Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes

Hannah L. Klein; Kenny K.H. Ang; Michelle R. Arkin; Emily C. Beckwitt; Yi Hsuan Chang; Jun Fan; Youngho Kwon; Michael J. Morten; Sucheta Mukherjee; Oliver J. Pambos; Hafez El Sayyed; Elizabeth S. Thrall; João P. Vieira-Da-Rocha; Quan Wang; Shuang Wang; Hsin Yi Yeh; Julie S. Biteen; Peter Chi; Wolf Dietrich Heyer; Achillefs N. Kapanidis; Joseph J. Loparo; Terence R. Strick; Patrick Sung; Bennett Van Houten; Hengyao Niu; Eli Rothenberg

doi:10.15698/mic2019.01.665

Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes

Hannah L. Klein, Kenny K.H. Ang, Michelle R. Arkin, Emily C. Beckwitt, Yi Hsuan Chang, Jun Fan, Youngho Kwon, Michael J. Morten, Sucheta Mukherjee, Oliver J. Pambos, Hafez El Sayyed, Elizabeth S. Thrall, João P. Vieira-Da-Rocha, Quan Wang, Shuang Wang, Hsin Yi Yeh, Julie S. Biteen, Peter Chi, Wolf Dietrich Heyer, Achillefs N. KapanidisJoseph J. Loparo, Terence R. Strick, Patrick Sung, Bennett Van Houten, Hengyao Niu, Eli Rothenberg

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

8 Scopus citations

Abstract

Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool 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)	65-101
Number of pages	37
Journal	Microbial Cell
Volume	6
Issue number	1
DOIs	https://doi.org/10.15698/mic2019.01.665
State	Published - Jan 2019

Keywords

Chromatin dynamics
Chromosome rearrangements
Crossovers
DNA breaks
DNA helicases
DNA repair centers
DNA repair synthesis
DNA resection
DSBs
Double strand break repair
Endonuclease protection assay
FRET
Fluorescent proteins
Genome instability
Gross chromosome rearrangements
Homologous recombination
Mismatch repair
Nonhomologous end joining
Nucleotide excision repair
PALM
Photoactivated fluorescent proteins
Recombinase filament assembly
Single-molecule
Single-particle tracking
Structure-selective endonucleases
Super resolution
Synthesis-dependent strand annealing
Transcription coupled repair

ASJC Scopus subject areas

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

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10.15698/mic2019.01.665

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Klein, H. L., Ang, K. K. H., Arkin, M. R., Beckwitt, E. C., Chang, Y. H., Fan, J., Kwon, Y., Morten, M. J., Mukherjee, S., Pambos, O. J., Sayyed, H. E., Thrall, E. S., Vieira-Da-Rocha, J. P., Wang, Q., Wang, S., Yeh, H. Y., Biteen, J. S., Chi, P., Heyer, W. D., ... Rothenberg, E. (2019). Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes. Microbial Cell, 6(1), 65-101. https://doi.org/10.15698/mic2019.01.665

Klein, HL, Ang, KKH, Arkin, MR, Beckwitt, EC, Chang, YH, Fan, J, Kwon, Y, Morten, MJ, Mukherjee, S, Pambos, OJ, Sayyed, HE, Thrall, ES, Vieira-Da-Rocha, JP, Wang, Q, Wang, S, Yeh, HY, Biteen, JS, Chi, P, Heyer, WD, Kapanidis, AN, Loparo, JJ, Strick, TR, Sung, P, Van Houten, B, Niu, H & Rothenberg, E 2019, 'Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes', Microbial Cell, vol. 6, no. 1, pp. 65-101. https://doi.org/10.15698/mic2019.01.665

@article{89b72fb170fd4344902190a1dd6619e7,

title = "Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes",

abstract = "Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool 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 helicases, DNA repair centers, DNA repair synthesis, DNA resection, DSBs, Double strand break repair, Endonuclease protection assay, FRET, Fluorescent proteins, Genome instability, Gross chromosome rearrangements, Homologous recombination, Mismatch repair, Nonhomologous end joining, Nucleotide excision repair, PALM, Photoactivated fluorescent proteins, Recombinase filament assembly, Single-molecule, Single-particle tracking, Structure-selective endonucleases, Super resolution, Synthesis-dependent strand annealing, Transcription coupled repair",

author = "Klein, {Hannah L.} and Ang, {Kenny K.H.} and Arkin, {Michelle R.} and Beckwitt, {Emily C.} and Chang, {Yi Hsuan} and Jun Fan and Youngho Kwon and Morten, {Michael J.} and Sucheta Mukherjee and Pambos, {Oliver J.} and Sayyed, {Hafez El} and Thrall, {Elizabeth S.} and Vieira-Da-Rocha, {Jo{\~a}o P.} and Quan Wang and Shuang Wang and Yeh, {Hsin Yi} and Biteen, {Julie S.} and Peter Chi and Heyer, {Wolf Dietrich} and Kapanidis, {Achillefs N.} and Loparo, {Joseph J.} and Strick, {Terence R.} and Patrick Sung and {Van Houten}, Bennett and Hengyao Niu and Eli Rothenberg",

note = "Funding Information: HLK was supported by NIH grant R01-CA146940. JB acknowledges support from NIH grant R21-GM-128022-01. PC was supported by the Taiwan Ministry of Science and Technology grant MOST 105-2314-B-002-073-MY4. W-DH was supported by NIH grants R01-GM58015, R01-CA92276, DOD grant W81XWH-14-1-0435 and T32-GM099608 (SM). BVH was supported by NIH grants R01-ES019566 (BVH) and T32-GM088119 (ECB). ANK was supported by grants to ANK from the European Research Council (261227), the Wellcome Trust (110164/Z/15/Z), the UK BBSRC (BB/H01795X/1, BB/J00054X/1, and BB/N018656/1). JJL was funded by Nation- Funding Information: HLK was supported by NIH grant R01-CA146940. JB acknowledges support from NIH grant R21-GM-128022-01. PC was supported by the Taiwan Ministry of Science and Technology grant MOST 105-2314-B-002-073-MY4. W-DH was supported by NIH grants R01-GM58015, R01-CA92276, DOD grant W81XWH-14-1-0435 and T32-GM099608 (SM). BVH was supported by NIH grants R01-ES019566 (BVH) and T32-GM088119 (ECB). ANK was supported by grants to ANK from the European Research Council (261227), the Wellcome Trust (110164/Z/15/Z), the UK BBSRC (BB/H01795X/1, BB/J00054X/1, and BB/N018656/1). JJL was funded by National Institutes of Health grants R01 GM114065 (to JJL) and F32 GM113516 (to EST). TRS would like to acknowledge grants RepOne and PrTxConf (French ANR), NanoRep (Universit{\'e} PSL) as well as the {"}Equipe Labelis{\'e}e{"} program of the French League Against Cancer. PS was supported by NIH grant R01-ES00761. HN was supported by NIH grant R35-GM124765. ER is funded by grants from NIH: R01 GM108119, ACS: 130304-RSG-16-241-01-DMC and V Foundation for Cancer Research: D2018-020. Publisher Copyright: {\textcopyright} 2019 Klein et al.",

year = "2019",

month = jan,

doi = "10.15698/mic2019.01.665",

language = "English (US)",

volume = "6",

pages = "65--101",

journal = "Microbial Cell",

issn = "2311-2638",

publisher = "Shared Science Publishers OG",

number = "1",

}

TY - JOUR

T1 - Guidelines for DNA recombination and repair studies

T2 - Mechanistic assays of DNA repair processes

AU - Klein, Hannah L.

AU - Ang, Kenny K.H.

AU - Arkin, Michelle R.

AU - Beckwitt, Emily C.

AU - Chang, Yi Hsuan

AU - Fan, Jun

AU - Kwon, Youngho

AU - Morten, Michael J.

AU - Mukherjee, Sucheta

AU - Pambos, Oliver J.

AU - Sayyed, Hafez El

AU - Thrall, Elizabeth S.

AU - Vieira-Da-Rocha, João P.

AU - Wang, Quan

AU - Wang, Shuang

AU - Yeh, Hsin Yi

AU - Biteen, Julie S.

AU - Chi, Peter

AU - Heyer, Wolf Dietrich

AU - Kapanidis, Achillefs N.

AU - Loparo, Joseph J.

AU - Strick, Terence R.

AU - Sung, Patrick

AU - Van Houten, Bennett

AU - Niu, Hengyao

AU - Rothenberg, Eli

N1 - Funding Information: HLK was supported by NIH grant R01-CA146940. JB acknowledges support from NIH grant R21-GM-128022-01. PC was supported by the Taiwan Ministry of Science and Technology grant MOST 105-2314-B-002-073-MY4. W-DH was supported by NIH grants R01-GM58015, R01-CA92276, DOD grant W81XWH-14-1-0435 and T32-GM099608 (SM). BVH was supported by NIH grants R01-ES019566 (BVH) and T32-GM088119 (ECB). ANK was supported by grants to ANK from the European Research Council (261227), the Wellcome Trust (110164/Z/15/Z), the UK BBSRC (BB/H01795X/1, BB/J00054X/1, and BB/N018656/1). JJL was funded by Nation- Funding Information: HLK was supported by NIH grant R01-CA146940. JB acknowledges support from NIH grant R21-GM-128022-01. PC was supported by the Taiwan Ministry of Science and Technology grant MOST 105-2314-B-002-073-MY4. W-DH was supported by NIH grants R01-GM58015, R01-CA92276, DOD grant W81XWH-14-1-0435 and T32-GM099608 (SM). BVH was supported by NIH grants R01-ES019566 (BVH) and T32-GM088119 (ECB). ANK was supported by grants to ANK from the European Research Council (261227), the Wellcome Trust (110164/Z/15/Z), the UK BBSRC (BB/H01795X/1, BB/J00054X/1, and BB/N018656/1). JJL was funded by National Institutes of Health grants R01 GM114065 (to JJL) and F32 GM113516 (to EST). TRS would like to acknowledge grants RepOne and PrTxConf (French ANR), NanoRep (Université PSL) as well as the "Equipe Labelisée" program of the French League Against Cancer. PS was supported by NIH grant R01-ES00761. HN was supported by NIH grant R35-GM124765. ER is funded by grants from NIH: R01 GM108119, ACS: 130304-RSG-16-241-01-DMC and V Foundation for Cancer Research: D2018-020. Publisher Copyright: © 2019 Klein et al.

PY - 2019/1

Y1 - 2019/1

N2 - Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool 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 - Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool 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 helicases

KW - DNA repair centers

KW - DNA repair synthesis

KW - DNA resection

KW - DSBs

KW - Double strand break repair

KW - Endonuclease protection assay

KW - FRET

KW - Fluorescent proteins

KW - Genome instability

KW - Gross chromosome rearrangements

KW - Homologous recombination

KW - Mismatch repair

KW - Nonhomologous end joining

KW - Nucleotide excision repair

KW - PALM

KW - Photoactivated fluorescent proteins

KW - Recombinase filament assembly

KW - Single-molecule

KW - Single-particle tracking

KW - Structure-selective endonucleases

KW - Super resolution

KW - Synthesis-dependent strand annealing

KW - Transcription coupled repair

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U2 - 10.15698/mic2019.01.665

DO - 10.15698/mic2019.01.665

M3 - Review article

AN - SCOPUS:85062960597

SN - 2311-2638

VL - 6

SP - 65

EP - 101

JO - Microbial Cell

JF - Microbial Cell

IS - 1

ER -

Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes

Abstract

Keywords

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