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  • 1
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    Mechanism of the ATP-dependent DNA end-resection machinery from Saccharomyces cerevisiae (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-09-03
    Description: If not properly processed and repaired, DNA double-strand breaks (DSBs) can give rise to deleterious chromosome rearrangements, which could ultimately lead to the tumour phenotype. DSB ends are resected in a 5' to 3' fashion in cells, to yield single-stranded DNA (ssDNA) for the recruitment of factors critical for DNA damage checkpoint activation and repair by homologous recombination. The resection process involves redundant pathways consisting of nucleases, DNA helicases and associated proteins. Being guided by recent genetic studies, we have reconstituted the first eukaryotic ATP-dependent DNA end-resection machinery comprising the Saccharomyces cerevisiae Mre11-Rad50-Xrs2 (MRX) complex, the Sgs1-Top3-Rmi1 complex, Dna2 protein and the heterotrimeric ssDNA-binding protein RPA. Here we show that DNA strand separation during end resection is mediated by the Sgs1 helicase function, in a manner that is enhanced by Top3-Rmi1 and MRX. In congruence with genetic observations, although the Dna2 nuclease activity is critical for resection, the Mre11 nuclease activity is dispensable. By examining the top3 Y356F allele and its encoded protein, we provide evidence that the topoisomerase activity of Top3, although critical for the suppression of crossover recombination, is not needed for resection either in cells or in the reconstituted system. Our results also unveil a multifaceted role of RPA, in the sequestration of ssDNA generated by DNA unwinding, enhancement of 5' strand incision, and protection of the 3' strand. Our reconstituted system should serve as a useful model for delineating the mechanistic intricacy of the DNA break resection process in eukaryotes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955862/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955862/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Niu, Hengyao -- Chung, Woo-Hyun -- Zhu, Zhu -- Kwon, Youngho -- Zhao, Weixing -- Chi, Peter -- Prakash, Rohit -- Seong, Changhyun -- Liu, Dongqing -- Lu, Lucy -- Ira, Grzegorz -- Sung, Patrick -- P01 CA092584/CA/NCI NIH HHS/ -- P01 CA092584-100007/CA/NCI NIH HHS/ -- R01 CA146940/CA/NCI NIH HHS/ -- R01 ES007061/ES/NIEHS NIH HHS/ -- R01 ES007061-18/ES/NIEHS NIH HHS/ -- R01 ES015252/ES/NIEHS NIH HHS/ -- R01 ES015252-04/ES/NIEHS NIH HHS/ -- R01 ES015632/ES/NIEHS NIH HHS/ -- R01 ES015632-04/ES/NIEHS NIH HHS/ -- R01 GM057814/GM/NIGMS NIH HHS/ -- R01 GM057814-11/GM/NIGMS NIH HHS/ -- R01 GM080600/GM/NIGMS NIH HHS/ -- R01 GM080600-03S1/GM/NIGMS NIH HHS/ -- R01 GM080600-04/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Sep 2;467(7311):108-11. doi: 10.1038/nature09318.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20811460" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/*metabolism ; *DNA Breaks, Double-Stranded ; DNA Helicases/metabolism ; *DNA Repair ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/metabolism ; RecQ Helicases/metabolism ; Replication Protein A/metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Migrating bubble during break-induced replication drives conservative DNA synthesis (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-09-13
    Description: The repair of chromosomal double strand breaks (DSBs) is crucial for the maintenance of genomic integrity. However, the repair of DSBs can also destabilize the genome by causing mutations and chromosomal rearrangements, the driving forces for carcinogenesis and hereditary diseases. Break-induced replication (BIR) is one of the DSB repair pathways that is highly prone to genetic instability. BIR proceeds by invasion of one broken end into a homologous DNA sequence followed by replication that can copy hundreds of kilobases of DNA from a donor molecule all the way through its telomere. The resulting repaired chromosome comes at a great cost to the cell, as BIR promotes mutagenesis, loss of heterozygosity, translocations, and copy number variations, all hallmarks of carcinogenesis. BIR uses most known replication proteins to copy large portions of DNA, similar to S-phase replication. It has therefore been suggested that BIR proceeds by semiconservative replication; however, the model of a bona fide, stable replication fork contradicts the known instabilities associated with BIR such as a 1,000-fold increase in mutation rate compared to normal replication. Here we demonstrate that in budding yeast the mechanism of replication during BIR is significantly different from S-phase replication, as it proceeds via an unusual bubble-like replication fork that results in conservative inheritance of the new genetic material. We provide evidence that this atypical mode of DNA replication, dependent on Pif1 helicase, is responsible for the marked increase in BIR-associated mutations. We propose that the BIR mode of synthesis presents a powerful mechanism that can initiate bursts of genetic instability in eukaryotes, including humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3804423/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3804423/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saini, Natalie -- Ramakrishnan, Sreejith -- Elango, Rajula -- Ayyar, Sandeep -- Zhang, Yu -- Deem, Angela -- Ira, Grzegorz -- Haber, James E -- Lobachev, Kirill S -- Malkova, Anna -- GM080600/GM/NIGMS NIH HHS/ -- GM76020/GM/NIGMS NIH HHS/ -- R01 GM080600/GM/NIGMS NIH HHS/ -- R01GM082950/GM/NIGMS NIH HHS/ -- R01GM084242/GM/NIGMS NIH HHS/ -- R03 ES016434/ES/NIEHS NIH HHS/ -- R03ES016434/ES/NIEHS NIH HHS/ -- R37 GM020056/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Oct 17;502(7471):389-92. doi: 10.1038/nature12584. Epub 2013 Sep 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24025772" target="_blank"〉PubMed〈/a〉
    Keywords: *Chromosome Breakage ; *DNA Breaks, Double-Stranded ; DNA Helicases/metabolism ; DNA Repair/genetics ; DNA Replication/*genetics ; DNA, Fungal/*biosynthesis/genetics ; Genomic Instability/genetics ; Mutagenesis/genetics ; S Phase/genetics ; Saccharomyces cerevisiae/cytology/enzymology/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-09-11
    Description: Chromosomal double-strand breaks (DSBs) are resected by 5' nucleases to form 3' single-stranded DNA substrates for binding by homologous recombination and DNA damage checkpoint proteins. Two redundant pathways of extensive resection have been described both in cells and in vitro, one relying on Exo1 exonuclease and the other on Sgs1 helicase and Dna2 nuclease. However, it remains unknown how resection proceeds within the context of chromatin, where histones and histone-bound proteins represent barriers for resection enzymes. Here we identify the yeast nucleosome-remodelling enzyme Fun30 as a factor promoting DSB end resection. Fun30 is the major nucleosome remodeller promoting extensive Exo1- and Sgs1-dependent resection of DSBs. The RSC and INO80 chromatin-remodelling complexes and Fun30 have redundant roles in resection adjacent to DSB ends. ATPase and helicase domains of Fun30, which are needed for nucleosome remodelling, are also required for resection. Fun30 is robustly recruited to DNA breaks and spreads along the DSB coincident with resection. Fun30 becomes less important for resection in the absence of the histone-bound Rad9 checkpoint adaptor protein known to block 5' strand processing and in the absence of either histone H3 K79 methylation or gamma-H2A, which mediate recruitment of Rad9 (refs 9, 10). Together these data suggest that Fun30 helps to overcome the inhibitory effect of Rad9 on DNA resection.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640768/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640768/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Xuefeng -- Cui, Dandan -- Papusha, Alma -- Zhang, Xiaotian -- Chu, Chia-Dwo -- Tang, Jiangwu -- Chen, Kaifu -- Pan, Xuewen -- Ira, Grzegorz -- GM080600/GM/NIGMS NIH HHS/ -- HG004840/HG/NHGRI NIH HHS/ -- R01 GM080600/GM/NIGMS NIH HHS/ -- R01 HG004840/HG/NHGRI NIH HHS/ -- England -- Nature. 2012 Sep 27;489(7417):576-80. doi: 10.1038/nature11355. Epub 2012 Sep 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22960743" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Cycle Proteins/metabolism ; *Chromatin Assembly and Disassembly ; *DNA Breaks, Double-Stranded ; *DNA Repair ; DNA, Fungal/genetics/*metabolism ; Exodeoxyribonucleases/metabolism ; Genes, Fungal/genetics ; Genome, Fungal/genetics ; Histones/metabolism ; Homologous Recombination ; Methylation ; Nucleosomes/genetics/*metabolism ; RecQ Helicases/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Transcription Factors/deficiency/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Pif1 helicase and Poldelta promote recombination-coupled DNA synthesis via bubble migration (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-09-13
    Description: During DNA repair by homologous recombination (HR), DNA synthesis copies information from a template DNA molecule. Multiple DNA polymerases have been implicated in repair-specific DNA synthesis, but it has remained unclear whether a DNA helicase is involved in this reaction. A good candidate DNA helicase is Pif1, an evolutionarily conserved helicase in Saccharomyces cerevisiae important for break-induced replication (BIR) as well as HR-dependent telomere maintenance in the absence of telomerase found in 10-15% of all cancers. Pif1 has a role in DNA synthesis across hard-to-replicate sites and in lagging-strand synthesis with polymerase delta (Poldelta). Here we provide evidence that Pif1 stimulates DNA synthesis during BIR and crossover recombination. The initial steps of BIR occur normally in Pif1-deficient cells, but Poldelta recruitment and DNA synthesis are decreased, resulting in premature resolution of DNA intermediates into half-crossovers. Purified Pif1 protein strongly stimulates Poldelta-mediated DNA synthesis from a D-loop made by the Rad51 recombinase. Notably, Pif1 liberates the newly synthesized strand to prevent the accumulation of topological constraint and to facilitate extensive DNA synthesis via the establishment of a migrating D-loop structure. Our results uncover a novel function of Pif1 and provide insights into the mechanism of HR.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3915060/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3915060/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, Marenda A -- Kwon, YoungHo -- Xu, Yuanyuan -- Chung, Woo-Hyun -- Chi, Peter -- Niu, Hengyao -- Mayle, Ryan -- Chen, Xuefeng -- Malkova, Anna -- Sung, Patrick -- Ira, Grzegorz -- ES007061/ES/NIEHS NIH HHS/ -- ES015632/ES/NIEHS NIH HHS/ -- GM057814/GM/NIGMS NIH HHS/ -- GM080600/GM/NIGMS NIH HHS/ -- GM084242/GM/NIGMS NIH HHS/ -- R01 ES007061/ES/NIEHS NIH HHS/ -- R01 ES015632/ES/NIEHS NIH HHS/ -- R01 GM057814/GM/NIGMS NIH HHS/ -- R01 GM080600/GM/NIGMS NIH HHS/ -- R01 GM084242/GM/NIGMS NIH HHS/ -- R03 ES016434/ES/NIEHS NIH HHS/ -- T32 GM008307/GM/NIGMS NIH HHS/ -- T32GM07526-34/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Oct 17;502(7471):393-6. doi: 10.1038/nature12585. Epub 2013 Sep 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Baylor College of Medicine, Department of Molecular & Human Genetics, One Baylor Plaza, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24025768" target="_blank"〉PubMed〈/a〉
    Keywords: *Crossing Over, Genetic ; DNA Helicases/deficiency/genetics/*metabolism ; DNA Polymerase III/*metabolism ; DNA Repair ; *DNA Replication ; DNA, Fungal/*biosynthesis/chemistry/metabolism ; Nucleic Acid Conformation ; Rad51 Recombinase/metabolism ; Saccharomyces cerevisiae/*enzymology/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    DNA REPAIR. Mus81 and converging forks limit the mutagenicity of replication fork breakage (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-08-15
    Description: Most spontaneous DNA double-strand breaks (DSBs) result from replication-fork breakage. Break-induced replication (BIR), a genome rearrangement-prone repair mechanism that requires the Pol32/POLD3 subunit of eukaryotic DNA Poldelta, was proposed to repair broken forks, but how genome destabilization is avoided was unknown. We show that broken fork repair initially uses error-prone Pol32-dependent synthesis, but that mutagenic synthesis is limited to within a few kilobases from the break by Mus81 endonuclease and a converging fork. Mus81 suppresses template switches between both homologous sequences and diverged human Alu repetitive elements, highlighting its importance for stability of highly repetitive genomes. We propose that lack of a timely converging fork or Mus81 may propel genome instability observed in cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mayle, Ryan -- Campbell, Ian M -- Beck, Christine R -- Yu, Yang -- Wilson, Marenda -- Shaw, Chad A -- Bjergbaek, Lotte -- Lupski, James R -- Ira, Grzegorz -- F31 NS083159/NS/NINDS NIH HHS/ -- GM080600/GM/NIGMS NIH HHS/ -- HG006542/HG/NHGRI NIH HHS/ -- NS058529/NS/NINDS NIH HHS/ -- NS083159/NS/NINDS NIH HHS/ -- R01 GM080600/GM/NIGMS NIH HHS/ -- R01 NS058529/NS/NINDS NIH HHS/ -- U54 HG006542/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2015 Aug 14;349(6249):742-7. doi: 10.1126/science.aaa8391.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. ; Department of Molecular Biology and Genetics, University of Aarhus, Aarhus 8000, Denmark. ; Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. Department of Pediatrics, and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. Texas Children's Hospital, Houston, TX 77030, USA. ; Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. gira@bcm.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26273056" target="_blank"〉PubMed〈/a〉
    Keywords: Alu Elements ; Base Sequence ; *DNA Breaks, Double-Stranded ; DNA Repair/*genetics ; DNA Replication/*genetics ; DNA-Binding Proteins/genetics/*metabolism ; DNA-Directed DNA Polymerase/metabolism ; Endonucleases/genetics/*metabolism ; *Genomic Instability ; Humans ; Molecular Sequence Data ; Neoplasms/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
    Electronic Resource
    Electronic Resource
    Protein Synthesis by Skeletal Muscle Ribosomes. Effect of Diabetes and Insulin* (1967)
    s.l. : American Chemical Society
    Biochemistry 6 (1967), S. 1231-1242 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00857a003
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  • 7
    Electronic Resource
    Electronic Resource
    Two physically and functionally distinct forms of eukaryotic 40S ribosomal subunits (1973)
    s.l. : American Chemical Society
    Biochemistry 12 (1973), S. 2403-2411 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00737a006
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  • 8
    Electronic Resource
    Electronic Resource
    Polyuridylic acid directed binding of phenylalanyl transfer ribonucleic acid to mammalian 40S ribosomal subunits (1970)
    s.l. : American Chemical Society
    Biochemistry 9 (1970), S. 1909-1916 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00811a008
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  • 9
    Electronic Resource
    Electronic Resource
    Skeletal muscle ribosome subunits and peptidyl transfer ribonucleic acid (1971)
    s.l. : American Chemical Society
    Biochemistry 10 (1971), S. 1594-1598 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00785a014
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  • 10
    Electronic Resource
    Electronic Resource
    Isolation of eukaryotic ribosomal proteins: purification and characterization of S25 and L16 (1979)
    s.l. : American Chemical Society
    Biochemistry 18 (1979), S. 1634-1637 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00575a040
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