当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > Quantifying deleterious effects of regulatory variants.

Quantifying deleterious effects of regulatory variants.

Abstract：

:The majority of genome-wide association study (GWAS) risk variants reside in non-coding DNA sequences. Understanding how these sequence modifications lead to transcriptional alterations and cell-to-cell variability can help unraveling genotype-phenotype relationships. Here, we describe a computational method, dubbed CAPE, which calculates the likelihood of a genetic variant deactivating enhancers by disrupting the binding of transcription factors (TFs) in a given cellular context. CAPE learns sequence signatures associated with putative enhancers originating from large-scale sequencing experiments (such as ChIP-seq or DNase-seq) and models the change in enhancer signature upon a single nucleotide substitution. CAPE accurately identifies causative cis-regulatory variation including expression quantitative trait loci (eQTLs) and DNase I sensitivity quantitative trait loci (dsQTLs) in a tissue-specific manner with precision superior to several currently available methods. The presented method can be trained on any tissue-specific dataset of enhancers and known functional variants and applied to prioritize disease-associated variants in the corresponding tissue.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Li S,Alvarez RV,Sharan R,Landsman D,Ovcharenko I

doi

10.1093/nar/gkw1263

subject

Has Abstract

pub_date

2017-03-17 00:00:00

pages

2307-2317

issue

5

eissn

0305-1048

issn

1362-4962

pii

gkw1263

journal_volume

45

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • Influence of loop size on the stability of intramolecular DNA quadruplexes.

    abstract：:We have determined the stability of intramolecular DNA quadruplexes in which the four G(3)-tracts are connected by non-nucleosidic linkers containing propanediol, octanediol or hexaethylene glycol, replacing the TTA loops in the human telomeric repeat sequence. We find that these sequences all fold to form intramolecu...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkh598

    authors： Risitano A,Fox KR

    更新日期：2004-05-11 00:00:00

  • Codon catalog usage and the genome hypothesis.

    abstract：:Frequencies for each of the 61 amino acid codons have been determined in every published mRNA sequence of 50 or more codons. The frequencies are shown for each kind of genome and for each individual gene. A surprising consistency of choices exists among genes of the same or similar genomes. Thus each genome, or kind o...

    journal_title：Nucleic acids research

    pub_type： 杂志文章,评审

    doi：10.1093/nar/8.1.197-c

    authors： Grantham R,Gautier C,Gouy M,Mercier R,Pavé A

    更新日期：1980-01-11 00:00:00

  • Spatial localization of co-regulated genes exceeds genomic gene clustering in the Saccharomyces cerevisiae genome.

    abstract：:While it has been long recognized that genes are not randomly positioned along the genome, the degree to which its 3D structure influences the arrangement of genes has remained elusive. In particular, several lines of evidence suggest that actively transcribed genes are spatially co-localized, forming transcription fa...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks1360

    authors： Ben-Elazar S,Yakhini Z,Yanai I

    更新日期：2013-02-01 00:00:00

  • A sigma factor toolbox for orthogonal gene expression in Escherichia coli.

    abstract：:Synthetic genetic sensors and circuits enable programmable control over timing and conditions of gene expression and, as a result, are increasingly incorporated into the control of complex and multi-gene pathways. Size and complexity of genetic circuits are growing, but stay limited by a shortage of regulatory parts t...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gky010

    authors： Bervoets I,Van Brempt M,Van Nerom K,Van Hove B,Maertens J,De Mey M,Charlier D

    更新日期：2018-02-28 00:00:00

  • CRISPR RNA binding and DNA target recognition by purified Cascade complexes from Escherichia coli.

    abstract：:Clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated Cas proteins comprise a prokaryotic RNA-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. The type I-E CRISPR interference complex Cascade from Escherichia coli is composed of...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku1285

    authors： Beloglazova N,Kuznedelov K,Flick R,Datsenko KA,Brown G,Popovic A,Lemak S,Semenova E,Severinov K,Yakunin AF

    更新日期：2015-01-01 00:00:00

  • Functional characterization of C. elegans Y-box-binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes.

    abstract：:The cold shock domain is one of the most highly conserved motifs between bacteria and higher eukaryotes. Y-box-binding proteins represent a subfamily of cold shock domain proteins with pleiotropic functions, ranging from transcription in the nucleus to translation in the cytoplasm. These proteins have been investigate...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku1077

    authors： Arnold A,Rahman MM,Lee MC,Muehlhaeusser S,Katic I,Gaidatzis D,Hess D,Scheckel C,Wright JE,Stetak A,Boag PR,Ciosk R

    更新日期：2014-12-01 00:00:00

  • Simple and straightforward construction of a mouse gene targeting vector using in vitro transposition reactions.

    abstract：:In a gene targeting experiment, the generation of a targeting construct often requires complex DNA manipulations. We developed a set of cassettes and plasmids useful for creating targeting vectors to modify the mammalian genome. A positive selection marker cassette (PGK/EM7p-npt), which included dual prokaryotic and e...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gni055

    authors： Aoyama M,Agari K,Sun-Wada GH,Futai M,Wada Y

    更新日期：2005-03-22 00:00:00

  • The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database.

    abstract：:The RESID Database is a comprehensive collection of annotations and structures for protein post-translational modifications including N-terminal, C-terminal and peptide chain cross-link modifications. The RESID Database includes systematic and frequently observed alternate names, Chemical Abstracts Service registry nu...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/29.1.199

    authors： Garavelli JS,Hou Z,Pattabiraman N,Stephens RM

    更新日期：2001-01-01 00:00:00

  • Serial analysis of gene expression: rapid RT-PCR analysis of unknown SAGE tags.

    abstract：:In a pilot study on SAGE on Reed-Sternberg cells we have sequenced 1055 tags representing 701 genes. Screening of the GenBank database resulted in the identification of a corresponding gene or EST for 490 of them. For 211 of the tags no homology could be detected. A major problem of the serial analysis of gene express...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/27.17.e17

    authors： van den Berg A,van der Leij J,Poppema S

    更新日期：1999-09-01 00:00:00

  • An adaptation of the LMS method to determine expression variations in profiling data.

    abstract：:One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expressio...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm093

    authors： Chuchana P,Marchand D,Nugoli M,Rodriguez C,Molinari N,Garcia-Sanz JA

    更新日期：2007-01-01 00:00:00

  • Circular dichroism studies of ethidium bromide binding to the isolated nucleolus.

    abstract：:Circular dichroism in the 300-360 nm region and fluorescence induced by intercaltating binding of ethidum bromide to both DNA and RNA components were studied in isolated HeLa nucleoli. Both DNA and RNA compoents contribute to the induced dichroic elliticity. Digestion of nucleoli by RNase or DNase shows that most of t...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/3.8.1857

    authors： Huang CH,Baserga R

    更新日期：1976-08-01 00:00:00

  • Characterization of the promoter for the rat and human link protein gene.

    abstract：:We have isolated the 5'-end of the gene for the rat and human link protein by screening genomic libraries with oligonucleotides corresponding to the 5'-cDNA sequence. Several overlapping clones were isolated for the human link protein gene, while only one clone was obtained for the rat. All the clones contained a sing...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/19.8.1933

    authors： Rhodes C,Savagner P,Line S,Sasaki M,Chirigos M,Doege K,Yamada Y

    更新日期：1991-04-25 00:00:00

  • Identification and partial characterization of an endogenous form of mouse mammary tumor virus that is transcribed into the virion-associated RNA genome.

    abstract：:Restriction mapping demonstrated the presence of several distinct proviral forms of mouse mammary tumor virus in the genome of GR mice. One of these proviruses (GR-MTV-2) was highly amplified in GR 3A cells, a cell line derived from a GR mammary tumor. By the criterion of restriction mapping, the amplified GR-MTV-2 pr...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/8.23.5715

    authors： Fanning TG,Puma JP,Cardiff RD

    更新日期：1980-12-11 00:00:00

  • IMP1 KH1 and KH2 domains create a structural platform with unique RNA recognition and re-modelling properties.

    abstract：:IGF2 mRNA-binding protein 1 (IMP1) is a key regulator of messenger RNA (mRNA) metabolism and transport in organismal development and, in cancer, its mis-regulation is an important component of tumour metastasis. IMP1 function relies on the recognition of a diverse set of mRNA targets that is mediated by the combinator...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz136

    authors： Dagil R,Ball NJ,Ogrodowicz RW,Hobor F,Purkiss AG,Kelly G,Martin SR,Taylor IA,Ramos A

    更新日期：2019-05-07 00:00:00

  • Apoptotic signals induce specific degradation of ribosomal RNA in yeast.

    abstract：:Organisms exposed to reactive oxygen species, generated endogenously during respiration or by environmental conditions, undergo oxidative stress. Stress response can either repair the damage or activate one of the programmed cell death (PCD) mechanisms, for example apoptosis, and finally end in cell death. One strikin...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm1100

    authors： Mroczek S,Kufel J

    更新日期：2008-05-01 00:00:00

  • 4EHP-independent repression of endogenous mRNAs by the RNA-binding protein GIGYF2.

    abstract：:Initially identified as a factor involved in tyrosine kinase receptor signaling, Grb10-interacting GYF protein 2 (GIGYF2) has later been shown to interact with the 5' cap-binding protein 4EHP as part of a translation repression complex, and to mediate post-transcriptional repression of tethered reporter mRNAs. A curre...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gky198

    authors： Amaya Ramirez CC,Hubbe P,Mandel N,Béthune J

    更新日期：2018-06-20 00:00:00

  • dbCAN2: a meta server for automated carbohydrate-active enzyme annotation.

    abstract：:Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active enzymes (CAZymes) are the most important enzymes for complex carbohydrate metabolism. With an increasing number of plant and plant-as...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gky418

    authors： Zhang H,Yohe T,Huang L,Entwistle S,Wu P,Yang Z,Busk PK,Xu Y,Yin Y

    更新日期：2018-07-02 00:00:00

  • Sequence-specific functions of the early palindrome domain within the SV40 core origin of replication.

    abstract：:The early palindrome domain within the SV40 core origin of replication is essential for the initiation of replication. Studies with single point mutants in this region suggested that the early palindrome domain does not function as a cruciform structure, but may be involved in the initiation of SV40 DNA replication in...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：

    authors： Kim YS,Kang HS

    更新日期：1989-11-25 00:00:00

  • Novel non-isotopic detection of MutY enzyme-recognized mismatches in DNA via ultrasensitive detection of aldehydes.

    abstract：:A highly sensitive method to detect traces of aldehyde-containing apurinic/apyrimidinic (AP) sites in nucleic acids has been developed. Based on this method, a novel approach to detect DNA base mismatches recognized by the mismatch repair glycosylase MutY is demonstrated. Open chain aldehydes generated in nucleic acid...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/27.5.1316

    authors： Maulik G,Botchway S,Chakrabarti S,Tetradis S,Price B,Makrigiorgos GM

    更新日期：1999-03-01 00:00:00

  • Structure of replication origin of the Escherichia coli K-12 chromosome: the presence of spacer sequences in the ori region carrying information for autonomous replication.

    abstract：:The replication origin region of the Escherichia coli K-12 chromosome has been cloned, and a region of 245 base-pairs has been shown to contain all the information for autonomous replication (defined ori). In order to obtain further information on the sequence organization in the defined ori stretch, various types of ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/10.12.3745

    authors： Asada K,Sugimoto K,Oka A,Takanami M,Hirota Y

    更新日期：1982-06-25 00:00:00

  • In vivo and in vitro studies of Mgs1 suggest a link between genome instability and Okazaki fragment processing.

    abstract：:The non-essential MGS1 gene of Saccharomyces cerevisiae is highly conserved in eukaryotes and encodes an enzyme containing both DNA-dependent ATPase and DNA annealing activities. MGS1 appears to function in post-replicational repair processes that contribute to genome stability. In this study, we identified MGS1 as a ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gki900

    authors： Kim JH,Kang YH,Kang HJ,Kim DH,Ryu GH,Kang MJ,Seo YS

    更新日期：2005-10-26 00:00:00

  • Specific hydrolysis of methionyl-tRNA Met f catalyzed by a purified peptide.

    abstract：:A peptide initiation factor purified from rat liver and promoting the binding of initiator tRNA and model initiators to 40S and 80S ribosome at an acid pH liberates methionine and N-acetylmethionine from Trna Met f at neutral reaction. Phenylalanyl-tRNA, N-acetylphenylalanyl-tRNA and methionyl-tRNA Met m are not hydro...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/2.11.2119

    authors： Hradec J

    更新日期：1975-11-01 00:00:00

  • Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon.

    abstract：:Mycobacterium tuberculosis (Mtb) Cmr (Rv1675c) is a CRP/FNR family transcription factor known to be responsive to cAMP levels and during macrophage infections. However, Cmr's DNA binding properties, cellular targets and overall role in tuberculosis (TB) complex bacteria have not been characterized. In this study, we u...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv889

    authors： Ranganathan S,Bai G,Lyubetskaya A,Knapp GS,Peterson MW,Gazdik M,C Gomes AL,Galagan JE,McDonough KA

    更新日期：2016-01-08 00:00:00

  • Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.

    abstract：:Genomic DNA methylation profiles exhibit substantial variation within the human population, with important functional implications for gene regulation. So far little is known about the characteristics and determinants of DNA methylation variation among healthy individuals. We performed bioinformatic analysis of high-r...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn122

    authors： Bock C,Walter J,Paulsen M,Lengauer T

    更新日期：2008-06-01 00:00:00

  • An in vitro RNA polymerase III system from S. cerevisiae: effects of deletions and point mutations upon SUP4 gene transcription.

    abstract：:A soluble cell-free extract containing RNA polymerase III and factors essential for selective transcription of the yeast SUP4-o tRNATyr gene was prepared from Saccharomyces cerevisiae cells. An intragenic promoter for yeast RNA polymerase III was identified within the yeast tRNATyr coding sequence by testing several s...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/10.24.8127

    authors： Koski RA,Allison DS,Worthington M,Hall BD

    更新日期：1982-12-20 00:00:00

  • Intracellular RNA cleavage by the hairpin ribozyme.

    abstract：:Studies involving ribozyme-directed inactivation of targeted RNA molecules have met with mixed success, making clear the importance of methods to measure and optimize ribozyme activity within cells. The interpretation of biochemical assays for determining ribozyme activity in the cellular environment have been complic...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/26.15.3494

    authors： Seyhan AA,Amaral J,Burke JM

    更新日期：1998-08-01 00:00:00

  • Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities.

    abstract：:An intronic hexanucleotide UGCAUG has been shown to play a critical role in the regulation of tissue-specific alternative splicing of pre-mRNAs in a wide range of tissues. Vertebrate Fox-1 has been shown to bind to this element, in a highly sequence-specific manner, through its RNA recognition motif (RRM). In mammals,...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gki338

    authors： Nakahata S,Kawamoto S

    更新日期：2005-04-11 00:00:00

  • Sinefungin resistance of Saccharomyces cerevisiae arising from Sam3 mutations that inactivate the AdoMet transporter or from increased expression of AdoMet synthase plus mRNA cap guanine-N7 methyltransferase.

    abstract：:The S-adenosylmethionine (AdoMet) analog sinefungin is a natural product antibiotic that inhibits nucleic acid methyltransferases and arrests the growth of unicellular eukarya and eukaryal viruses. The basis for the particular sensitivity of fungi and protozoa to sinefungin is not known. Here we report the isolation a...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm817

    authors： Zheng S,Shuman S,Schwer B

    更新日期：2007-01-01 00:00:00

  • Triple helix formation at distant sites: hybrid oligonucleotides containing a polymeric linker.

    abstract：:An oligonucleotide hybrid is described which possesses two triple helix forming oligonucleotides which have been connected by a flexible polymeric linker chain. As a prototype, binding of this class of oligonucleotide to duplex DNA has been studied using a segment of the HSV-1 D-glycoprotein promoter, which possesses ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/21.20.4810

    authors： Kessler DJ,Pettitt BM,Cheng YK,Smith SR,Jayaraman K,Vu HM,Hogan ME

    更新日期：1993-10-11 00:00:00

  • Structural basis of the XPB-Bax1 complex as a dynamic helicase-nuclease machinery for DNA repair.

    abstract：:Nucleotide excision repair (NER) is a major DNA repair pathway for a variety of DNA lesions. XPB plays a key role in DNA opening at damage sites and coordinating damage incision by nucleases. XPB is conserved from archaea to human. In archaea, XPB is associated with a nuclease Bax1. Here we report crystal structures o...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkaa324

    authors： DuPrez K,He F,Chen Z,Hilario E,Fan L

    更新日期：2020-06-19 00:00:00