Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways

Authors:

Hannah L. Klein1, Giedrė Bačinskaja2, Jun Che3, Anais Cheblal4, Rajula Elango5, Anastasiya Epshtein1, Devon M. Fitzgerald6-9, Belén Gómez-González10, Sharik R. Khan11, Sandeep Kumar7, Bryan A. Leland12, Léa Marie13, Qian Mei14, Judith Miné-Hattab16,17, Alicja Piotrowska18, Erica J. Polleys19, Christopher D. Putnam20,21, Elina A. Radchenko19, Anissia Ait Saada22,23, Cynthia J. Sakofsky24, Eun Yong Shim3, Mathew Stracy25, Jun Xia6-9, Zhenxin Yan7, Yi Yin26, Andrés Aguilera10, Juan Lucas Argueso27, Catherine H. Freudenreich19,28, Susan M. Gasser4, Dmitry A. Gordenin24, James E. Haber29, Grzegorz Ira7, Sue Jinks-Robertson30, Megan C. King12, Richard D. Kolodner20, 31-33, Andrei Kuzminov11, Sarah AE Lambert22,23, Sang Eun Lee3, Kyle M. Miller6,15, Sergei M. Mirkin19, Thomas D. Petes26, Susan M. Rosenberg6-9,14, Rodney Rothstein34, Lorraine S. Symington13, Pawel Zawadzki18, Nayun Kim35, Michael Lisby2 and Anna Malkova5

doi: 10.15698/mic2019.01.664
Volume 6, pp. 1 to 64, published 07/01/2019.

Affiliations:

1 Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA. 2 Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark. 3 Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA. 4 Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland. 5 Department of Biology, University of Iowa, Iowa City, IA, USA. 6 Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA. 7 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. 8 Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA. 9 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA. 10 Centro Andaluz de BIología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain. 11 Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. 12 Yale School of Medicine, New Haven, CT, USA. 13 Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA. 14 Systems, Synthetic and Physical Biology Graduate Program, Rice University, Houston, TX, USA. 15 Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
16 Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France. 17 Sorbonne Université, Institut Curie, CNRS, UMR3664, F-75005 Paris, France. 18 NanoBioMedical Centre, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland. 19 Department of Biology, Tufts University, Medford, MA USA. 20 Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, CA, USA. 21 Department of Medicine, University of California School of Medicine, San Diego, La Jolla, CA, USA. 22 Institut Curie, PSL Research University, CNRS, UMR3348 F-91405, Orsay, France. 23 University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405, Orsay, France. 24 Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA. 25 Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK. 26 Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC USA. 27 Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA. 28 Program in Genetics, Tufts University, Boston, MA, USA. 29 Department of Biology and Rosenstiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, USA. 30 Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC USA. 31 Department of Cellular and Molecular Medicine, University of California School of Medicine, San Diego, La Jolla, CA, USA. 32 Moores-UCSD Cancer Center, University of California School of Medicine, San Diego, La Jolla, CA, USA. 33 Institute of Genomic Medicine, University of California School of Medicine, San Diego, La Jolla, CA, USA. 34 Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA. 35 Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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.

Corresponding Author(s):

Hannah Klein, New York University School of Medicine, New York, NY USA; hannah.klein@nyumc.org Nayun Kim, The University of Texas Health Science Center, Houston, TX, USA; Nayun.Kim@uth.tmc.edu

Conflict of interest statement:

The authors declare no conflict of interest.

Please cite this article as:

Hannah L. Klein, et al. (2019). Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways. Microbial Cell 6(1): 1-64. doi: 10.15698/mic2019.01.664

© 2019 Klein et al. This is an open-access article released under the terms of the Creative Commons Attribution (CC BY) license, which allows the unrestricted use, distribution, and reproduction in any medium, provided the original author and source are acknowledged.

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.