Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways.

Abstract:

:Nucleotide excision repair is initiated by two different damage recognition subpathways, global genome repair (GGR) and transcription-coupled repair (TCR). In GGR, XPC detects DNA lesions and recruits TFIIH via interaction with the pleckstrin homology (PH) domain of TFIIH subunit p62. In TCR, an elongating form of RNA Polymerase II detects a lesion on the transcribed strand and recruits TFIIH by an unknown mechanism. Here, we found that the TCR initiation factor UVSSA forms a stable complex with the PH domain of p62 via a short acidic string in the central region of UVSSA, and determined the complex structure by NMR. The acidic string of UVSSA binds strongly to the basic groove of the PH domain by inserting Phe408 and Val411 into two pockets, highly resembling the interaction mechanism of XPC with p62. Mutational binding analysis validated the structure and identified residues crucial for binding. TCR activity was markedly diminished in UVSSA-deficient cells expressing UVSSA mutated at Phe408 or Val411. Thus, a common TFIIH recruitment mechanism is shared by UVSSA in TCR and XPC in GGR.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Okuda M,Nakazawa Y,Guo C,Ogi T,Nishimura Y

doi

10.1093/nar/gkx970

subject

Has Abstract

pub_date

2017-12-15 00:00:00

pages

13043-13055

issue

22

eissn

0305-1048

issn

1362-4962

pii

4563304

journal_volume

45

pub_type

杂志文章
  • The gene II proteins of the filamentous phages IKe and Ff (M13, fd and f1) are not functionally interchangeable during viral strand replication.

    abstract::Gene II protein is the only phage-encoded protein required for the double-stranded DNA replication of the distantly related filamentous phages IKe and Ff (M13, fd and f1). Complementation studies have demonstrated that, despite a significant degree of homology between the nucleotide sequences of the gene II's of IKe a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.12.5067

    authors: Peeters BP,Schoenmakers JG,Konings RN

    更新日期:1986-06-25 00:00:00

  • Helicobacter pylori oriC--the first bipartite origin of chromosome replication in Gram-negative bacteria.

    abstract::Binding of the DnaA protein to oriC leads to DNA melting within the DNA unwinding element (DUE) and initiates replication of the bacterial chromosome. Helicobacter pylori oriC was previously identified as a region localized upstream of dnaA and containing a cluster of DnaA boxes bound by DnaA protein with a high affin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks742

    authors: Donczew R,Weigel C,Lurz R,Zakrzewska-Czerwinska J,Zawilak-Pawlik A

    更新日期:2012-10-01 00:00:00

  • Fluoride-cleavable biotinylation phosphoramidite for 5'-end-labeling and affinity purification of synthetic oligonucleotides.

    abstract::A fluoride-cleavable phosphoramidite for biotinylation was designed, synthesized and coupled efficiently to the 5'-end of DNA on an automatic synthesizer. The diisopropylsilyl acetal functionality was used to link the biotin moiety through a tertiary hydroxide group to the 5'-end of DNA. This linkage proved to be comp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg130

    authors: Fang S,Bergstrom DE

    更新日期:2003-01-15 00:00:00

  • High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.

    abstract::The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt1070

    authors: Amir A,Zeisel A,Zuk O,Elgart M,Stern S,Shamir O,Turnbaugh PJ,Soen Y,Shental N

    更新日期:2013-12-01 00:00:00

  • The Comparative Toxicogenomics Database: update 2019.

    abstract::The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a premier public resource for literature-based, manually curated associations between chemicals, gene products, phenotypes, diseases, and environmental exposures. In this biennial update, we present our new chemical-phenotype module that codes chemi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky868

    authors: Davis AP,Grondin CJ,Johnson RJ,Sciaky D,McMorran R,Wiegers J,Wiegers TC,Mattingly CJ

    更新日期:2019-01-08 00:00:00

  • EMdeCODE: a novel algorithm capable of reading words of epigenetic code to predict enhancers and retroviral integration sites and to identify H3R2me1 as a distinctive mark of coding versus non-coding genes.

    abstract::Existence of some extra-genetic (epigenetic) codes has been postulated since the discovery of the primary genetic code. Evident effects of histone post-translational modifications or DNA methylation over the efficiency and the regulation of DNA processes are supporting this postulation. EMdeCODE is an original algorit...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1214

    authors: Santoni FA

    更新日期:2013-02-01 00:00:00

  • Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases.

    abstract::The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers the entire element with the ability to invade genomic targets. The persistence of a homing endonuclease lineage depends in part on conservation of its DNA target site. One such rDNA sequence has been invaded both in archaea a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn846

    authors: Nomura N,Nomura Y,Sussman D,Klein D,Stoddard BL

    更新日期:2008-12-01 00:00:00

  • Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer.

    abstract::Clustered regularly interspaced short palindromic repeats (CRISPR), in combination with CRISPR associated (cas) genes, constitute CRISPR-Cas bacterial adaptive immune systems. To generate immunity, these systems acquire short sequences of nucleic acids from foreign invaders and incorporate these into their CRISPR arra...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku527

    authors: Richter C,Dy RL,McKenzie RE,Watson BN,Taylor C,Chang JT,McNeil MB,Staals RH,Fineran PC

    更新日期:2014-07-01 00:00:00

  • A novel nuclear inhibitor I-92 regulates DNA binding activity of octamer binding protein p92 during the cell cycle.

    abstract::Nuclear DNA binding protein p92 is a sequence specific octamer binding protein with identical molecular weight as the ubiquitous octamer binding protein Oct-1. It binds to octamer related sequences from the enhancer of human papillomavirus type 18. The activity and intracellular distribution of p92 is regulated by ext...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.20.5725

    authors: Weitz J,Kopun M,Stoehr M,Napierski I,Royer HD

    更新日期:1991-10-25 00:00:00

  • The human apolipoprotein A-II gene: complete nucleic acid sequence and genomic organization.

    abstract::The gene for human apolipoprotein (apo) A-II has been isolated from a human genomic DNA library. The cloned fragment was approximately 14 kilobase-pair (kb) long, and extended about 9.0 kb upstream as well as 3.5 kb downstream from the apoA-II gene, which was contained within a 3.1 kb HindIII fragment of human DNA. Th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.12.4597

    authors: Lackner KJ,Law SW,Brewer HB Jr

    更新日期:1985-06-25 00:00:00

  • ECO, the Evidence & Conclusion Ontology: community standard for evidence information.

    abstract::The Evidence and Conclusion Ontology (ECO) contains terms (classes) that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this inform...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky1036

    authors: Giglio M,Tauber R,Nadendla S,Munro J,Olley D,Ball S,Mitraka E,Schriml LM,Gaudet P,Hobbs ET,Erill I,Siegele DA,Hu JC,Mungall C,Chibucos MC

    更新日期:2019-01-08 00:00:00

  • Stimuli of differentiation regulate RNA elongation in the transcription units for the major stage-specific antigens of Trypanosoma brucei.

    abstract::In Trypanosoma brucei, the mutually exclusive expression of the major surface antigens, the variant surface glycoprotein (VSG) of the bloodstream form and procyclin of the procyclic form, is due to a stage-specific accumulation of the respective mRNAs. Through the targeting of a reporter construct in the procyclin pro...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.11.1862

    authors: Vanhamme L,Berberof M,Le Ray D,Pays E

    更新日期:1995-06-11 00:00:00

  • 3CAPS - a structural AP-site analogue as a tool to investigate DNA base excision repair.

    abstract::Abasic sites (AP-sites) are frequent DNA lesions, arising by spontaneous base hydrolysis or as intermediates of base excision repair (BER). The hemiacetal at the anomeric centre renders them chemically reactive, which presents a challenge to biochemical and structural investigation. Chemically more stable AP-site anal...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1520

    authors: Schuermann D,Scheidegger SP,Weber AR,Bjørås M,Leumann CJ,Schär P

    更新日期:2016-03-18 00:00:00

  • Cloning and expression of the hypoxanthine-guanine phosphoribosyltransferase gene from Trypanosoma brucei.

    abstract::The hypoxanthine-guanine phosphoribosyltransferase (HGPRT) enzyme of Trypanosoma brucei and related parasites provides a rational target for the treatment of African sleeping sickness and several other parasitic diseases. To characterize the T. brucei HGPRT enzyme in detail, the T. brucei hgprt was isolated within a 4...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.23.5431

    authors: Allen TE,Ullman B

    更新日期:1993-11-25 00:00:00

  • PipeAlign: A new toolkit for protein family analysis.

    abstract::PipeAlign is a protein family analysis tool integrating a five step process ranging from the search for sequence homologues in protein and 3D structure databases to the definition of the hierarchical relationships within and between subfamilies. The complete, automatic pipeline takes a single sequence or a set of sequ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg518

    authors: Plewniak F,Bianchetti L,Brelivet Y,Carles A,Chalmel F,Lecompte O,Mochel T,Moulinier L,Muller A,Muller J,Prigent V,Ripp R,Thierry JC,Thompson JD,Wicker N,Poch O

    更新日期:2003-07-01 00:00:00

  • Lack of a requirement for strict rotational alignment among transcription factor binding sites in yeast.

    abstract::The MF alpha 1 gene of Saccharomyces cerevisiae is an alpha specific gene whose expression is regulated by two upstream activation sites (UASMF alpha 1S), which are the binding sites for activator proteins, MAT alpha 1 and MCM1. UASMF alpha 1 elements act in a synergistic fashion; lack of either element causes reduced...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.11.3099

    authors: Inokuchi K,Nakayama A

    更新日期:1991-06-11 00:00:00

  • An RNA-based transcription activator derived from an inhibitory aptamer.

    abstract::According to the recruitment model of transcriptional activation, an activator helps initiate transcription by bringing the RNA polymerase to a specific location on the DNA through interaction with components of the transcriptional machinery. However, it is difficult to isolate and define the activities of specific ac...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp1227

    authors: Wang S,Shepard JR,Shi H

    更新日期:2010-04-01 00:00:00

  • The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode.

    abstract::Transcription termination defines accurate transcript 3'-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination fa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa702

    authors: Yue L,Li J,Zhang B,Qi L,Li Z,Zhao F,Li L,Zheng X,Dong X

    更新日期:2020-09-25 00:00:00

  • Femtosecond near-infrared laser microirradiation reveals a crucial role for PARP signaling on factor assemblies at DNA damage sites.

    abstract::Laser microirradiation is a powerful tool for real-time single-cell analysis of the DNA damage response (DDR). It is often found, however, that factor recruitment or modification profiles vary depending on the laser system employed. This is likely due to an incomplete understanding of how laser conditions/dosages affe...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv976

    authors: Saquilabon Cruz GM,Kong X,Silva BA,Khatibzadeh N,Thai R,Berns MW,Yokomori K

    更新日期:2016-02-18 00:00:00

  • Improving the predictive value of the competence transcription factor (ComK) binding site in Bacillus subtilis using a genomic approach.

    abstract::Generally, the presence of a consensus sequence in the promoter of a gene is taken as indication for regulation by the transcription factor that binds to this sequence. In light of the recent developments in genome research, we were interested to what extent this supposition is valid. We examined the relationship betw...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkf698

    authors: Hamoen LW,Smits WK,de Jong A,Holsappel S,Kuipers OP

    更新日期:2002-12-15 00:00:00

  • Engineering an Acinetobacter regulon for biosensing and high-throughput enzyme screening in E. coli via flow cytometry.

    abstract::We created a single cell sorting system to screen for enzyme activity in Escherichia coli producing 3,4 dihydroxy benzoate (34DHB). To do so, we engineered a transcription factor regulon controlling the expression of green fluorescent protein (GFP) for induction by 34DHB. An autoregulated transcription factor, pcaU, w...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku444

    authors: Jha RK,Kern TL,Fox DT,M Strauss CE

    更新日期:2014-07-01 00:00:00

  • Telomere length regulation and transcriptional silencing in KU80-deficient Trypanosoma brucei.

    abstract::KU is a heterodimer, consisting of approximately 70 and approximately 80 kDa subunits (KU70 and KU80, respectively), which is involved in a variety of nuclear functions. We generated tbKU80-deficient trypanosomes to explore the potential role of the tbKU complex in telomere maintenance and transcriptional regulation o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh991

    authors: Janzen CJ,Lander F,Dreesen O,Cross GA

    更新日期:2004-12-15 00:00:00

  • Expression of the arylsulfatase gene from the beta 2-tubulin promoter in Chlamydomonas reinhardtii.

    abstract::Arylsulfatase, produced by Chlamydomonas reinhardtii during sulfur-limited growth, is secreted into the periplasmic space and is readily assayed using a chromogenic substrate. To assess the usefulness of the gene encoding arylsulfatase (ars) as a reporter gene in C. reinhardtii, we have fused the promoter region of th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.12.2959

    authors: Davies JP,Weeks DP,Grossman AR

    更新日期:1992-06-25 00:00:00

  • OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.

    abstract::A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt216

    authors: Wu J,Anczuków O,Krainer AR,Zhang MQ,Zhang C

    更新日期:2013-05-01 00:00:00

  • alpha-DNA. I. Synthesis, characterization by high field 1H-NMR, and base-pairing properties of the unnatural hexadeoxyribonucleotide alpha-[d(CpCpTpTpCpC)] with its complement beta-[d(GpGpApApGpG)].

    abstract::The novel deoxyribonucleotide alpha-[d(CpCpTpTpCpC)] and its complement beta-[d(GpGpApApGpG)] were synthesized by the phosphotriester method. 1H-NMR-NOE examination of the alpha-hexamer revealed that the cytosine and thymine bases appear to adopt anti conformations in this strand. In addition the deoxyribose of the th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.12.5019

    authors: Morvan F,Rayner B,Imbach JL,Chang DK,Lown JW

    更新日期:1986-06-25 00:00:00

  • Relative stabilities of DNA three-way, four-way and five-way junctions (multi-helix junction loops): unpaired nucleotides can be stabilizing or destabilizing.

    abstract::Competition binding and UV melting studies of a DNA model system consisting of three, four or five mutually complementary oligonucleotides demonstrate that unpaired bases at the branch point stabilize three- and five-way junction loops but destabilize four-way junctions. The inclusion of unpaired nucleotides permits t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.12.2212

    authors: Kadrmas JL,Ravin AJ,Leontis NB

    更新日期:1995-06-25 00:00:00

  • Does the 'non-coding' strand code?

    abstract::The hypothesis that DNA strands complementary to the coding strand contain in phase coding sequences has been investigated. Statistical analysis of the 50 genes of bacteriophage T7 shows no significant correlation between patterns of codon usage on the coding and non-coding strands. In Bacillus and yeast genes the cor...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.4.1389

    authors: Sharp PM

    更新日期:1985-02-25 00:00:00

  • High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

    abstract::In silico prediction of transcription factor binding sites (TFBSs) is central to the task of gene regulatory network elucidation. Genomic DNA sequence information provides a basis for these predictions, due to the sequence specificity of TF-binding events. However, DNA sequence alone is an impoverished source of infor...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn866

    authors: Whitington T,Perkins AC,Bailey TL

    更新日期:2009-01-01 00:00:00

  • The genomic organisation and nucleotide sequence of the HLA-SB(DP) alpha gene.

    abstract::We have isolated a unique fragment of the HLA-DR alpha gene and probed human genomic DNA at low stringency to search for homologous sequences. A minimum of six non-polymorphic cross-hybridizing high molecular weight fragments were found in all DNAs examined. In order to obtain molecular clones of these cross-hybridizi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.20.7515

    authors: Lawrance SK,Das HK,Pan J,Weissman SM

    更新日期:1985-10-25 00:00:00

  • A consensus sequence for cleavage by vertebrate DNA topoisomerase II.

    abstract::Topoisomerase II, purified from chicken erythrocytes, was reacted with a large number of different DNA fragments and cleavages were catalogued in the presence and absence of drugs that stabilize the cleavage intermediate. Cleavages were sequenced to derive a consensus for topoisomerase II that predicts catalytic sites...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.12.5533

    authors: Spitzner JR,Muller MT

    更新日期:1988-06-24 00:00:00