T,Morris AP,Medland SE,Genetic Investigation of ANthropometric Traits (GIANT) Consortium.,DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium.,Madden PA,Heath AC,Martin NG,Montgomery GW,Weedon MN,Lo

    更新日期:2012-03-18 00:00:00

  • The gene encoding ganglioside-induced differentiation-associated protein 1 is mutated in axonal Charcot-Marie-Tooth type 4A disease.

    abstract::We identified three distinct mutations and six mutant alleles in GDAP1 in three families with axonal Charcot-Marie-Tooth (CMT) neuropathy and vocal cord paresis, which were previously linked to the CMT4A locus on chromosome 8q21.1. These results establish the molecular etiology of CMT4A (MIM 214400) and suggest that i...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng798

    authors: Cuesta A,Pedrola L,Sevilla T,García-Planells J,Chumillas MJ,Mayordomo F,LeGuern E,Marín I,Vílchez JJ,Palau F

    更新日期:2002-01-01 00:00:00

  • Genetic analysis of quantitative traits in the Japanese population links cell types to complex human diseases.

    abstract::Clinical measurements can be viewed as useful intermediate phenotypes to promote understanding of complex human diseases. To acquire comprehensive insights into the underlying genetics, here we conducted a genome-wide association study (GWAS) of 58 quantitative traits in 162,255 Japanese individuals. Overall, we ident...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-018-0047-6

    authors: Kanai M,Akiyama M,Takahashi A,Matoba N,Momozawa Y,Ikeda M,Iwata N,Ikegawa S,Hirata M,Matsuda K,Kubo M,Okada Y,Kamatani Y

    更新日期:2018-03-01 00:00:00

  • Regulatory defects in liver and intestine implicate abnormal hepcidin and Cybrd1 expression in mouse hemochromatosis.

    abstract::Individuals with hereditary hemochromatosis suffer from systemic iron overload due to duodenal hyperabsorption. Most cases arise from a founder mutation in HFE (845G-->A; ref. 2) that results in the amino-acid substitution C282Y and prevents the association of HFE with beta2-microglobulin. Mice homozygous with respect...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1152

    authors: Muckenthaler M,Roy CN,Custodio AO,Miñana B,deGraaf J,Montross LK,Andrews NC,Hentze MW

    更新日期:2003-05-01 00:00:00

  • Microarray databases: standards and ontologies.

    abstract::A single microarray can provide information on the expression of tens of thousands of genes. The amount of information generated by a microarray-based experiment is sufficiently large that no single study can be expected to mine each nugget of scientific information. As a consequence, the scale and complexity of micro...

    journal_title:Nature genetics

    pub_type: 杂志文章,评审

    doi:10.1038/ng1028

    authors: Stoeckert CJ Jr,Causton HC,Ball CA

    更新日期:2002-12-01 00:00:00

  • A literature network of human genes for high-throughput analysis of gene expression.

    abstract::We have carried out automated extraction of explicit and implicit biomedical knowledge from publicly available gene and text databases to create a gene-to-gene co-citation network for 13,712 named human genes by automated analysis of titles and abstracts in over 10 million MEDLINE records. The associations between gen...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0501-21

    authors: Jenssen TK,Laegreid A,Komorowski J,Hovig E

    更新日期:2001-05-01 00:00:00

  • Meta-analysis of genome-wide association data identifies two loci influencing age at menarche.

    abstract::We conducted a meta-analysis of genome-wide association data to detect genes influencing age at menarche in 17,510 women. The strongest signal was at 9q31.2 (P = 1.7 × 10(-9)), where the nearest genes include TMEM38B, FKTN, FSD1L, TAL2 and ZNF462. The next best signal was near the LIN28B gene (rs7759938; P = 7.0 × 10(...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.386

    authors: Perry JR,Stolk L,Franceschini N,Lunetta KL,Zhai G,McArdle PF,Smith AV,Aspelund T,Bandinelli S,Boerwinkle E,Cherkas L,Eiriksdottir G,Estrada K,Ferrucci L,Folsom AR,Garcia M,Gudnason V,Hofman A,Karasik D,Kiel DP,Lau

    更新日期:2009-06-01 00:00:00

  • Natural variation at the DEP1 locus enhances grain yield in rice.

    abstract::Grain yield is controlled by quantitative trait loci (QTLs) derived from natural variations in many crop plants. Here we report the molecular characterization of a major rice grain yield QTL that acts through the determination of panicle architecture. The dominant allele at the DEP1 locus is a gain-of-function mutatio...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.352

    authors: Huang X,Qian Q,Liu Z,Sun H,He S,Luo D,Xia G,Chu C,Li J,Fu X

    更新日期:2009-04-01 00:00:00

  • Direct detection of novel expanded trinucleotide repeats in the human genome.

    abstract::Expansion of trinucleotide repeats can give rise to genetic disease. We have developed a technique, repeat expansion detection (RED), that can identify potentially pathological repeat expansion without prior knowledge of chromosomal location. Human genomic DNA is used as a template for a two-step cycling process that ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0693-135

    authors: Schalling M,Hudson TJ,Buetow KH,Housman DE

    更新日期:1993-06-01 00:00:00

  • Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures.

    abstract::Advances in sequencing technologies have enabled the identification of mutations acquired by bacterial pathogens during infection. However, it remains unclear whether adaptive mutations fix in the population or lead to pathogen diversification within the patient. Here we study the genotypic diversity of Burkholderia d...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.2848

    authors: Lieberman TD,Flett KB,Yelin I,Martin TR,McAdam AJ,Priebe GP,Kishony R

    更新日期:2014-01-01 00:00:00

  • Common variants near ATM are associated with glycemic response to metformin in type 2 diabetes.

    abstract::Metformin is the most commonly used pharmacological therapy for type 2 diabetes. We report a genome-wide association study for glycemic response to metformin in 1,024 Scottish individuals with type 2 diabetes with replication in two cohorts including 1,783 Scottish individuals and 1,113 individuals from the UK Prospec...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.735

    authors: GoDARTS and UKPDS Diabetes Pharmacogenetics Study Group.,Wellcome Trust Case Control Consortium 2.,Zhou K,Bellenguez C,Spencer CC,Bennett AJ,Coleman RL,Tavendale R,Hawley SA,Donnelly LA,Schofield C,Groves CJ,Burch L,Carr F,St

    更新日期:2011-02-01 00:00:00

  • A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element.

    abstract::The Charcot-Marie Tooth disease type 1A (CMT1A) duplication and hereditary neuropathy with liability to pressure palsies (HNPP) deletion are reciprocal products of an unequal crossing-over event between misaligned flanking CMT1A-REP repeats. The molecular aetiology of this apparently homologous recombination event was...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0396-288

    authors: Reiter LT,Murakami T,Koeuth T,Pentao L,Muzny DM,Gibbs RA,Lupski JR

    更新日期:1996-03-01 00:00:00

  • Zinc transport and diabetes risk.

    abstract::Genome-wide association studies have previously identified variants in SLC30A8, encoding the zinc transporter ZnT8, associated with diabetes risk. A rare variant association study has now established the direction of effect, surprisingly showing that loss-of-function mutations in SLC30A8 are protective against diabete...

    journal_title:Nature genetics

    pub_type: 评论,杂志文章

    doi:10.1038/ng.2934

    authors: Pearson E

    更新日期:2014-04-01 00:00:00