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 A.E. 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

doi:10.15698/mic2019.01.664

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. SakofskyEun 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 A.E. 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

Microbiology

Research output: Contribution to journal › Review article › peer-review

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.

Original language	English (US)
Pages (from-to)	1-64
Number of pages	64
Journal	Microbial Cell
Volume	6
Issue number	1
DOIs	https://doi.org/10.15698/mic2019.01.664
State	Published - Jan 2019

Keywords

Chromatin dynamics
Chromosome rearrangements
Crossovers
DNA breaks
DNA repair centers
DNA resection
DSBs
Fluorescent proteins
Gene amplification
Gene conversion
Genome instability
Gross chromosome rearrangements
Holliday junctions
Homologous recombination
Mitotic recombination
Mutagenesis
Pulsed field gel electrophoresis
R-loops
Replication fork stalling
Single-particle tracking
Sister chromatid recombination
Sister repetitive sequences
Site-specific chromosome breaks
Toxic recombination intermediates
Yeast artificial chromosome

ASJC Scopus subject areas

Parasitology
Microbiology
Applied Microbiology and Biotechnology
Biochemistry, Genetics and Molecular Biology (miscellaneous)
Molecular Biology
Genetics
Cell Biology
Virology

Online availability

10.15698/mic2019.01.664

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Klein, H. L., Bačinskaja, G., Che, J., Cheblal, A., Elango, R., Epshtein, A., Fitzgerald, D. M., Gómez-González, B., Khan, S. R., Kumar, S., Leland, B. A., Marie, L., Mei, Q., Miné-Hattab, J., Piotrowska, A., Polleys, E. J., Putnam, C. D., Radchenko, E. A., Saada, A. A., ... Malkova, A. (2019). Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways. Microbial Cell, 6(1), 1-64. https://doi.org/10.15698/mic2019.01.664

Klein, HL, Bačinskaja, G, Che, J, Cheblal, A, Elango, R, Epshtein, A, Fitzgerald, DM, Gómez-González, B, Khan, SR, Kumar, S, Leland, BA, Marie, L, Mei, Q, Miné-Hattab, J, Piotrowska, A, Polleys, EJ, Putnam, CD, Radchenko, EA, Saada, AA, Sakofsky, CJ, Shim, EY, Stracy, M, Xia, J, Yan, Z, Yin, Y, Aguilera, A, Argueso, JL, Freudenreich, CH, Gasser, SM, Gordenin, DA, Haber, JE, Ira, G, Jinks-Robertson, S, King, MC, Kolodner, RD, Kuzminov, A, Lambert, SAE, Lee, SE, Miller, KM, Mirkin, SM, Petes, TD, Rosenberg, SM, Rothstein, R, Symington, LS, Zawadzki, P, Kim, N, Lisby, M & Malkova, A 2019, 'Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways', Microbial Cell, vol. 6, no. 1, pp. 1-64. https://doi.org/10.15698/mic2019.01.664

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title = "Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways",

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, Fluorescent proteins, Gene amplification, Gene conversion, Genome instability, Gross chromosome rearrangements, Holliday junctions, Homologous recombination, Mitotic recombination, Mutagenesis, Pulsed field gel electrophoresis, R-loops, Replication fork stalling, Single-particle tracking, Sister chromatid recombination, Sister repetitive sequences, Site-specific chromosome breaks, Toxic recombination intermediates, Yeast artificial chromosome",

author = "Klein, {Hannah L.} and Giedrė Ba{\v c}inskaja and Jun Che and Anais Cheblal and Rajula Elango and Anastasiya Epshtein and Fitzgerald, {Devon M.} and Bel{\'e}n G{\'o}mez-Gonz{\'a}lez and Khan, {Sharik R.} and Sandeep Kumar and Leland, {Bryan A.} and L{\'e}a Marie and Qian Mei and Judith Min{\'e}-Hattab and Alicja Piotrowska and Polleys, {Erica J.} and Putnam, {Christopher D.} and Radchenko, {Elina A.} and Saada, {Anissia Ait} and Sakofsky, {Cynthia J.} and Shim, {Eun Yong} and Mathew Stracy and Jun Xia and Zhenxin Yan and Yi Yin and Andr{\'e}s Aguilera and Argueso, {Juan Lucas} and Freudenreich, {Catherine H.} and Gasser, {Susan M.} and Gordenin, {Dmitry A.} and Haber, {James E.} and Grzegorz Ira and Sue Jinks-Robertson and King, {Megan C.} and Kolodner, {Richard D.} and Andrei Kuzminov and Lambert, {Sarah A.E.} and Lee, {Sang Eun} and Miller, {Kyle M.} and Mirkin, {Sergei M.} and Petes, {Thomas D.} and Rosenberg, {Susan M.} and Rodney Rothstein and Symington, {Lorraine S.} and Pawel Zawadzki and Nayun Kim and Michael Lisby and Anna Malkova",

note = "Funding Information: HLK was supported by NIH grant R01-CA146940. AA was supported by the European research Council (ERC2014-ADG669898 TARLOOP), the Spanish Ministry of Economy and Competitiveness (BFU2016-75058-P), and the Junta de Andaluc{\'i}a (BIO1238). JLA was supported by NIH grant R35G-GM119788. CHF was supported by NIH grants P01-GM105473 and R01-GM122880. SMG was supported by the Swiss national Science Foundation and the Novartis Research Foundation. DAG was supported by National Institutes of Health (Intramural Research Program Project Z1AES103266. JEH was supported by NIH grants R35-GM127029 and P01-GM105473. GI was supported by NIH grants R01-GM125650 and R01-GM080600. SJ-R was supported by NIH grant R35-GM118077. MCK was supported by National Science Foundation Graduate Research Fellowship DGE-1122492, NIH training grant T32-GM007223 and NIH grant DP20D008429. RDK and CDP were supported by NIH grants R01-GM26017 and R01-GM50006. AK was supported by NIH grant R01-GM073115. SAEL was supported by grants from Agence Nationale de la Recherche ANR-14-CE10-0010-01 and the Foundation pour la Recherche M{\'e}-dicale Equipe FRM DEQ20160334889. SEL was supported by NIH grant R01-GM071011. SMM was supported by NIH grants R01-GM60987 and P01-GM105473. TDP was supported by NIH grant R35-GM118020. SMR was supported by a gift from WM <eck Foundation ? NIH Director ?s ?ioneer Award DP1-CA174424 and NIH grant R35-GM122598. DMF was supported by the Cancer Prevention and Research Institute of Texas, Baylor College of Medicine Comprehensive Cancer Training Program Postdoctoral Fellowship RP160283. RR was supported by NIH grant R35-GM118180 and JM-H was supported by a Marie Curie International Outgoing Fellowship and the ANR-12-PDOC-0035-01. LSS was supported by NIH grant R35-GM126997. PZ was supported by National Science Centre Poland 2015/19/103859 and FNP First TEAM/2016-1/9. NK was supported by NIH grant R01-GM116007 and the Welch Foundation (AU1875). ML was supported by grants from the Danish Agency for Science, Technology and Innovation, the Villum Foundation and the Danish National Research Foundation (DNRF115). AM was supported by NIH grants R35-GM127006 and R03-ES029306. Publisher Copyright: {\textcopyright} 2019 Klein et al.",

year = "2019",

month = jan,

doi = "10.15698/mic2019.01.664",

language = "English (US)",

volume = "6",

pages = "1--64",

journal = "Microbial Cell",

issn = "2311-2638",

publisher = "Shared Science Publishers OG",

number = "1",

}

TY - JOUR

T1 - Guidelines for DNA recombination and repair studies

T2 - Cellular assays of DNA repair pathways

AU - Klein, Hannah L.

AU - Bačinskaja, Giedrė

AU - Che, Jun

AU - Cheblal, Anais

AU - Elango, Rajula

AU - Epshtein, Anastasiya

AU - Fitzgerald, Devon M.

AU - Gómez-González, Belén

AU - Khan, Sharik R.

AU - Kumar, Sandeep

AU - Leland, Bryan A.

AU - Marie, Léa

AU - Mei, Qian

AU - Miné-Hattab, Judith

AU - Piotrowska, Alicja

AU - Polleys, Erica J.

AU - Putnam, Christopher D.

AU - Radchenko, Elina A.

AU - Saada, Anissia Ait

AU - Sakofsky, Cynthia J.

AU - Shim, Eun Yong

AU - Stracy, Mathew

AU - Xia, Jun

AU - Yan, Zhenxin

AU - Yin, Yi

AU - Aguilera, Andrés

AU - Argueso, Juan Lucas

AU - Freudenreich, Catherine H.

AU - Gasser, Susan M.

AU - Gordenin, Dmitry A.

AU - Haber, James E.

AU - Ira, Grzegorz

AU - Jinks-Robertson, Sue

AU - King, Megan C.

AU - Kolodner, Richard D.

AU - Kuzminov, Andrei

AU - Lambert, Sarah A.E.

AU - Lee, Sang Eun

AU - Miller, Kyle M.

AU - Mirkin, Sergei M.

AU - Petes, Thomas D.

AU - Rosenberg, Susan M.

AU - Rothstein, Rodney

AU - Symington, Lorraine S.

AU - Zawadzki, Pawel

AU - Kim, Nayun

AU - Lisby, Michael

AU - Malkova, Anna

N1 - Funding Information: HLK was supported by NIH grant R01-CA146940. AA was supported by the European research Council (ERC2014-ADG669898 TARLOOP), the Spanish Ministry of Economy and Competitiveness (BFU2016-75058-P), and the Junta de Andalucía (BIO1238). JLA was supported by NIH grant R35G-GM119788. CHF was supported by NIH grants P01-GM105473 and R01-GM122880. SMG was supported by the Swiss national Science Foundation and the Novartis Research Foundation. DAG was supported by National Institutes of Health (Intramural Research Program Project Z1AES103266. JEH was supported by NIH grants R35-GM127029 and P01-GM105473. GI was supported by NIH grants R01-GM125650 and R01-GM080600. SJ-R was supported by NIH grant R35-GM118077. MCK was supported by National Science Foundation Graduate Research Fellowship DGE-1122492, NIH training grant T32-GM007223 and NIH grant DP20D008429. RDK and CDP were supported by NIH grants R01-GM26017 and R01-GM50006. AK was supported by NIH grant R01-GM073115. SAEL was supported by grants from Agence Nationale de la Recherche ANR-14-CE10-0010-01 and the Foundation pour la Recherche Mé-dicale Equipe FRM DEQ20160334889. SEL was supported by NIH grant R01-GM071011. SMM was supported by NIH grants R01-GM60987 and P01-GM105473. TDP was supported by NIH grant R35-GM118020. SMR was supported by a gift from WM <eck Foundation ? NIH Director ?s ?ioneer Award DP1-CA174424 and NIH grant R35-GM122598. DMF was supported by the Cancer Prevention and Research Institute of Texas, Baylor College of Medicine Comprehensive Cancer Training Program Postdoctoral Fellowship RP160283. RR was supported by NIH grant R35-GM118180 and JM-H was supported by a Marie Curie International Outgoing Fellowship and the ANR-12-PDOC-0035-01. LSS was supported by NIH grant R35-GM126997. PZ was supported by National Science Centre Poland 2015/19/103859 and FNP First TEAM/2016-1/9. NK was supported by NIH grant R01-GM116007 and the Welch Foundation (AU1875). ML was supported by grants from the Danish Agency for Science, Technology and Innovation, the Villum Foundation and the Danish National Research Foundation (DNRF115). AM was supported by NIH grants R35-GM127006 and R03-ES029306. Publisher Copyright: © 2019 Klein et al.

PY - 2019/1

Y1 - 2019/1

N2 - 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.

AB - 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.

KW - Chromatin dynamics

KW - Chromosome rearrangements

KW - Crossovers

KW - DNA breaks

KW - DNA repair centers

KW - DNA resection

KW - DSBs

KW - Fluorescent proteins

KW - Gene amplification

KW - Gene conversion

KW - Genome instability

KW - Gross chromosome rearrangements

KW - Holliday junctions

KW - Homologous recombination

KW - Mitotic recombination

KW - Mutagenesis

KW - Pulsed field gel electrophoresis

KW - R-loops

KW - Replication fork stalling

KW - Single-particle tracking

KW - Sister chromatid recombination

KW - Sister repetitive sequences

KW - Site-specific chromosome breaks

KW - Toxic recombination intermediates

KW - Yeast artificial chromosome

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UR - http://www.scopus.com/inward/citedby.url?scp=85063010098&partnerID=8YFLogxK

U2 - 10.15698/mic2019.01.664

DO - 10.15698/mic2019.01.664

M3 - Review article

C2 - 30652105

AN - SCOPUS:85063010098

SN - 2311-2638

VL - 6

SP - 1

EP - 64

JO - Microbial Cell

JF - Microbial Cell

IS - 1

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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