Publications by authors named "Grzegorz Ira"

44Publications

A Rad51-independent pathway promotes single-strand template repair in gene editing.

PLoS Genet 2020 Oct 15;16(10):e1008689. Epub 2020 Oct 15.

Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7591047PMC
October 2020

Analysis of DNA Double-Strand Break End Resection and Single-Strand Annealing in S. pombe.

Methods Mol Biol 2021 ;2153:47-57

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

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http://dx.doi.org/10.1007/978-1-0716-0644-5_4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7647126PMC
January 2021

Rad52 Restrains Resection at DNA Double-Strand Break Ends in Yeast.

Mol Cell 2019 12 18;76(5):699-711.e6. Epub 2019 Sep 18.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.08.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6898758PMC
December 2019

Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2.

Cell 2019 03 28;176(6):1310-1324.e10. Epub 2019 Feb 28.

Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA; Department of Pediatrics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.01.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438178PMC
March 2019

Dna2 nuclease deficiency results in large and complex DNA insertions at chromosomal breaks.

Nature 2018 12 5;564(7735):287-290. Epub 2018 Dec 5.

Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, USA.

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http://www.nature.com/articles/s41586-018-0769-8
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http://dx.doi.org/10.1038/s41586-018-0769-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346745PMC
December 2018

Bre1-dependent H2B ubiquitination promotes homologous recombination by stimulating histone eviction at DNA breaks.

Nucleic Acids Res 2018 11;46(21):11326-11339

Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265479PMC
November 2018

Predicting human genes susceptible to genomic instability associated with /-mediated rearrangements.

Genome Res 2018 08 15;28(8):1228-1242. Epub 2018 Jun 15.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1101/gr.229401.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6071635PMC
August 2018

Role of the Pif1-PCNA Complex in Pol δ-Dependent Strand Displacement DNA Synthesis and Break-Induced Replication.

Cell Rep 2017 Nov;21(7):1707-1714

Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.10.079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5842794PMC
November 2017

MRE11 and EXO1 nucleases degrade reversed forks and elicit MUS81-dependent fork rescue in BRCA2-deficient cells.

Nat Commun 2017 10 16;8(1):860. Epub 2017 Oct 16.

Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, 63104, USA.

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http://dx.doi.org/10.1038/s41467-017-01180-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5643552PMC
October 2017

Yeast Sub1 and human PC4 are G-quadruplex binding proteins that suppress genome instability at co-transcriptionally formed G4 DNA.

Nucleic Acids Res 2017 Jun;45(10):5850-5862

Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/nar/gkx201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5449603PMC
June 2017

A novel role of the Dna2 translocase function in DNA break resection.

Genes Dev 2017 03 23;31(5):503-510. Epub 2017 Mar 23.

Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1101/gad.295659.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5393064PMC
March 2017

Differential regulation of the anti-crossover and replication fork regression activities of Mph1 by Mte1.

Genes Dev 2016 Mar 10;30(6):687-99. Epub 2016 Mar 10.

Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA;

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http://dx.doi.org/10.1101/gad.276139.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4803054PMC
March 2016

Enrichment of Cdk1-cyclins at DNA double-strand breaks stimulates Fun30 phosphorylation and DNA end resection.

Nucleic Acids Res 2016 Apr 21;44(6):2742-53. Epub 2016 Jan 21.

Department of Molecular ad Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA

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http://dx.doi.org/10.1093/nar/gkv1544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824098PMC
April 2016

Translesion Polymerases Drive Microhomology-Mediated Break-Induced Replication Leading to Complex Chromosomal Rearrangements.

Mol Cell 2015 Dec 6;60(6):860-72. Epub 2015 Dec 6.

Department of Biology, University of Iowa, Iowa City, IA 52242, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.10.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4688117PMC
December 2015

DNA REPAIR. Mus81 and converging forks limit the mutagenicity of replication fork breakage.

Science 2015 Aug;349(6249):742-7

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/science.aaa8391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4782627PMC
August 2015

Selective modulation of the functions of a conserved DNA motor by a histone fold complex.

Genes Dev 2015 May 8;29(10):1000-5. Epub 2015 May 8.

Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA; Programs in Biochemistry, Cell, and Molecular Biology, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10065, USA;

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http://dx.doi.org/10.1101/gad.259143.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441048PMC
May 2015

Absence of heterozygosity due to template switching during replicative rearrangements.

Am J Hum Genet 2015 Apr 19;96(4):555-64. Epub 2015 Mar 19.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.01.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385179PMC
April 2015

A new Riff: Rif1 eats its cake and has it too.

EMBO Rep 2014 Jun 27;15(6):622-4. Epub 2014 Apr 27.

Laboratory of Genome Integrity, Center for Cancer Research National Cancer Institute National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1002/embr.201438825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4197870PMC
June 2014

Migrating bubble during break-induced replication drives conservative DNA synthesis.

Nature 2013 Oct 11;502(7471):389-92. Epub 2013 Sep 11.

School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.

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http://dx.doi.org/10.1038/nature12584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3804423PMC
October 2013

Pif1 helicase and Polδ promote recombination-coupled DNA synthesis via bubble migration.

Nature 2013 Oct 11;502(7471):393-6. Epub 2013 Sep 11.

Baylor College of Medicine, Department of Molecular & Human Genetics, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature12585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3915060PMC
October 2013

Break-induced replication: functions and molecular mechanism.

Curr Opin Genet Dev 2013 Jun 18;23(3):271-9. Epub 2013 Jun 18.

Department of Biology, School of Science, IUPUI, Indianapolis, IN 46202, USA.

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http://dx.doi.org/10.1016/j.gde.2013.05.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3915057PMC
June 2013

The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends.

Nature 2012 Sep 9;489(7417):576-80. Epub 2012 Sep 9.

Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature11355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640768PMC
September 2012

DNA breakage drives nuclear search.

Nat Cell Biol 2012 May 2;14(5):448-50. Epub 2012 May 2.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/ncb2494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495951PMC
May 2012

Human nuclease/helicase DNA2 alleviates replication stress by promoting DNA end resection.

Cancer Res 2012 Jun 9;72(11):2802-13. Epub 2012 Apr 9.

Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-11-3152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367086PMC
June 2012

Cell cycle regulation of DNA double-strand break end resection by Cdk1-dependent Dna2 phosphorylation.

Nat Struct Mol Biol 2011 Aug 14;18(9):1015-9. Epub 2011 Aug 14.

Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA.

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http://www.nature.com/articles/nsmb.2105
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http://dx.doi.org/10.1038/nsmb.2105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3168961PMC
August 2011

RSC facilitates Rad59-dependent homologous recombination between sister chromatids by promoting cohesin loading at DNA double-strand breaks.

Mol Cell Biol 2011 Oct 1;31(19):3924-37. Epub 2011 Aug 1.

Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 15355 Lambda Drive, San Antonio, TX 78245, USA.

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http://dx.doi.org/10.1128/MCB.01269-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187356PMC
October 2011

Saccharomyces cerevisiae Mre11/Rad50/Xrs2 and Ku proteins regulate association of Exo1 and Dna2 with DNA breaks.

EMBO J 2010 Oct 10;29(19):3370-80. Epub 2010 Sep 10.

Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.

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http://emboj.embopress.org/cgi/doi/10.1038/emboj.2010.219
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http://dx.doi.org/10.1038/emboj.2010.219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957216PMC
October 2010

Mechanism of the ATP-dependent DNA end-resection machinery from Saccharomyces cerevisiae.

Nature 2010 Sep;467(7311):108-11

Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1038/nature09318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955862PMC
September 2010

Defective resection at DNA double-strand breaks leads to de novo telomere formation and enhances gene targeting.

PLoS Genet 2010 May 13;6(5):e1000948. Epub 2010 May 13.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1000948
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http://dx.doi.org/10.1371/journal.pgen.1000948DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869328PMC
May 2010

Mechanisms of change in gene copy number.

Nat Rev Genet 2009 Aug;10(8):551-64

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nrg2593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864001PMC
August 2009

A microhomology-mediated break-induced replication model for the origin of human copy number variation.

PLoS Genet 2009 Jan 30;5(1):e1000327. Epub 2009 Jan 30.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1000327
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http://dx.doi.org/10.1371/journal.pgen.1000327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2621351PMC
January 2009

Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends.

Cell 2008 Sep;134(6):981-94

Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.cell.2008.08.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2662516PMC
September 2008

Conservative inheritance of newly synthesized DNA in double-strand break-induced gene conversion.

Mol Cell Biol 2006 Dec 9;26(24):9424-9. Epub 2006 Oct 9.

Rosenstiel Center and Department of Biology, Brandeis University, Waltham, MA 02453-2728, USA.

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http://dx.doi.org/10.1128/MCB.01654-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1698534PMC
December 2006

RAD51-dependent break-induced replication differs in kinetics and checkpoint responses from RAD51-mediated gene conversion.

Mol Cell Biol 2005 Feb;25(3):933-44

Rosenstiel Center, Brandeis University, 415 South St., Mail Stop 029, Waltham, MA 02454-9110, USA.

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http://dx.doi.org/10.1128/MCB.25.3.933-944.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC544012PMC
February 2005

Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break.

Curr Biol 2004 Oct;14(19):1703-11

Laboratory of Biochemistry, Center for Cancer Research, National Cancer Institute, Building 37, Room 6124, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.cub.2004.09.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493763PMC
October 2004

Role of DNA replication proteins in double-strand break-induced recombination in Saccharomyces cerevisiae.

Mol Cell Biol 2004 Aug;24(16):6891-9

Rosenstiel Center and Department of Biology, Brandeis University, Waltham, MA 02454-9110, USA.

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http://dx.doi.org/10.1128/MCB.24.16.6891-6899.2004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC479734PMC
August 2004

Mapping of the hotspots of recombination in human DNA cloned as yeast artificial chromosomes.

Methods Mol Biol 2004 ;240:35-52

Laboratory of Genetics, N Copernicus University, Toruñ, Poland.

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http://dx.doi.org/10.1385/1-59259-434-4:35DOI Listing
April 2004

Srs2 and Sgs1-Top3 suppress crossovers during double-strand break repair in yeast.

Cell 2003 Nov;115(4):401-11

Rosenstiel Center and Department of Biology, Brandeis University, Waltham, MA 02454, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493758PMC
http://dx.doi.org/10.1016/s0092-8674(03)00886-9DOI Listing
November 2003

Characterization of RAD51-independent break-induced replication that acts preferentially with short homologous sequences.

Mol Cell Biol 2002 Sep;22(18):6384-92

Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachussetts 02454-9110, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC135638PMC
http://dx.doi.org/10.1128/mcb.22.18.6384-6392.2002DOI Listing
September 2002

Recovery from checkpoint-mediated arrest after repair of a double-strand break requires Srs2 helicase.

Mol Cell 2002 Aug;10(2):373-85

Rosenstiel Center and Department of Biology, Brandeis University, Waltham, MA 02454, USA.

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http://dx.doi.org/10.1016/s1097-2765(02)00593-2DOI Listing
August 2002