Microbial Cell (Jan 2019)
Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways
- 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
Affiliations
- Hannah L. Klein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
- Giedrė Bačinskaja
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
- Jun Che
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA.
- Anais Cheblal
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland.
- Rajula Elango
- Department of Biology, University of Iowa, Iowa City, IA, USA.
- Anastasiya Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
- Devon M. Fitzgerald
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Belén Gómez-González
- Centro Andaluz de BIología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain.
- Sharik R. Khan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Sandeep Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Bryan A. Leland
- Yale School of Medicine, New Haven, CT, USA.
- Léa Marie
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.
- Qian Mei
- Systems, Synthetic and Physical Biology Graduate Program, Rice University, Houston, TX, USA.
- Judith Miné-Hattab
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France.
- Alicja Piotrowska
- NanoBioMedical Centre, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland.
- Erica J. Polleys
- Department of Biology, Tufts University, Medford, MA USA.
- Christopher D. Putnam
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, CA, USA.
- Elina A. Radchenko
- Department of Biology, Tufts University, Medford, MA USA.
- Anissia Ait Saada
- Institut Curie, PSL Research University, CNRS, UMR3348 F-91405, Orsay, France.
- Cynthia J. Sakofsky
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA.
- Eun Yong Shim
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA.
- Mathew Stracy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Jun Xia
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Zhenxin Yan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Yi Yin
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC USA.
- Andrés Aguilera
- Centro Andaluz de BIología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain.
- Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
- Catherine H. Freudenreich
- Department of Biology, Tufts University, Medford, MA USA.
- Susan M. Gasser
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland.
- Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA.
- James E. Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, USA.
- Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC USA.
- Megan C. King
- Yale School of Medicine, New Haven, CT, USA.
- Richard D. Kolodner
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, CA, USA.
- Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Sarah AE Lambert
- Institut Curie, PSL Research University, CNRS, UMR3348 F-91405, Orsay, France.
- Sang Eun Lee
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA.
- Kyle M. Miller
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Sergei M. Mirkin
- Department of Biology, Tufts University, Medford, MA USA.
- Thomas D. Petes
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC USA.
- Susan M. Rosenberg
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Rodney Rothstein
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA.
- Lorraine S. Symington
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.
- Pawel Zawadzki
- NanoBioMedical Centre, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland.
- Nayun Kim
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, USA.
- Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
- Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA, USA.
- DOI
- https://doi.org/10.15698/mic2019.01.664
- Journal volume & issue
-
Vol. 6,
no. 1
pp. 1 – 64
Abstract
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.
Keywords
- 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
