Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways
Understanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic,...
| Published in: | Microbial Cell |
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| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format: | Article |
| Language: | English |
| Published: |
Shared Science Publishers OG
2019-01-01
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| Online Access: | http://microbialcell.com/researcharticles/2019a-klein-microbial-cell/ |
| _version_ | 1849511333361352704 |
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| author | Hannah L. Klein Giedrė Bačinskaja Jun Che Anais Cheblal Rajula Elango Anastasiya Epshtein Devon M. Fitzgerald Belén Gómez-González Sharik R. Khan Sandeep Kumar Bryan A. Leland Léa Marie Qian Mei Judith Miné-Hattab Alicja Piotrowska Erica J. Polleys Christopher D. Putnam Elina A. Radchenko Anissia Ait Saada Cynthia J. Sakofsky Eun Yong Shim Mathew Stracy Jun Xia Zhenxin Yan Yi Yin Andrés Aguilera Juan Lucas Argueso Catherine H. Freudenreich Susan M. Gasser Dmitry A. Gordenin James E. Haber Grzegorz Ira Sue Jinks-Robertson Megan C. King Richard D. Kolodner Andrei Kuzminov Sarah AE Lambert Sang Eun Lee Kyle M. Miller Sergei M. Mirkin Thomas D. Petes Susan M. Rosenberg Rodney Rothstein Lorraine S. Symington Pawel Zawadzki Nayun Kim Michael Lisby Anna Malkova |
| author_facet | Hannah L. Klein Giedrė Bačinskaja Jun Che Anais Cheblal Rajula Elango Anastasiya Epshtein Devon M. Fitzgerald Belén Gómez-González Sharik R. Khan Sandeep Kumar Bryan A. Leland Léa Marie Qian Mei Judith Miné-Hattab Alicja Piotrowska Erica J. Polleys Christopher D. Putnam Elina A. Radchenko Anissia Ait Saada Cynthia J. Sakofsky Eun Yong Shim Mathew Stracy Jun Xia Zhenxin Yan Yi Yin Andrés Aguilera Juan Lucas Argueso Catherine H. Freudenreich Susan M. Gasser Dmitry A. Gordenin James E. Haber Grzegorz Ira Sue Jinks-Robertson Megan C. King Richard D. Kolodner Andrei Kuzminov Sarah AE Lambert Sang Eun Lee Kyle M. Miller Sergei M. Mirkin Thomas D. Petes Susan M. Rosenberg Rodney Rothstein Lorraine S. Symington Pawel Zawadzki Nayun Kim Michael Lisby Anna Malkova |
| author_sort | Hannah L. Klein |
| collection | DOAJ |
| container_title | Microbial Cell |
| description | Understanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic, molecular, and cytological reporters. The assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies. |
| format | Article |
| id | doaj-art-9deb4e4edc524ec78e599b9f614eaef3 |
| institution | Directory of Open Access Journals |
| issn | 2311-2638 |
| language | English |
| publishDate | 2019-01-01 |
| publisher | Shared Science Publishers OG |
| record_format | Article |
| spelling | doaj-art-9deb4e4edc524ec78e599b9f614eaef32025-08-20T02:57:37ZengShared Science Publishers OGMicrobial Cell2311-26382019-01-016116410.15698/mic2019.01.664Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathwaysHannah L. Klein0Giedrė Bačinskaja1Jun Che2Anais Cheblal3Rajula Elango4Anastasiya Epshtein5Devon M. Fitzgerald6Belén Gómez-González7Sharik R. Khan8Sandeep Kumar9Bryan A. Leland10Léa Marie11Qian Mei12Judith Miné-Hattab13Alicja Piotrowska14Erica J. Polleys15Christopher D. Putnam16Elina A. Radchenko17Anissia Ait Saada18Cynthia J. Sakofsky19Eun Yong Shim20Mathew Stracy21Jun Xia22Zhenxin Yan23Yi Yin24Andrés Aguilera25Juan Lucas Argueso26Catherine H. Freudenreich27Susan M. Gasser28Dmitry A. Gordenin29James E. Haber30Grzegorz Ira31Sue Jinks-Robertson32Megan C. King33Richard D. Kolodner34Andrei Kuzminov35Sarah AE Lambert36Sang Eun Lee37Kyle M. Miller38Sergei M. Mirkin39Thomas D. Petes40Susan M. Rosenberg41Rodney Rothstein42Lorraine S. Symington43Pawel Zawadzki44Nayun Kim45Michael Lisby46Anna Malkova47Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA.Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland.Department of Biology, University of Iowa, Iowa City, IA, USA.Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.Centro Andaluz de BIología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain.Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.Yale School of Medicine, New Haven, CT, USA.Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.Systems, Synthetic and Physical Biology Graduate Program, Rice University, Houston, TX, USA.Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France.NanoBioMedical Centre, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland.Department of Biology, Tufts University, Medford, MA USA.Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, CA, USA. Department of Biology, Tufts University, Medford, MA USA.Institut Curie, PSL Research University, CNRS, UMR3348 F-91405, Orsay, France.Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA.Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA.Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC USA.Centro Andaluz de BIología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain.Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA. Department of Biology, Tufts University, Medford, MA USA.Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland.Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA.Department of Biology and Rosenstiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, USA.Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC USA.Yale School of Medicine, New Haven, CT, USA.Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, CA, USA. Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.Institut Curie, PSL Research University, CNRS, UMR3348 F-91405, Orsay, France.Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA.Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.Department of Biology, Tufts University, Medford, MA USA.Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC USA.Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA.Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.NanoBioMedical Centre, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland.Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, USA.Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.Department of Biology, University of Iowa, Iowa City, IA, USA.Understanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic, molecular, and cytological reporters. The assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.http://microbialcell.com/researcharticles/2019a-klein-microbial-cell/chromatin dynamicschromosome rearrangementscrossoversDNA breaksDNA repair centersDNA resectionDSBsgene amplificationgene conversiongenome instabilitygross chromosome rearrangementsfluorescent proteinsHolliday junctionshomologous recombinationmitotic recombinationmutagenesispulsed field gel electrophoresisR-loopssingle-particle trackingreplication fork stallingsister repetitive sequencessister chromatid recombinationsite-specific chromosome breakstoxic recombination intermediatesyeast artificial chromosome |
| spellingShingle | Hannah L. Klein Giedrė Bačinskaja Jun Che Anais Cheblal Rajula Elango Anastasiya Epshtein Devon M. Fitzgerald Belén Gómez-González Sharik R. Khan Sandeep Kumar Bryan A. Leland Léa Marie Qian Mei Judith Miné-Hattab Alicja Piotrowska Erica J. Polleys Christopher D. Putnam Elina A. Radchenko Anissia Ait Saada Cynthia J. Sakofsky Eun Yong Shim Mathew Stracy Jun Xia Zhenxin Yan Yi Yin Andrés Aguilera Juan Lucas Argueso Catherine H. Freudenreich Susan M. Gasser Dmitry A. Gordenin James E. Haber Grzegorz Ira Sue Jinks-Robertson Megan C. King Richard D. Kolodner Andrei Kuzminov Sarah AE Lambert Sang Eun Lee Kyle M. Miller Sergei M. Mirkin Thomas D. Petes Susan M. Rosenberg Rodney Rothstein Lorraine S. Symington Pawel Zawadzki Nayun Kim Michael Lisby Anna Malkova Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways chromatin dynamics chromosome rearrangements crossovers DNA breaks DNA repair centers DNA resection DSBs gene amplification gene conversion genome instability gross chromosome rearrangements fluorescent proteins Holliday junctions homologous recombination mitotic recombination mutagenesis pulsed field gel electrophoresis R-loops single-particle tracking replication fork stalling sister repetitive sequences sister chromatid recombination site-specific chromosome breaks toxic recombination intermediates yeast artificial chromosome |
| title | Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways |
| title_full | Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways |
| title_fullStr | Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways |
| title_full_unstemmed | Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways |
| title_short | Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways |
| title_sort | guidelines for dna recombination and repair studies cellular assays of dna repair pathways |
| topic | chromatin dynamics chromosome rearrangements crossovers DNA breaks DNA repair centers DNA resection DSBs gene amplification gene conversion genome instability gross chromosome rearrangements fluorescent proteins Holliday junctions homologous recombination mitotic recombination mutagenesis pulsed field gel electrophoresis R-loops single-particle tracking replication fork stalling sister repetitive sequences sister chromatid recombination site-specific chromosome breaks toxic recombination intermediates yeast artificial chromosome |
| url | http://microbialcell.com/researcharticles/2019a-klein-microbial-cell/ |
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