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  1 / 3614 MEDLINE  
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[PMID]:29320758
[Au] Autor:Voutsadakis IA
[Ad] Endereço:Division of Medical Oncology, Department of Internal Medicine, Sault Area Hospital, Sault Ste Marie, Ontario, Canada; Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, Ontario, Canada. Electronic address: ivoutsadakis@nosm.ca.
[Ti] Título:Polymerase epsilon mutations and concomitant ß2-microglobulin mutations in cancer.
[So] Source:Gene;647:31-38, 2018 Mar 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Mutations in the exonuclease domain of polymerase epsilon (POLE), an enzyme of DNA synthesis, are involved in a newly described syndrome of colorectal polyposis and cancer, and have been associated with a high mutation burden with or without microsatellite instability (MSI) phenotype. The exonuclease domain of POLE executes a proofreading function that decreases the mutation rate during DNA replication by an estimated of one to two orders. The high mutation burden resulting from its loss of function could create a load of neo-antigens that would put the neoplastic cells in severe disadvantage of an immune attack if properly presented to the immune system. This paper investigates the mutagenic effect of different POLE mutations in various cancers, in published genomic studies and the effect that these POLE mutations have in selecting for mutations of the ß2 microglobulin (B2M) gene involved in antigen presentation.
[Mh] Termos MeSH primário: DNA Polimerase II/genética
Globulinas/genética
Mutação/genética
Neoplasias/genética
Proteínas de Ligação a Poli-ADP-Ribose/genética
[Mh] Termos MeSH secundário: Replicação do DNA/genética
Exodesoxirribonucleases/genética
Seres Humanos
Instabilidade de Microssatélites
Mutagênese/genética
Taxa de Mutação
Fenótipo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Globulins); 0 (Poly-ADP-Ribose Binding Proteins); EC 2.7.7.- (DNA Polymerase II); EC 2.7.7.7 (POLE protein, human); EC 3.1.- (Exodeoxyribonucleases)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180209
[Lr] Data última revisão:
180209
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180111
[St] Status:MEDLINE


  2 / 3614 MEDLINE  
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[PMID]:29321179
[Au] Autor:Reginato G; Cannavo E; Cejka P
[Ad] Endereço:Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland.
[Ti] Título:Physiological protein blocks direct the Mre11-Rad50-Xrs2 and Sae2 nuclease complex to initiate DNA end resection.
[So] Source:Genes Dev;31(23-24):2325-2330, 2017 12 01.
[Is] ISSN:1549-5477
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:DNA double-strand break repair by homologous recombination is initiated by DNA end resection, which is commenced by the Mre11-Rad50-Xrs2 complex and Sae2 in yeast. Here we report that the nonhomologous end joining factor Ku limits the exonuclease activity of Mre11 and promotes its endonuclease to cleave 5'-terminated DNA strands at break sites. Following initial endonucleolytic cleavage past the obstacle, Exo1 specifically extends the resection track, leading to the generation of long 3' overhangs that are required for homologous recombination. These experiments provide mechanistic insights into how short-range and long-range DNA end resection enzymes overcome obstacles near broken DNA ends to initiate recombination.
[Mh] Termos MeSH primário: Reparo do DNA por Junção de Extremidades
Endonucleases/metabolismo
Exonucleases/metabolismo
Proteínas de Saccharomyces cerevisiae/metabolismo
Saccharomyces cerevisiae/fisiologia
[Mh] Termos MeSH secundário: Animais
Clivagem do DNA
Proteínas de Ligação a DNA/metabolismo
Endodesoxirribonucleases/metabolismo
Ativação Enzimática/genética
Exodesoxirribonucleases/metabolismo
Complexos Multiproteicos/metabolismo
Saccharomyces cerevisiae/enzimologia
Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/genética
Células Sf9
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA-Binding Proteins); 0 (Multiprotein Complexes); 0 (RAD50 protein, S cerevisiae); 0 (SAE2 protein, S cerevisiae); 0 (Saccharomyces cerevisiae Proteins); 0 (XRS2 protein, S cerevisiae); 0 (high affinity DNA-binding factor, S cerevisiae); EC 3.1.- (Endodeoxyribonucleases); EC 3.1.- (Endonucleases); EC 3.1.- (Exodeoxyribonucleases); EC 3.1.- (Exonucleases); EC 3.1.- (MRE11 protein, S cerevisiae); EC 3.1.11.1 (exodeoxyribonuclease I)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180208
[Lr] Data última revisão:
180208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180112
[St] Status:MEDLINE
[do] DOI:10.1101/gad.308254.117


  3 / 3614 MEDLINE  
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[PMID]:29321177
[Au] Autor:Wang W; Daley JM; Kwon Y; Krasner DS; Sung P
[Ad] Endereço:Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
[Ti] Título:Plasticity of the Mre11-Rad50-Xrs2-Sae2 nuclease ensemble in the processing of DNA-bound obstacles.
[So] Source:Genes Dev;31(23-24):2331-2336, 2017 12 01.
[Is] ISSN:1549-5477
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The budding yeast Mre11-Rad50-Xrs2 (MRX) complex and Sae2 function together in DNA end resection during homologous recombination. Here we show that the Ku complex shields DNA ends from exonucleolytic digestion but facilitates endonucleolytic scission by MRX with a dependence on ATP and Sae2. The incision site is enlarged into a DNA gap via the exonuclease activity of MRX, which is stimulated by Sae2 without ATP being present. RPA renders a partially resected or palindromic DNA structure susceptible to MRX-Sae2, and internal protein blocks also trigger DNA cleavage. We present models for how MRX-Sae2 creates entry sites for the long-range resection machinery.
[Mh] Termos MeSH primário: Reparo do DNA por Junção de Extremidades
Reparo do DNA/fisiologia
Endonucleases/metabolismo
Exonucleases/metabolismo
Complexos Multienzimáticos/metabolismo
Proteínas de Saccharomyces cerevisiae/metabolismo
Saccharomyces cerevisiae/fisiologia
[Mh] Termos MeSH secundário: Clivagem do DNA
Proteínas de Ligação a DNA/metabolismo
Endodesoxirribonucleases/metabolismo
Ativação Enzimática/genética
Exodesoxirribonucleases/metabolismo
Complexos Multiproteicos/metabolismo
Saccharomyces cerevisiae/enzimologia
Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (DNA-Binding Proteins); 0 (Multienzyme Complexes); 0 (Multiprotein Complexes); 0 (RAD50 protein, S cerevisiae); 0 (SAE2 protein, S cerevisiae); 0 (Saccharomyces cerevisiae Proteins); 0 (XRS2 protein, S cerevisiae); 0 (high affinity DNA-binding factor, S cerevisiae); EC 3.1.- (Endodeoxyribonucleases); EC 3.1.- (Endonucleases); EC 3.1.- (Exodeoxyribonucleases); EC 3.1.- (Exonucleases); EC 3.1.- (MRE11 protein, S cerevisiae); EC 3.1.11.1 (exodeoxyribonuclease I)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180208
[Lr] Data última revisão:
180208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180112
[St] Status:MEDLINE
[do] DOI:10.1101/gad.307900.117


  4 / 3614 MEDLINE  
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[PMID]:29352017
[Au] Autor:Gnügge R; Symington LS
[Ad] Endereço:Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York 10032, USA.
[Ti] Título:Keeping it real: MRX-Sae2 clipping of natural substrates.
[So] Source:Genes Dev;31(23-24):2311-2312, 2017 12 01.
[Is] ISSN:1549-5477
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The yeast Mre11-Rad50-Xrs2 (MRX) complex and Sae2 function together to initiate DNA end resection, an essential early step in homology-dependent repair of DNA double-strand breaks (DSBs). In this issue of , Wang and colleagues (pp. 2331-2336) and Reginato and colleagues (pp. 2325-2330) report that a variety of physiological protein blocks, including Ku, RPA, and nucleosomes, stimulate MRX-Sae2 endonuclease cleavage in vitro. These studies have important implications for how cells deal with a range of barriers to end resection and highlight the crucial role of Sae2 in activating MRX cleavage at the correct cell cycle stage.
[Mh] Termos MeSH primário: Endodesoxirribonucleases/genética
Proteínas de Saccharomyces cerevisiae/genética
[Mh] Termos MeSH secundário: Quebras de DNA de Cadeia Dupla
Reparo do DNA
Proteínas de Ligação a DNA/genética
Exodesoxirribonucleases/genética
Saccharomyces cerevisiae/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; REVIEW; COMMENT
[Nm] Nome de substância:
0 (DNA-Binding Proteins); 0 (Saccharomyces cerevisiae Proteins); EC 3.1.- (Endodeoxyribonucleases); EC 3.1.- (Exodeoxyribonucleases)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180207
[Lr] Data última revisão:
180207
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180121
[St] Status:MEDLINE
[do] DOI:10.1101/gad.310771.117


  5 / 3614 MEDLINE  
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[PMID]:28459543
[Au] Autor:Jensen M; Davis R
[Ad] Endereço:Stanford Genome Technology Center, Department of Biochemistry, Stanford University , Palo Alto, California 94304, United States.
[Ti] Título:RecJ 5' Exonuclease Digestion of Oligonucleotide Failure Strands: A "Green" Method of Trityl-On Purification.
[So] Source:Biochemistry;56(18):2417-2424, 2017 05 09.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Methods of error filtration and correction post-gene assembly are a major bottleneck in the synthetic biology pipeline. Current oligonucleotide purification strategies, including polyacrylamide gel electrophoresis and high-performance liquid chromatography, are often expensive and labor-intensive, give low mass recovery, and contain hazardous chemicals. To circumvent these limitations, we explored an enzymatic means of oligonucleotide purification using RecJ, which is the only known exonuclease to digest single-stranded DNA (ssDNA) in the 5' to 3' direction. As a potential application to remove failure strands generated in oligonucleotide synthesis, we found RecJ does not recognize the 5' dimethoxytrityl blocking group and could therefore be used to specifically target and digest unblocked failure strands. In combination with ssDNA binding protein (SSBP), which acts to recruit RecJ via C-terminal recognition, secondary structure formation is precluded, allowing for enhanced RecJ processivity. Using this method to purify crude trityl-on oligonucleotides, we also found on average 30 units of RecJ with 0.5 µg of SSBP digests 53 pmol of 5' hydroxylated ssDNA (60 min at 37 °C). With these parameters, the average purity is increased by 8%. As such, this novel method can be adapted to most laboratory practices, particularly those with DNA synthesis automation as a simple, inexpensive (<$4), and eco-friendly means of oligonucleotide trityl-on purification.
[Mh] Termos MeSH primário: Proteínas de Bactérias/química
DNA de Cadeia Simples/química
Proteínas de Ligação a DNA/química
Exodesoxirribonucleases/química
Química Verde
Oligonucleotídeos/isolamento & purificação
[Mh] Termos MeSH secundário: Proteínas de Bactérias/genética
DNA de Cadeia Simples/genética
Proteínas de Ligação a DNA/genética
Exodesoxirribonucleases/genética
Conformação de Ácido Nucleico
Ligação Proteica
Compostos de Tritil/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (DNA, Single-Stranded); 0 (DNA-Binding Proteins); 0 (Oligonucleotides); 0 (Trityl Compounds); EC 3.1.- (Exodeoxyribonucleases); EC 3.1.11.- (recJ protein, Bacteria)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:171205
[Lr] Data última revisão:
171205
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE
[do] DOI:10.1021/acs.biochem.7b00010


  6 / 3614 MEDLINE  
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[PMID]:29069084
[Au] Autor:Dahal BK; Kadyrova LY; Delfino KR; Rogozin IB; Gujar V; Lobachev KS; Kadyrov FA
[Ad] Endereço:Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, United States of America.
[Ti] Título:Involvement of DNA mismatch repair in the maintenance of heterochromatic DNA stability in Saccharomyces cerevisiae.
[So] Source:PLoS Genet;13(10):e1007074, 2017 Oct.
[Is] ISSN:1553-7404
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Heterochromatin contains a significant part of nuclear DNA. Little is known about the mechanisms that govern heterochromatic DNA stability. We show here that in the yeast Saccharomyces cerevisiae (i) DNA mismatch repair (MMR) is required for the maintenance of heterochromatic DNA stability, (ii) MutLα (Mlh1-Pms1 heterodimer), MutSα (Msh2-Msh6 heterodimer), MutSß (Msh2-Msh3 heterodimer), and Exo1 are involved in MMR at heterochromatin, (iii) Exo1-independent MMR at heterochromatin frequently leads to the formation of Pol ζ-dependent mutations, (iv) MMR cooperates with the proofreading activity of Pol ε and the histone acetyltransferase Rtt109 in the maintenance of heterochromatic DNA stability, (v) repair of base-base mismatches at heterochromatin is less efficient than repair of base-base mismatches at euchromatin, and (vi) the efficiency of repair of 1-nt insertion/deletion loops at heterochromatin is similar to the efficiency of repair of 1-nt insertion/deletion loops at euchromatin.
[Mh] Termos MeSH primário: Reparo de Erro de Pareamento de DNA
DNA Fúngico/química
Heterocromatina
Proteínas de Saccharomyces cerevisiae/genética
Saccharomyces cerevisiae/genética
[Mh] Termos MeSH secundário: Sequência de Bases
Dano ao DNA
DNA Fúngico/genética
Exodesoxirribonucleases/genética
Genes pol
Histona Acetiltransferases/genética
Proteínas MutL/genética
Proteína MutS de Ligação de DNA com Erro de Pareamento/genética
Homologia de Sequência
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Fungal); 0 (Heterochromatin); 0 (Saccharomyces cerevisiae Proteins); EC 2.3.1.48 (Histone Acetyltransferases); EC 2.3.1.48 (Rtt109 protein, S cerevisiae); EC 3.1.- (Exodeoxyribonucleases); EC 3.1.11.1 (exodeoxyribonuclease I); EC 3.6.1.3 (MutL Proteins); EC 3.6.1.3 (MutS DNA Mismatch-Binding Protein)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171119
[Lr] Data última revisão:
171119
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171026
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1007074


  7 / 3614 MEDLINE  
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[PMID]:28977567
[Au] Autor:Nagata M; Ishino S; Yamagami T; Ogino H; Simons JR; Kanai T; Atomi H; Ishino Y
[Ad] Endereço:Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Fukuoka 812-8581, Japan.
[Ti] Título:The Cdc45/RecJ-like protein forms a complex with GINS and MCM, and is important for DNA replication in Thermococcus kodakarensis.
[So] Source:Nucleic Acids Res;45(18):10693-10705, 2017 Oct 13.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The archaeal minichromosome maintenance (MCM) has DNA helicase activity, which is stimulated by GINS in several archaea. In the eukaryotic replicative helicase complex, Cdc45 forms a complex with MCM and GINS, named as CMG (Cdc45-MCM-GINS). Cdc45 shares sequence similarity with bacterial RecJ. A Cdc45/RecJ-like protein from Thermococcus kodakarensis shows a bacterial RecJ-like exonuclease activity, which is stimulated by GINS in vitro. Therefore, this archaeal Cdc45/RecJ is designated as GAN, from GINS-associated nuclease. In this study, we identified the CMG-like complex in T. kodakarensis cells. The GAN·GINS complex stimulated the MCM helicase, but MCM did not affect the nuclease activity of GAN in vitro. The gene disruption analysis showed that GAN was non-essential for its viability but the Δgan mutant did not grow at 93°C. Furthermore, the Δgan mutant showed a clear retardation in growth as compared with the parent cells under optimal conditions at 85°C. These deficiencies were recovered by introducing the gan gene encoding the nuclease deficient GAN protein back to the genome. These results suggest that the replicative helicase complex without GAN may become unstable and ineffective in replication fork progression. The nuclease activity of GAN is not related to the growth defects of the Δgan mutant cells.
[Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo
Replicação do DNA
Exodesoxirribonucleases/metabolismo
Componente 3 do Complexo de Manutenção de Minicromossomo/metabolismo
Thermococcus/enzimologia
Thermococcus/genética
[Mh] Termos MeSH secundário: Proteínas Arqueais/genética
Exodesoxirribonucleases/genética
Deleção de Genes
Metais
Thermococcus/crescimento & desenvolvimento
Thermococcus/metabolismo
Raios Ultravioleta
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (Metals); EC 3.1.- (Exodeoxyribonucleases); EC 3.6.4.12 (Minichromosome Maintenance Complex Component 3)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171107
[Lr] Data última revisão:
171107
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171005
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx740


  8 / 3614 MEDLINE  
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[PMID]:28934474
[Au] Autor:Liu D; Frederiksen JH; Liberti SE; Lützen A; Keijzers G; Pena-Diaz J; Rasmussen LJ
[Ad] Endereço:Center for Healthy Aging, University of Copenhagen, Denmark.
[Ti] Título:Human DNA polymerase delta double-mutant D316A;E318A interferes with DNA mismatch repair in vitro.
[So] Source:Nucleic Acids Res;45(16):9427-9440, 2017 Sep 19.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:DNA mismatch repair (MMR) is a highly-conserved DNA repair mechanism, whose primary role is to remove DNA replication errors preventing them from manifesting as mutations, thereby increasing the overall genome stability. Defects in MMR are associated with increased cancer risk in humans and other organisms. Here, we characterize the interaction between MMR and a proofreading-deficient allele of the human replicative DNA polymerase delta, PolδD316A;E318A, which has a higher capacity for strand displacement DNA synthesis than wild type Polδ. Human cell lines overexpressing PolδD316A;E318A display a mild mutator phenotype, while nuclear extracts of these cells exhibit reduced MMR activity in vitro, and these defects are complemented by overexpression or addition of exogenous human Exonuclease 1 (EXO1). By contrast, another proofreading-deficient mutant, PolδD515V, which has a weaker strand displacement activity, does not decrease the MMR activity as significantly as PolδD316A;E318A. In addition, PolδD515V does not increase the mutation frequency in MMR-proficient cells. Based on our findings, we propose that the proofreading activity restricts the strand displacement activity of Polδ in MMR. This contributes to maintain the nicks required for EXO1 entry, and in this manner ensures the dominance of the EXO1-dependent MMR pathway.
[Mh] Termos MeSH primário: Reparo de Erro de Pareamento de DNA
DNA Polimerase III/metabolismo
Mutação
[Mh] Termos MeSH secundário: Metilação de DNA/efeitos dos fármacos
DNA Polimerase III/genética
Enzimas Reparadoras do DNA/genética
Enzimas Reparadoras do DNA/metabolismo
Exodesoxirribonucleases/genética
Exodesoxirribonucleases/metabolismo
Células HeLa
Seres Humanos
Metilnitronitrosoguanidina/farmacologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
12H3O2UGSF (Methylnitronitrosoguanidine); EC 2.7.7.- (DNA Polymerase III); EC 3.1.- (EXO1 protein, human); EC 3.1.- (Exodeoxyribonucleases); EC 6.5.1.- (DNA Repair Enzymes)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171024
[Lr] Data última revisão:
171024
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170922
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx611


  9 / 3614 MEDLINE  
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[PMID]:28922417
[Au] Autor:Sanchez A; Gadaleta MC; Limbo O; Russell P
[Ad] Endereço:Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America.
[Ti] Título:Lingering single-strand breaks trigger Rad51-independent homology-directed repair of collapsed replication forks in the polynucleotide kinase/phosphatase mutant of fission yeast.
[So] Source:PLoS Genet;13(9):e1007013, 2017 Sep.
[Is] ISSN:1553-7404
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The DNA repair enzyme polynucleotide kinase/phosphatase (PNKP) protects genome integrity by restoring ligatable 5'-phosphate and 3'-hydroxyl termini at single-strand breaks (SSBs). In humans, PNKP mutations underlie the neurological disease known as MCSZ, but these individuals are not predisposed for cancer, implying effective alternative repair pathways in dividing cells. Homology-directed repair (HDR) of collapsed replication forks was proposed to repair SSBs in PNKP-deficient cells, but the critical HDR protein Rad51 is not required in PNKP-null (pnk1Δ) cells of Schizosaccharomyces pombe. Here, we report that pnk1Δ cells have enhanced requirements for Rad3 (ATR/Mec1) and Chk1 checkpoint kinases, and the multi-BRCT domain protein Brc1 that binds phospho-histone H2A (γH2A) at damaged replication forks. The viability of pnk1Δ cells depends on Mre11 and Ctp1 (CtIP/Sae2) double-strand break (DSB) resection proteins, Rad52 DNA strand annealing protein, Mus81-Eme1 Holliday junction resolvase, and Rqh1 (BLM/WRN/Sgs1) DNA helicase. Coupled with increased sister chromatid recombination and Rad52 repair foci in pnk1Δ cells, these findings indicate that lingering SSBs in pnk1Δ cells trigger Rad51-independent homology-directed repair of collapsed replication forks. From these data, we propose models for HDR-mediated tolerance of persistent SSBs with 3' phosphate in pnk1Δ cells.
[Mh] Termos MeSH primário: Enzimas Reparadoras do DNA/genética
Reparo do DNA/genética
Polinucleotídeo 5´-Hidroxiquinase/genética
Rad51 Recombinase/genética
[Mh] Termos MeSH secundário: Quinase do Ponto de Checagem 1/genética
Quinase do Ponto de Checagem 2/genética
Quebras de DNA de Cadeia Dupla
Quebras de DNA de Cadeia Simples
Dano ao DNA/genética
Replicação do DNA/genética
Proteínas de Ligação a DNA/genética
Endonucleases/genética
Exodesoxirribonucleases/genética
Resolvases de Junção Holliday/genética
Seres Humanos
Mutação
Reparo de DNA por Recombinação/genética
Schizosaccharomyces/genética
Proteínas de Schizosaccharomyces pombe/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Brc1 protein, S pombe); 0 (Ctp1 protein, S pombe); 0 (DNA-Binding Proteins); 0 (MUS81 protein, S pombe); 0 (Schizosaccharomyces pombe Proteins); 0 (rad52 protein, S pombe); EC 2.7.1.11 (Checkpoint Kinase 2); EC 2.7.1.78 (Polynucleotide 5'-Hydroxyl-Kinase); EC 2.7.11.1 (Checkpoint Kinase 1); EC 2.7.11.1 (Chk1 protein, S pombe); EC 2.7.11.1 (rad3 protein, S pombe); EC 2.7.7.- (Rad51 Recombinase); EC 3.1.- (Eme1protein, S pombe); EC 3.1.- (Endonucleases); EC 3.1.- (Exodeoxyribonucleases); EC 3.1.- (Mre11 protein, S pombe); EC 3.1.21.- (Holliday Junction Resolvases); EC 6.5.1.- (DNA Repair Enzymes)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171018
[Lr] Data última revisão:
171018
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170919
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1007013


  10 / 3614 MEDLINE  
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[PMID]:28911122
[Au] Autor:Welch R; Chung D; Grass J; Landick R; Keles S
[Ad] Endereço:Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA.
[Ti] Título:Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments.
[So] Source:Nucleic Acids Res;45(15):e145, 2017 Sep 06.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:ChIP-exo/nexus experiments rely on innovative modifications of the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a novel statistical quality control pipeline and accompanying R/Bioconductor package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments. ChIPexoQual evaluates a number of key issues including strand imbalance, library complexity, and signal enrichment of data. Assessment of these features are facilitated through diagnostic plots and summary statistics computed over regions of the genome with varying levels of coverage. We evaluated our QC pipeline with both large collections of public ChIP-exo/nexus data and multiple, new ChIP-exo datasets from Escherichia coli. ChIPexoQual analysis of these datasets resulted in guidelines for using these QC metrics across a wide range of sequencing depths and provided further insights for modelling ChIP-exo data.
[Mh] Termos MeSH primário: Imunoprecipitação da Cromatina/métodos
DNA/metabolismo
Acurácia dos Dados
Interpretação Estatística de Dados
Exodesoxirribonucleases/metabolismo
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Análise de Sequência de DNA/métodos
[Mh] Termos MeSH secundário: Sítios de Ligação/genética
Imunoprecipitação da Cromatina/normas
DNA/análise
DNA Ligases/metabolismo
Conjuntos de Dados como Assunto
Escherichia coli/genética
Escherichia coli/metabolismo
Sequenciamento de Nucleotídeos em Larga Escala/normas
Análise de Sequência com Séries de Oligonucleotídeos/métodos
Análise de Sequência com Séries de Oligonucleotídeos/normas
Ligação Proteica
Controle de Qualidade
Análise de Sequência de DNA/normas
Software
Fatores de Transcrição/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; VALIDATION STUDIES
[Nm] Nome de substância:
0 (Transcription Factors); 9007-49-2 (DNA); EC 3.1.- (Exodeoxyribonucleases); EC 6.5.1.- (DNA Ligases)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171107
[Lr] Data última revisão:
171107
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170916
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx594



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