当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > Significant expansion of the REST/NRSF cistrome in human versus mouse embryonic stem cells: potential implications for neural development.

Significant expansion of the REST/NRSF cistrome in human versus mouse embryonic stem cells: potential implications for neural development.

Abstract：

:Recent studies have employed cross-species comparisons of transcription factor binding, reporting significant regulatory network 'rewiring' between species. Here, we address how a transcriptional repressor targets and regulates neural genes differentially between human and mouse embryonic stem cells (ESCs). We find that the transcription factor, Repressor Element 1 Silencing Transcription factor (REST; also called neuron restrictive silencer factor) binds to a core group of ∼1200 syntenic genomic regions in both species, with these conserved sites highly enriched with co-factors, selective histone modifications and DNA hypomethylation. Genes with conserved REST binding are enriched with neural functions and more likely to be upregulated upon REST depletion. Interestingly, we identified twice as many REST peaks in human ESCs compared to mouse ESCs. Human REST cistrome expansion involves additional peaks in genes targeted by REST in both species and human-specific gene targets. Genes with expanded REST occupancy in humans are enriched for learning or memory functions. Analysis of neurological disorder associated genes reveals that Amyotrophic Lateral Sclerosis and oxidative stress genes are particularly enriched with human-specific REST binding. Overall, our results demonstrate that there is substantial rewiring of human and mouse REST cistromes, and that REST may have human-specific roles in brain development and functions.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Rockowitz S,Zheng D

doi

10.1093/nar/gkv514

subject

Has Abstract

pub_date

2015-07-13 00:00:00

pages

5730-43

issue

12

eissn

0305-1048

issn

1362-4962

pii

gkv514

journal_volume

43

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • Reverse genetics-based biochemical studies of the ribosomal exit tunnel constriction region in eukaryotic ribosome stalling: spatial allocation of the regulatory nascent peptide at the constriction.

    abstract：:A number of regulatory nascent peptides have been shown to regulate gene expression by causing programmed ribosome stalling during translation. Nascent peptide emerges from the ribosome through the exit tunnel, and one-third of the way along which β-loop structures of ribosomal proteins uL4 and uL22 protrude into the ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz1190

    authors： Takamatsu S,Ohashi Y,Onoue N,Tajima Y,Imamichi T,Yonezawa S,Morimoto K,Onouchi H,Yamashita Y,Naito S

    更新日期：2020-02-28 00:00:00

  • Improved programs for DNA and protein sequence analysis on the IBM personal computer and other standard computer systems.

    abstract：:We have previously described programs for a variety of types of sequence analysis (1-4). These programs have now been integrated into a single package. They are written in the standard C programming language and run on virtually any computer system with a C compiler, such as the IBM/PC and other computers running unde...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/14.1.443

    authors： Mount DW,Conrad B

    更新日期：1986-01-10 00:00:00

  • Controlled loading of oligodeoxyribonucleotide monolayers onto unoxidized crystalline silicon; fluorescence-based determination of the surface coverage and of the hybridization efficiency; parallel imaging of the process by Atomic Force Microscopy.

    abstract：:Unoxidized crystalline silicon, characterized by high purity, high homogeneity, sturdiness and an atomically flat surface, offers many advantages for the construction of electronic miniaturized biosensor arrays upon attachment of biomolecules (DNA, proteins or small organic compounds). This allows to study the inciden...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gnj034

    authors： Cattaruzza F,Cricenti A,Flamini A,Girasole M,Longo G,Prosperi T,Andreano G,Cellai L,Chirivino E

    更新日期：2006-02-28 00:00:00

  • The effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine.

    abstract：:The effect of amino groups attached at positions 2 and 8 of the hypoxanthine moiety in the structure, reactivity and stability of DNA duplexes and triplexes is studied by means of quantum mechanical calculations, as well as extended molecular dynamics (MD) and thermodynamic integration (MD/TI) simulations. Theoretical...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/29.12.2522

    authors： Cubero E,Güimil-García R,Luque FJ,Eritja R,Orozco M

    更新日期：2001-06-15 00:00:00

  • Short antisense-locked nucleic acids (all-LNAs) correct alternative splicing abnormalities in myotonic dystrophy.

    abstract：:Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystemic disorder caused by expansion of CTG triplet repeats in 3'-untranslated region of DMPK gene. The pathomechanism of DM1 is driven by accumulation of toxic transcripts containing expanded CUG repeats (CUG(exp)) in nuclear foci which sequester several ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv163

    authors： Wojtkowiak-Szlachcic A,Taylor K,Stepniak-Konieczna E,Sznajder LJ,Mykowska A,Sroka J,Thornton CA,Sobczak K

    更新日期：2015-03-31 00:00:00

  • Capping of vesicular stomatitis virus pre-mRNA is required for accurate selection of transcription stop-start sites and virus propagation.

    abstract：:The multifunctional RNA-dependent RNA polymerase L protein of vesicular stomatitis virus catalyzes unconventional pre-mRNA capping via the covalent enzyme-pRNA intermediate formation, which requires the histidine-arginine (HR) motif in the polyribonucleotidyltransferase domain. Here, the effects of cap-defective mutat...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku901

    authors： Ogino T

    更新日期：2014-10-29 00:00:00

  • HDAC3 functions as a positive regulator in Notch signal transduction.

    abstract：:Aberrant Notch signaling plays a pivotal role in T-cell acute lymphoblastic leukemia (T-ALL) and chronic lymphocytic leukemia (CLL). Amplitude and duration of the Notch response is controlled by ubiquitin-dependent proteasomal degradation of the Notch1 intracellular domain (NICD1), a hallmark of the leukemogenic proce...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkaa088

    authors： Ferrante F,Giaimo BD,Bartkuhn M,Zimmermann T,Close V,Mertens D,Nist A,Stiewe T,Meier-Soelch J,Kracht M,Just S,Klöble P,Oswald F,Borggrefe T

    更新日期：2020-04-17 00:00:00

  • Topological structure analysis of the protein-protein interaction network in budding yeast.

    abstract：:Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large-scale data sets is important to present-day biology. Here, a spectral method derived from graph theory was introduced to uncover hidden topological structures (i.e. quasi-cliques...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkg340

    authors： Bu D,Zhao Y,Cai L,Xue H,Zhu X,Lu H,Zhang J,Sun S,Ling L,Zhang N,Li G,Chen R

    更新日期：2003-05-01 00:00:00

  • Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance.

    abstract：:Fully modified 4'-thioDNA, an oligonucleotide only comprising 2'-deoxy-4'-thionucleosides, exhibited resistance to an endonuclease, in addition to preferable hybridization with RNA. Therefore, 4'-thioDNA is promising for application as a functional oligonucleotide. Fully modified 4'-thioDNA was found to behave like an...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn011

    authors： Matsugami A,Ohyama T,Inada M,Inoue N,Minakawa N,Matsuda A,Katahira M

    更新日期：2008-04-01 00:00:00

  • Oligonucleotide immobilization on micropatterned streptavidin surfaces.

    abstract：:We describe a simple procedure for photolithographic patterning of streptavidin on silicon substrates. Long wavelength UV (365 nm) light was used to direct the covalent attachment of photoactivatable biotin onto silylated silicon wafers. Fluorescently labeled streptavidin was found to bind only in areas exposed to the...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/28.8.e33

    authors： Sabanayagam CR,Smith CL,Cantor CR

    更新日期：2000-04-15 00:00:00

  • A novel occluded RNA recognition motif in Prp24 unwinds the U6 RNA internal stem loop.

    abstract：:The essential splicing factor Prp24 contains four RNA Recognition Motif (RRM) domains, and functions to anneal U6 and U4 RNAs during spliceosome assembly. Here, we report the structure and characterization of the C-terminal RRM4. This domain adopts a novel non-canonical RRM fold with two additional flanking α-helices ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkr455

    authors： Martin-Tumasz S,Richie AC,Clos LJ 2nd,Brow DA,Butcher SE

    更新日期：2011-09-01 00:00:00

  • Single locus microsatellites isolated using 5' anchored PCR.

    abstract：:Microsatellites are widely used as genetic markers because they are co-dominant, multiallelic, easily scored and highly polymorphic. A major drawback of microsatellite markers is the time and cost required to characterise them. We have developed a novel technique to reduce this cost by producing a microsatellite-rich ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/24.21.4369

    authors： Fisher PJ,Gardner RC,Richardson TE

    更新日期：1996-11-01 00:00:00

  • The transcription factors ATF-1 and CREB-1 bind constitutively to the hypoxia-inducible factor-1 (HIF-1) DNA recognition site.

    abstract：:The hypoxia-inducible factor-1 (HIF-1) was first described as a DNA binding activity that specifically recognizes an 8 bp motif known to be essential for hypoxia-inducible erythropoietin gene transcription. Subsequently HIF-1 activity has also been found in cell lines which do not express erythropoietin, suggesting th...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/23.22.4542

    authors： Kvietikova I,Wenger RH,Marti HH,Gassmann M

    更新日期：1995-11-25 00:00:00

  • A synthetic DNA-binding inhibitor of SOX2 guides human induced pluripotent stem cells to differentiate into mesoderm.

    abstract：:Targeted differentiation of human induced pluripotent stem cells (hiPSCs) using only chemicals would have value-added clinical potential in the regeneration of complex cell types including cardiomyocytes. Despite the availability of several chemical inhibitors targeting proteins involved in signaling pathways, no bioa...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx693

    authors： Taniguchi J,Pandian GN,Hidaka T,Hashiya K,Bando T,Kim KK,Sugiyama H

    更新日期：2017-09-19 00:00:00

  • Novel internucleotide 3'-NH-P(CH3)(O)-O-5' linkage. Oligo(deoxyribonucleoside methanephosphonamidates); synthesis, structure and hybridization properties.

    abstract：:Diastereomeric dithymidine methanephosphonamidates (TnpmT) were synthesized by reaction of 3'-amino-3'-deoxythymidine with 3'- O -acetylthymidin-5-yl-methanephosphonochloridate. Separated dinucleotide TnpmT(fast) and TnpmT(slow) diastereomers were used as building blocks to prepare chimeric dodecathy-midylates, posses...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/26.11.2650

    authors： Nawrot B,Boczkowska M,Wójcik M,Sochacki M,Kazmierski S,Stec WJ

    更新日期：1998-06-01 00:00:00

  • MutSβ and histone deacetylase complexes promote expansions of trinucleotide repeats in human cells.

    abstract：:Trinucleotide repeat (TNR) expansions cause at least 17 heritable neurological diseases, including Huntington's disease. Expansions are thought to arise from abnormal processing of TNR DNA by specific trans-acting proteins. For example, the DNA repair complex MutSβ (MSH2-MSH3 heterodimer) is required in mice for on-go...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks810

    authors： Gannon AM,Frizzell A,Healy E,Lahue RS

    更新日期：2012-11-01 00:00:00

  • Alternative-splicing-based bicistronic vectors for ratio-controlled protein expression and application to recombinant antibody production.

    abstract：:In the last decade polycistronic vectors have become essential tools for both basic science and gene therapy applications. In order to co-express heterologous polypeptides, different systems have been developed from Internal Ribosome Entry Site (IRES) based vectors to the use of the 2A peptide. Unfortunately, these me...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkp716

    authors： Fallot S,Ben Naya R,Hieblot C,Mondon P,Lacazette E,Bouayadi K,Kharrat A,Touriol C,Prats H

    更新日期：2009-11-01 00:00:00

  • The telomere resolvase of the Lyme disease spirochete, Borrelia burgdorferi, promotes DNA single-strand annealing and strand exchange.

    abstract：:Spirochetes of the genus Borrelia include the tick-transmitted causative agents of Lyme disease and relapsing fever. They possess unusual genomes composed mainly of linear replicons terminated by closed DNA hairpin telomeres. Hairpin telomeres present an uninterrupted DNA chain to the replication machinery overcoming ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt832

    authors： Mir T,Huang SH,Kobryn K

    更新日期：2013-12-01 00:00:00

  • Hydropathic analysis of the free energy differences in anthracycline antibiotic binding to DNA.

    abstract：:Molecular models of six anthracycline antibiotics and their complexes with 32 distinct DNA octamer sequences were created and analyzed using HINT (Hydropathic INTeractions) to describe binding. The averaged binding scores were then used to calculate the free energies of binding for comparison with experimentally deter...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkg645

    authors： Cashman DJ,Scarsdale JN,Kellogg GE

    更新日期：2003-08-01 00:00:00

  • Role of nucleotide identity in effective CRISPR target escape mutations.

    abstract：:Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly infl...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gky687

    authors： Künne T,Zhu Y,da Silva F,Konstantinides N,McKenzie RE,Jackson RN,Brouns SJ

    更新日期：2018-11-02 00:00:00

  • Monitoring the spatio-temporal organization and dynamics of the genome.

    abstract：:The spatio-temporal organization of chromatin in the eukaryotic cell nucleus is of vital importance for transcription, DNA replication and genome maintenance. Each of these activities is tightly regulated in both time and space. While we have a good understanding of chromatin organization in space, for example in fixe...

    journal_title：Nucleic acids research

    pub_type： 杂志文章,评审

    doi：10.1093/nar/gkaa135

    authors： Shaban HA,Seeber A

    更新日期：2020-04-17 00:00:00

  • Primer specific and mispair extension analysis (PSMEA) as a simple approach to fast genotyping.

    abstract：:A simple method, primer specific and mispair extension analysis (PSMEA) with pfu DNA polymerase was developed for genotyping. PSMEA is based on the unique properties of 3'-->5' exonuclease proofreading activity. In the presence of an incomplete set of dNTPs, pfu was found to be extremely discriminative in nucleotide i...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/26.21.5013

    authors： Hu YW,Balaskas E,Kessler G,Issid C,Scully LJ,Murphy DG,Rinfret A,Giulivi A,Scalia V,Gill P

    更新日期：1998-11-01 00:00:00

  • Identification of a distal regulatory element in the 5' flanking region of the bovine prolactin gene.

    abstract：:The 5'-flanking region of the bovine prolactin gene was cloned and sequenced. The expression of chimeric gene constructs containing 5'-flanking DNA fragments from the prolactin gene joined to a reporter gene encoding human growth hormone (hGH) was examined using transiently transfected rat pituitary cells. Prolactin n...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：

    authors： Wolf JB,David VA,Deutch AH

    更新日期：1990-08-25 00:00:00

  • GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure.

    abstract：:Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx246

    authors： Baek M,Park T,Heo L,Park C,Seok C

    更新日期：2017-07-03 00:00:00

  • Quantitative analysis of conditional gene inactivation using rationally designed, tetracycline-controlled miRNAs.

    abstract：:The combination of RNA interference (RNAi) with the tetracycline-controlled transcription activation (tet) system promises to become a powerful method for conditional gene inactivation in cultured cells and in whole organisms. Here, we tested critical sequence elements that originated from miRNA mR-30 for optimal effi...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq616

    authors： Berger SM,Pesold B,Reber S,Schönig K,Berger AJ,Weidenfeld I,Miao J,Berger MR,Gruss OJ,Bartsch D

    更新日期：2010-09-01 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

  • Conditional genome engineering reveals canonical and divergent roles for the Hus1 component of the 9-1-1 complex in the maintenance of the plastic genome of Leishmania.

    abstract：:Leishmania species are protozoan parasites whose remarkably plastic genome limits the establishment of effective genetic manipulation and leishmaniasis treatment. The strategies used by Leishmania to maintain its genome while allowing variability are not fully understood. Here, we used DiCre-mediated conditional gene ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gky1017

    authors： Damasceno JD,Obonaga R,Silva GLA,Reis-Cunha JL,Duncan SM,Bartholomeu DC,Mottram JC,McCulloch R,Tosi LRO

    更新日期：2018-12-14 00:00:00

  • Methods to increase reproducibility in differential gene expression via meta-analysis.

    abstract：:Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, ge...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw797

    authors： Sweeney TE,Haynes WA,Vallania F,Ioannidis JP,Khatri P

    更新日期：2017-01-09 00:00:00

  • A nascent micronuclear pseudogene in the ciliate Euplotes crassus.

    abstract：:The macronuclear genome of Euplotes crassus contains two different genes, EFA1 and EFA2, encoding EF-1alpha proteins. They are derived from micronuclear precursors in the course of a sexual process termed conjugation. We have found that two apparent micronuclear precursors exist for EFA1. They differ in their potentia...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/24.16.3195

    authors： Florian V,Klein A

    更新日期：1996-08-15 00:00:00

  • Characterization of human Spartan/C1orf124, an ubiquitin-PCNA interacting regulator of DNA damage tolerance.

    abstract：:Unrepaired DNA damage may arrest ongoing replication forks, potentially resulting in fork collapse, increased mutagenesis and genomic instability. Replication through DNA lesions depends on mono- and polyubiquitylation of proliferating cell nuclear antigen (PCNA), which enable translesion synthesis (TLS) and template ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks850

    authors： Juhasz S,Balogh D,Hajdu I,Burkovics P,Villamil MA,Zhuang Z,Haracska L

    更新日期：2012-11-01 00:00:00