Different types of interaction between PCNA and PIP boxes contribute to distinct cellular functions of Y-family DNA polymerases.

Abstract:

:Translesion DNA synthesis (TLS) by the Y-family DNA polymerases Polη, Polι and Polκ, mediated via interaction with proliferating cell nuclear antigen (PCNA), is a crucial pathway that protects human cells against DNA damage. We report that Polη has three PCNA-interacting protein (PIP) boxes (PIP1, 2, 3) that contribute differentially to two distinct functions, stimulation of DNA synthesis and promotion of PCNA ubiquitination. The latter function is strongly associated with formation of nuclear Polη foci, which co-localize with PCNA. We also show that Polκ has two functionally distinct PIP boxes, like Polη, whereas Polι has a single PIP box involved in stimulation of DNA synthesis. All three polymerases were additionally stimulated by mono-ubiquitinated PCNA in vitro. The three PIP boxes and a ubiquitin-binding zinc-finger of Polη exert redundant and additive effects in vivo via distinct molecular mechanisms. These findings provide an integrated picture of the orchestration of TLS polymerases.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Masuda Y,Kanao R,Kaji K,Ohmori H,Hanaoka F,Masutani C

doi

10.1093/nar/gkv712

subject

Has Abstract

pub_date

2015-09-18 00:00:00

pages

7898-910

issue

16

eissn

0305-1048

issn

1362-4962

pii

gkv712

journal_volume

43

pub_type

杂志文章
  • Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter.

    abstract::Increasing evidence indicates that active DNA demethylation is involved in several processes in mammals, resulting in developmental stage-specificity and cell lineage-specificity. The recently discovered Ten-Eleven Translocation (TET) dioxygenases are accepted to be involved in DNA demethylation by initiating 5-mC oxi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt1019

    authors: Chen H,Kazemier HG,de Groote ML,Ruiters MH,Xu GL,Rots MG

    更新日期:2014-02-01 00:00:00

  • Master regulatory GATA transcription factors: mechanistic principles and emerging links to hematologic malignancies.

    abstract::Numerous examples exist of how disrupting the actions of physiological regulators of blood cell development yields hematologic malignancies. The master regulator of hematopoietic stem/progenitor cells GATA-2 was cloned almost 20 years ago, and elegant genetic analyses demonstrated its essential function to promote hem...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审

    doi:10.1093/nar/gks281

    authors: Bresnick EH,Katsumura KR,Lee HY,Johnson KD,Perkins AS

    更新日期:2012-07-01 00:00:00

  • Distribution of 5-methylcytosine in the DNA of somatic and germline cells from bovine tissues.

    abstract::Genomic DNA of calf thymus contains 1.5 times as much 5-methylcytosine as similar sperm DNA, but the major EcoRI repeat fragment from satellite I of thymus contains ten times as much 5-methylcytosine as the corresponding fragment from sperm DNA. Restriction enzyme analyses of the total DNA and the satellite I fragment...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/9.18.4537

    authors: Sturm KS,Taylor JH

    更新日期:1981-09-25 00:00:00

  • A database of macromolecular motions.

    abstract::We describe a database of macromolecular motions meant to be of general use to the structural community. The database, which is accessible on the World Wide Web with an entry point at http://bioinfo.mbb.yale.edu/MolMovDB , attempts to systematize all instances of protein and nucleic acid movement for which there is at...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.18.4280

    authors: Gerstein M,Krebs W

    更新日期:1998-09-15 00:00:00

  • The structural integrity exerted by N-terminal pyroglutamate is crucial for the cytotoxicity of frog ribonuclease from Rana pipiens.

    abstract::Onconase, a cytotoxic ribonuclease from Rana pipiens, possesses pyroglutamate (Pyr) at the N-terminus and has a substrate preference for uridine-guanine (UG). To identify residues responsible for onconase's cytotoxicity, we cloned the rpr gene from genomic DNA and expressed it in Escherichia coli BL21(DE3). The recomb...

    journal_title:Nucleic acids research

    pub_type: 评论,杂志文章

    doi:10.1093/nar/gkg746

    authors: Liao YD,Wang SC,Leu YJ,Wang CF,Chang ST,Hong YT,Pan YR,Chen C

    更新日期:2003-09-15 00:00:00

  • CAMP: Collection of sequences and structures of antimicrobial peptides.

    abstract::Antimicrobial peptides (AMPs) are gaining importance as anti-infective agents. Here we describe the updated Collection of Antimicrobial Peptide (CAMP) database, available online at http://www.camp.bicnirrh.res.in/. The 3D structures of peptides are known to influence antimicrobial activity. Although there exists datab...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt1157

    authors: Waghu FH,Gopi L,Barai RS,Ramteke P,Nizami B,Idicula-Thomas S

    更新日期:2014-01-01 00:00:00

  • Immunofluorescence assay and flow-cytometry selection of bead-bound aptamers.

    abstract::An immunofluorescence assay was developed to identify proteins specifically binding to oligonucleoside phosphorodithioate (ODN) aptamers from a bead-bound ODN library. Accordingly, NF-kappaB p50 protein was incubated with either bead-bound NF-kappaB consensus sequence or a bead-bound ODN combinatorial library and adso...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gng054

    authors: Yang X,Li X,Prow TW,Reece LM,Bassett SE,Luxon BA,Herzog NK,Aronson J,Shope RE,Leary JF,Gorenstein DG

    更新日期:2003-05-15 00:00:00

  • Recent enhancements to the Blocks Database servers.

    abstract::The Blocks Database contains multiple alignments of conserved regions in protein families which can be searched by e-mail (blocks@blocks.fhcrc.org) and World Wide Web (http://blocks.fhcrc.org/ ) servers to classify protein and nucleotide sequences. Recent enhancements to the servers include: (i) improved calculation o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.1.222

    authors: Henikoff JG,Pietrokovski S,Henikoff S

    更新日期:1997-01-01 00:00:00

  • FAF-Drugs: free ADME/tox filtering of compound collections.

    abstract::In silico screening based on the structures of the ligands or of the receptors has become an essential tool to facilitate the drug discovery process but compound collections are needed to carry out such in silico experiments. It has been recognized that absorption, distribution, metabolism, excretion and toxicity (ADM...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl065

    authors: Miteva MA,Violas S,Montes M,Gomez D,Tuffery P,Villoutreix BO

    更新日期:2006-07-01 00:00:00

  • Pseudomonas aeruginosa MutL promotes large chromosomal deletions through non-homologous end joining to prevent bacteriophage predation.

    abstract::Pseudomonas aeruginosa is an opportunistic pathogen with a relatively large genome, and has been shown to routinely lose genomic fragments during environmental selection. However, the underlying molecular mechanisms that promote chromosomal deletion are still poorly understood. In a recent study, we showed that by del...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky160

    authors: Shen M,Zhang H,Shen W,Zou Z,Lu S,Li G,He X,Agnello M,Shi W,Hu F,Le S

    更新日期:2018-05-18 00:00:00

  • HSCARG, a novel regulator of H2A ubiquitination by downregulating PRC1 ubiquitin E3 ligase activity, is essential for cell proliferation.

    abstract::Histone H2A ubiquitination plays critical roles in transcriptional repression and deoxyribonucleic acid (DNA) damage response. More attention has been focused on ubiquitin E3 ligases of H2A, however, less is known about the negative regulators of H2A ubiquitination. Here we identified HSCARG as a new negative regulato...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku230

    authors: Hu B,Li S,Zhang X,Zheng X

    更新日期:2014-05-01 00:00:00

  • NEpiC: a network-assisted algorithm for epigenetic studies using mean and variance combined signals.

    abstract::DNA methylation plays an important role in many biological processes. Existing epigenome-wide association studies (EWAS) have successfully identified aberrantly methylated genes in many diseases and disorders with most studies focusing on analysing methylation sites one at a time. Incorporating prior biological inform...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw546

    authors: Ruan P,Shen J,Santella RM,Zhou S,Wang S

    更新日期:2016-09-19 00:00:00

  • A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals.

    abstract::Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa550

    authors: Turakhia Y,Chen HI,Marcovitz A,Bejerano G

    更新日期:2020-09-18 00:00:00

  • Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins.

    abstract::eIF4E-binding proteins (4E-BPs) regulate translation of mRNAs in eukaryotes. However the extent to which specific mRNA targets are regulated by 4E-BPs remains unknown. We performed translational profiling by microarray analysis of polysome and monosome associated mRNAs in wild-type and mutant cells to identify mRNAs i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq686

    authors: Cridge AG,Castelli LM,Smirnova JB,Selley JN,Rowe W,Hubbard SJ,McCarthy JE,Ashe MP,Grant CM,Pavitt GD

    更新日期:2010-12-01 00:00:00

  • Uranyl photofootprinting of triple helical DNA.

    abstract::Two triple helix structures (15-mers containing only T.A-T triplets or containing mixed T.A-T and C.G-C triplets) have been studied by uranyl mediated DNA photocleavage to probe the accessibility of the phosphates of the DNA backbone. Whereas the phosphates of the pyrimidine strand are at least as accessible as in dou...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.11.2735

    authors: Nielsen PE

    更新日期:1992-06-11 00:00:00

  • Update of the Diatom EST Database: a new tool for digital transcriptomics.

    abstract::The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130,000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77,000 Thalassiosira pseudonana ESTs from seven libraries...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn905

    authors: Maheswari U,Mock T,Armbrust EV,Bowler C

    更新日期:2009-01-01 00:00:00

  • RaftProt: mammalian lipid raft proteome database.

    abstract::RaftProt (http://lipid-raft-database.di.uq.edu.au/) is a database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids thought to act as dynamic signalling and sorting platforms....

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1131

    authors: Shah A,Chen D,Boda AR,Foster LJ,Davis MJ,Hill MM

    更新日期:2015-01-01 00:00:00

  • ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants.

    abstract::Genome-wide mapping in the identification of novel candidate genes has always been the standard method in genetics and genomics to correlate a clinically interesting phenotypic trait with a genotype. However, the performance of a mapping experiment using classical microsatellite approaches can be very time consuming. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki430

    authors: Klaften M,Hrabé de Angelis M

    更新日期:2005-07-01 00:00:00

  • MIPModDB: a central resource for the superfamily of major intrinsic proteins.

    abstract::The channel proteins belonging to the major intrinsic proteins (MIP) superfamily are diverse and are found in all forms of life. Water-transporting aquaporin and glycerol-specific aquaglyceroporin are the prototype members of the MIP superfamily. MIPs have also been shown to transport other neutral molecules and gases...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr914

    authors: Gupta AB,Verma RK,Agarwal V,Vajpai M,Bansal V,Sankararamakrishnan R

    更新日期:2012-01-01 00:00:00

  • Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

    abstract::Aberrant DNA methylation at CpG dinucleotides can result in epigenetic silencing of tumour suppressor genes and represents one of the earliest events in tumourigenesis. To date, however, high-throughput tools that are capable of surveying the methylation status of multiple gene promoters have been restricted to a limi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gni072

    authors: Mund C,Beier V,Bewerunge P,Dahms M,Lyko F,Hoheisel JD

    更新日期:2005-04-28 00:00:00

  • Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues.

    abstract::Most human genes generate multiple transcript isoforms. The differential expression of these isoforms can help specify cell types. Diverse transcript isoforms arise from the use of alternative transcription start sites, polyadenylation sites and splice sites; however, the relative contribution of these processes to is...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx1165

    authors: Reyes A,Huber W

    更新日期:2018-01-25 00:00:00

  • Large polypeptides of 10S DNA polymerase alpha from calf thymus: rapid isolation using monoclonal antibody and tryptic peptide mapping analysis.

    abstract::The polypeptides recognized by a monoclonal antibody against calf thymus DNA polymerase alpha (secreted from a hybridoma CL22 -2- 42B , Nucleic Acids Res. (1982) 10, 4703-4713) were identified by the immunoblot method as the large polypeptides of the partially-purified 10S DNA polymerase alpha fraction. Using an immun...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.11.4455

    authors: Masaki S,Tanabe K,Yoshida S

    更新日期:1984-06-11 00:00:00

  • Random DNA fragmentation with endonuclease V: application to DNA shuffling.

    abstract::The enzyme endonuclease V nicks uracil-containing DNA at the second or third phosphodiester bond 3' to uracil sites. I applied the enzyme to random fragmentation of DNA to revise the complex DNA shuffling protocol. The merit of using endonuclease V is that cleavage occurs at random sites and the length of the fragment...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gnf139

    authors: Miyazaki K

    更新日期:2002-12-15 00:00:00

  • The CATH Database provides insights into protein structure/function relationships.

    abstract::We report the latest release (version 1.4) of the CATH protein domains database (http://www.biochem.ucl.ac.uk/bsm/cath). This is a hierarchical classification of 13 359 protein domain structures into evolutionary families and structural groupings. We currently identify 827 homologous families in which the proteins hav...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.1.275

    authors: Orengo CA,Pearl FM,Bray JE,Todd AE,Martin AC,Lo Conte L,Thornton JM

    更新日期:1999-01-01 00:00:00

  • Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase.

    abstract::Nitrated polycyclic aromatic hydrocarbons are common environmental pollutants, of which many are mutagenic and carcinogenic. 1-Nitropyrene is the most abundant nitrated polycyclic aromatic hydrocarbon, which causes DNA damage and is carcinogenic in experimental animals. Error-prone translesion synthesis of 1-nitropyre...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1296

    authors: Kirouac KN,Basu AK,Ling H

    更新日期:2013-02-01 00:00:00

  • DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites.

    abstract::The Dnd (DNA degradation) phenotype, reflecting a novel DNA modification by sulfur in Streptomyces lividans 1326, was strongly aggravated when one (dndB) of the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear change...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm176

    authors: Liang J,Wang Z,He X,Li J,Zhou X,Deng Z

    更新日期:2007-01-01 00:00:00

  • Plasmodium falciparum heterochromatin protein 1 binds to tri-methylated histone 3 lysine 9 and is linked to mutually exclusive expression of var genes.

    abstract::Increasing experimental evidence shows a prominent role of histone modifications in the coordinated control of gene expression in the human malaria parasite Plasmodium falciparum. The search for the histone-mark-reading machinery that translates histone modifications into biological processes, such as formation of het...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp115

    authors: Pérez-Toledo K,Rojas-Meza AP,Mancio-Silva L,Hernández-Cuevas NA,Delgadillo DM,Vargas M,Martínez-Calvillo S,Scherf A,Hernandez-Rivas R

    更新日期:2009-05-01 00:00:00

  • Spectral clustering of protein sequences.

    abstract::An important problem in genomics is automatically clustering homologous proteins when only sequence information is available. Most methods for clustering proteins are local, and are based on simply thresholding a measure related to sequence distance. We first show how locality limits the performance of such methods by...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkj515

    authors: Paccanaro A,Casbon JA,Saqi MA

    更新日期:2006-03-17 00:00:00

  • Kinetic analysis of N-alkylaryl carboxamide hexitol nucleotides as substrates for evolved polymerases.

    abstract::Six 1',5'-anhydrohexitol uridine triphosphates were synthesized with aromatic substitutions appended via a carboxamide linker to the 5-position of their bases. An improved method for obtaining such 5-substituted hexitol nucleosides and nucleotides is described. The incorporation profile of the nucleotide analogues int...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz008

    authors: Renders M,Dumbre S,Abramov M,Kestemont D,Margamuljana L,Largy E,Cozens C,Vandenameele J,Pinheiro VB,Toye D,Frère JM,Herdewijn P

    更新日期:2019-03-18 00:00:00

  • Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease.

    abstract::The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw644

    authors: Probst M,Aeschimann W,Chau TT,Langenegger SM,Stocker A,Häner R

    更新日期:2016-09-06 00:00:00