A phospho-dependent mechanism involving NCoR and KMT2D controls a permissive chromatin state at Notch target genes.

Abstract:

:The transcriptional shift from repression to activation of target genes is crucial for the fidelity of Notch responses through incompletely understood mechanisms that likely involve chromatin-based control. To activate silenced genes, repressive chromatin marks are removed and active marks must be acquired. Histone H3 lysine-4 (H3K4) demethylases are key chromatin modifiers that establish the repressive chromatin state at Notch target genes. However, the counteracting histone methyltransferase required for the active chromatin state remained elusive. Here, we show that the RBP-J interacting factor SHARP is not only able to interact with the NCoR corepressor complex, but also with the H3K4 methyltransferase KMT2D coactivator complex. KMT2D and NCoR compete for the C-terminal SPOC-domain of SHARP. We reveal that the SPOC-domain exclusively binds to phosphorylated NCoR. The balance between NCoR and KMT2D binding is shifted upon mutating the phosphorylation sites of NCoR or upon inhibition of the NCoR kinase CK2β. Furthermore, we show that the homologs of SHARP and KMT2D in Drosophila also physically interact and control Notch-mediated functions in vivo Together, our findings reveal how signaling can fine-tune a committed chromatin state by phosphorylation of a pivotal chromatin-modifier.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Oswald F,Rodriguez P,Giaimo BD,Antonello ZA,Mira L,Mittler G,Thiel VN,Collins KJ,Tabaja N,Cizelsky W,Rothe M,Kühl SJ,Kühl M,Ferrante F,Hein K,Kovall RA,Dominguez M,Borggrefe T

doi

10.1093/nar/gkw105

subject

Has Abstract

pub_date

2016-06-02 00:00:00

pages

4703-20

issue

10

eissn

0305-1048

issn

1362-4962

pii

gkw105

journal_volume

44

pub_type

杂志文章
  • NMR solution structures of LNA (locked nucleic acid) modified quadruplexes.

    abstract::We have determined the NMR solution structures of the quadruplexes formed by d(TGLGLT) and d(TL4T), where L denotes LNA (locked nucleic acid) modified G-residues. Both structures are tetrameric, parallel and right-handed and the native global fold of the corresponding DNA quadruplex is retained upon introduction of th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl144

    authors: Nielsen JT,Arar K,Petersen M

    更新日期:2006-04-13 00:00:00

  • The gapped duplex DNA approach to oligonucleotide-directed mutation construction.

    abstract::A simple and efficient method is described to introduce structurally pre-determined mutations into recombinant genomes of filamentous phage M13. The method rests on gapped duplex DNA (gdDNA) molecules of the phage M13 genome as the key intermediate. In this gdDNA, the (+) and the (shorter) (-) strand carry different g...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.24.9441

    authors: Kramer W,Drutsa V,Jansen HW,Kramer B,Pflugfelder M,Fritz HJ

    更新日期:1984-12-21 00:00:00

  • The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.

    abstract::FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger stand...

    journal_title:Nucleic acids research

    pub_type: 历史文章,杂志文章,评审

    doi:10.1093/nar/gkp1137

    authors: Cock PJ,Fields CJ,Goto N,Heuer ML,Rice PM

    更新日期:2010-04-01 00:00:00

  • f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome.

    abstract::The ability to integrate 'omics' (i.e. transcriptomics and proteomics) is becoming increasingly important to the understanding of regulatory mechanisms. There are currently no tools available to identify differentially expressed genes (DEGs) across different 'omics' data types or multi-dimensional data including time ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw157

    authors: Tang S,Hemberg M,Cansizoglu E,Belin S,Kosik K,Kreiman G,Steen H,Steen J

    更新日期:2016-06-02 00:00:00

  • Isolation and characterization of the DNA fraction of rat liver chromatin which binds polylysine.

    abstract::The structure of eukaryotic chromatin has been investigated by isolating and analyzing the "accessible" DNA fraction of rat liver chromatin. This DNA fraction has been isolated by titrating the chromatin with the protese-resistant D isomer of polylysine to bind the "accessible" DNA sites. After removal of chromosomal ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/2.5.667

    authors: Arnold EA,Wahn U,Young KE

    更新日期:1975-05-01 00:00:00

  • Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions.

    abstract::The Neurospora VS ribozyme is a catalytic RNA that has the unique ability to specifically recognize and cleave a stem-loop substrate through formation of a highly stable kissing-loop interaction (KLI). In order to explore the engineering potential of the VS ribozyme to cleave alternate substrates, we substituted the w...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw401

    authors: Lacroix-Labonté J,Girard N,Dagenais P,Legault P

    更新日期:2016-08-19 00:00:00

  • Human Disease Ontology 2018 update: classification, content and workflow expansion.

    abstract::The Human Disease Ontology (DO) (http://www.disease-ontology.org), database has undergone significant expansion in the past three years. The DO disease classification includes specific formal semantic rules to express meaningful disease models and has expanded from a single asserted classification to include multiple-...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky1032

    authors: Schriml LM,Mitraka E,Munro J,Tauber B,Schor M,Nickle L,Felix V,Jeng L,Bearer C,Lichenstein R,Bisordi K,Campion N,Hyman B,Kurland D,Oates CP,Kibbey S,Sreekumar P,Le C,Giglio M,Greene C

    更新日期:2019-01-08 00:00:00

  • Molecular recognition of RhlB and RNase D in the Caulobacter crescentus RNA degradosome.

    abstract::The endoribonuclease RNase E is a key enzyme in RNA metabolism for many bacterial species. In Escherichia coli, RNase E contributes to the majority of RNA turnover and processing events, and the enzyme has been extensively characterized as the central component of the RNA degradosome assembly. A similar RNA degradosom...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1134

    authors: Voss JE,Luisi BF,Hardwick SW

    更新日期:2014-12-01 00:00:00

  • Regulation of yeast DNA polymerase δ-mediated strand displacement synthesis by 5'-flaps.

    abstract::The strand displacement activity of DNA polymerase δ is strongly stimulated by its interaction with proliferating cell nuclear antigen (PCNA). However, inactivation of the 3'-5' exonuclease activity is sufficient to allow the polymerase to carry out strand displacement even in the absence of PCNA. We have examined in ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv260

    authors: Koc KN,Stodola JL,Burgers PM,Galletto R

    更新日期:2015-04-30 00:00:00

  • Intracellular stability of 2'-OMe-4'-thioribonucleoside modified siRNA leads to long-term RNAi effect.

    abstract::Chemically modified siRNAs are expected to have resistance toward nuclease degradation and good thermal stability in duplex formation for in vivo applications. We have recently found that 2'-OMe-4'-thioRNA, a hybrid chemical modification based on 2'-OMeRNA and 4'-thioRNA, has high hybridization affinity for complement...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks204

    authors: Takahashi M,Nagai C,Hatakeyama H,Minakawa N,Harashima H,Matsuda A

    更新日期:2012-07-01 00:00:00

  • Facile preparation of nuclease resistant 3' modified oligodeoxynucleotides.

    abstract::An efficient chemical procedure for the immobilization of carboxylate containing conjugate groups onto controlled pore glass (CPG) is described. The derivatized supports were used in the automated synthesis of an oligodeoxynucleotide (20-mer ODN) containing a 3' phosphodiester linked hexanol, aminohexyl, acridine, or ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.1.145

    authors: Gamper HB,Reed MW,Cox T,Virosco JS,Adams AD,Gall AA,Scholler JK,Meyer RB Jr

    更新日期:1993-01-11 00:00:00

  • Interference activity of a minimal Type I CRISPR-Cas system from Shewanella putrefaciens.

    abstract::Type I CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR-associated) systems exist in bacterial and archaeal organisms and provide immunity against foreign DNA. The Cas protein content of the DNA interference complexes (termed Cascade) varies between different CRISPR-Cas subtypes. A minima...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv882

    authors: Dwarakanath S,Brenzinger S,Gleditzsch D,Plagens A,Klingl A,Thormann K,Randau L

    更新日期:2015-10-15 00:00:00

  • Fission yeast with DNA polymerase delta temperature-sensitive alleles exhibits cell division cycle phenotype.

    abstract::DNA polymerases alpha and delta are essential enzymes believed to play critical roles in initiation and replication of chromosome DNA. In this study, we show that the genes for Schizosaccharomyces pombe (S.pombe) DNA polymerase alpha and delta (pol alpha+ and pol delta+) are essential for cell viability. Disruption of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.16.3821

    authors: Francesconi S,Park H,Wang TS

    更新日期:1993-08-11 00:00:00

  • The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of mouse fold-back RNA.

    abstract::Three copies of a highly repetitive DNA sequence B1 which is complementary to the most abundant class of mouse fold-back RNA have been cloned in pBR322 plasmid and sequenced by the method of Maxam and Gilbert. All the three have a length of about 130 base pairs and are very similar in their base sequence. The deviatio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.6.1201

    authors: Krayev AS,Kramerov DA,Skryabin KG,Ryskov AP,Bayev AA,Georgiev GP

    更新日期:1980-03-25 00:00:00

  • Visualization of novel simian virus 40 DNA recombination intermediates induced by ultraviolet light irradiation.

    abstract::Electron microscopic technique was used to examine the structures of SV40 DNA recombination intermediates induced by ultraviolet irradiation as an approach for understanding recombination mechanisms in animal cells. Putative recombination intermediate with the characteristic Holliday junction was observed in both SV40...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.25.7193

    authors: Hsu MT

    更新日期:1991-12-01 00:00:00

  • The mechanisms of a mammalian splicing enhancer.

    abstract::Exonic splicing enhancer (ESE) sequences are bound by serine & arginine-rich (SR) proteins, which in turn enhance the recruitment of splicing factors. It was inferred from measurements of splicing around twenty years ago that Drosophila doublesex ESEs are bound stably by SR proteins, and that the bound proteins intera...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky056

    authors: Jobbins AM,Reichenbach LF,Lucas CM,Hudson AJ,Burley GA,Eperon IC

    更新日期:2018-03-16 00:00:00

  • EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis.

    abstract::EpoDB is a database of genes expressed in vertebrate red blood cells. It is also a prototype for the creation of cell and tissue-specific databases from multiple external sources. The information in EpoDB obtained from GenBank, SWISS-PROT, Transfac, TRRD and GERD is curated to provide high quality data for sequence an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.1.200

    authors: Stoeckert CJ Jr,Salas F,Brunk B,Overton GC

    更新日期:1999-01-01 00:00:00

  • Human apolipoprotein B: identification of cDNA clones and characterization of mRNA.

    abstract::Apolipoprotein B (apoB) is a major protein component of low density and very low density lipoproteins. Because of its large size and heterogeneity, molecular studies of apoB have been difficult, and its structure and regulation remain poorly understood. We now report the identification of human apoB cDNA clones by ant...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.19.6937

    authors: Mehrabian M,Schumaker VN,Fareed GC,West R,Johnson DF,Kirchgessner T,Lin HC,Wang XB,Ma YH,Mendiaz E

    更新日期:1985-10-11 00:00:00

  • Sensitive detection of p53 gene mutations by a 'mutant enriched' PCR-SSCP technique.

    abstract::For the rapid and sensitive detection of p53 'hot spot' mutations, we combined polymerase chain reaction based single-strand conformational polymorphism (PCR-SSCP) analysis with sequence specific-clamping by peptide nucleic acids (PNAs) in a one-step reaction tube protocol. For this purpose, we designed two PNA molecu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.5.1356

    authors: Behn M,Schuermann M

    更新日期:1998-03-01 00:00:00

  • In vitro 3'-end endonucleolytic processing defect in a human mitochondrial tRNA(Ser(UCN)) precursor with the U7445C substitution, which causes non-syndromic deafness.

    abstract::Eukaryotic tRNAs are transcribed as precursors. A 5'-end leader and 3'-end trailer are endonucleolytically removed by RNase P and 3'-tRNase before 3'-end CCA addition, aminoacylation, nuclear export and translation. 3'-End -CC can be a 3'-tRNase anti-determinant with the ability to prevent mature tRNA from recycling t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.21.4334

    authors: Levinger L,Jacobs O,James M

    更新日期:2001-11-01 00:00:00

  • Structural characterization of a ribonuclease III processing signal.

    abstract::The structure of a ribonuclease III processing signal from bacteriophage T7 was examined by NMR spectroscopy, optical melting, and chemical and enzymatic modification. A 41 nucleotide variant of the T7 R1.1 processing signal has two Watson-Crick base-paired helices separated by an internal loop, consistent with its pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.4.604

    authors: Schweisguth DC,Chelladurai BS,Nicholson AW,Moore PB

    更新日期:1994-02-25 00:00:00

  • Identification and characterization of the mouse nuclear export factor (Nxf) family members.

    abstract::TAP/hNXF1 is a key factor that mediates general cellular mRNA export from the nucleus, and its orthologs are structurally and functionally conserved from yeast to humans. Metazoans encode additional proteins that share homology and domain organization with TAP/hNXF1, suggesting their participation in mRNA metabolism; ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki706

    authors: Tan W,Zolotukhin AS,Tretyakova I,Bear J,Lindtner S,Smulevitch SV,Felber BK

    更新日期:2005-07-13 00:00:00

  • A deep learning framework for modeling structural features of RNA-binding protein targets.

    abstract::RNA-binding proteins (RBPs) play important roles in the post-transcriptional control of RNAs. Identifying RBP binding sites and characterizing RBP binding preferences are key steps toward understanding the basic mechanisms of the post-transcriptional gene regulation. Though numerous computational methods have been dev...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1025

    authors: Zhang S,Zhou J,Hu H,Gong H,Chen L,Cheng C,Zeng J

    更新日期:2016-02-29 00:00:00

  • X-ray induced DNA double strand break production and repair in mammalian cells as measured by neutral filter elution.

    abstract::This work presents a neutral filter elution method for detecting DNA double strand breaks in mouse L1210 cells after X-ray. The assay will detect the number of double strand breaks induced by as little as 1000 rad of X-ray. The rate of DNA elution through the filters under neutral conditions increases with X-ray dose....

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/7.3.793

    authors: Bradley MO,Kohn KW

    更新日期:1979-10-10 00:00:00

  • Protection of discrete DNA fragments by the complex H1-octamerhistones or H5-octamerhistones after micrococcal nuclease digestion.

    abstract::Several authors, including ourselves, have reported the existence of chromatosomes with DNA size larger than 166 bp in bird erythrocyte chromatin. It was tempting to correlate this increased DNA size with the presence of histone H5. In order to substantiate this hypothesis, we performed a micrococcal nuclease digestio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/9.15.3671

    authors: Muyldermans S,Lasters I,Wyns L,Hamers R

    更新日期:1981-08-11 00:00:00

  • Solid-phase synthesis and hybridization properties of DNA containing sulfide-linked dinucleosides.

    abstract::Oligodeoxyribonucleotides incorporating non-hydrolyzable dialkyl sulfide linked thymidine dimers (TsT) were synthesized chemically by the solid-phase approach. The sulfide dimer TsT was stable to degradation by snake-venom phosphodiesterase, calf spleen phosphodiesterase, Nuclease P1 and Nuclease S1. Thermal denaturat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.6.1473

    authors: Kawai SH,Wang D,Giannaris PA,Damha MJ,Just G

    更新日期:1993-03-25 00:00:00

  • Ultrasensitive isolation, identification and quantification of DNA-protein adducts by ELISA-based RADAR assay.

    abstract::Enzymes that form transient DNA-protein covalent complexes are targets for several potent classes of drugs used to treat infectious disease and cancer, making it important to establish robust and rapid procedures for analysis of these complexes. We report a method for isolation of DNA-protein adducts and their identif...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku490

    authors: Kiianitsa K,Maizels N

    更新日期:2014-07-01 00:00:00

  • Unusual duplex formation in purine rich oligodeoxyribonucleotides.

    abstract::The purine rich oligodeoxyribonucleotides 1C, d(ATGACGGAATA) and 2C, d(ATGAGCGAATA) alone exhibit highly cooperative melting transitions. Analysis of the concentration dependence of melting, and electrophoretic studies indicate that these oligomers can form an unusual purine rich offset double helix. The unusual duple...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.11.5137

    authors: Wilson WD,Dotrong MH,Zuo ET,Zon G

    更新日期:1988-06-10 00:00:00

  • DNA-like duplexes with repetitions. I. Properties of concatemer duplexes formed by d(T-G-C-A-C-A-T-G).

    abstract::A new class of synthetic DNA duplexes containing repeating oligonucleotide sequences, double-helical concatemers, is characterized. The UV-absorption and circular dichroism of a concatemer formed in self-association of d(T-G-C-A-C-A-T-G) have been studied. The thermodynamical parameters of complex formation are the fo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.11.2413

    authors: Shabarova ZA,Dolinnaya NG,Turkin SI,Gromova ES

    更新日期:1980-06-11 00:00:00

  • mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

    abstract::High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku370

    authors: Hach F,Sarrafi I,Hormozdiari F,Alkan C,Eichler EE,Sahinalp SC

    更新日期:2014-07-01 00:00:00