Strand-specific ChIP-seq at DNA breaks distinguishes ssDNA versus dsDNA binding and refutes single-stranded nucleosomes

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

Standard

Strand-specific ChIP-seq at DNA breaks distinguishes ssDNA versus dsDNA binding and refutes single-stranded nucleosomes. / Peritore, Martina; Reusswig, Karl Uwe; Bantele, Susanne C.S.; Straub, Tobias; Pfander, Boris.

In: Molecular Cell, Vol. 81, No. 8, 2021, p. 1841-1853.e4.

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

Harvard

Peritore, M, Reusswig, KU, Bantele, SCS, Straub, T & Pfander, B 2021, 'Strand-specific ChIP-seq at DNA breaks distinguishes ssDNA versus dsDNA binding and refutes single-stranded nucleosomes', Molecular Cell, vol. 81, no. 8, pp. 1841-1853.e4. https://doi.org/10.1016/j.molcel.2021.02.005

APA

Peritore, M., Reusswig, K. U., Bantele, S. C. S., Straub, T., & Pfander, B. (2021). Strand-specific ChIP-seq at DNA breaks distinguishes ssDNA versus dsDNA binding and refutes single-stranded nucleosomes. Molecular Cell, 81(8), 1841-1853.e4. https://doi.org/10.1016/j.molcel.2021.02.005

Vancouver

Peritore M, Reusswig KU, Bantele SCS, Straub T, Pfander B. Strand-specific ChIP-seq at DNA breaks distinguishes ssDNA versus dsDNA binding and refutes single-stranded nucleosomes. Molecular Cell. 2021;81(8):1841-1853.e4. https://doi.org/10.1016/j.molcel.2021.02.005

Author

Peritore, Martina ; Reusswig, Karl Uwe ; Bantele, Susanne C.S. ; Straub, Tobias ; Pfander, Boris. / Strand-specific ChIP-seq at DNA breaks distinguishes ssDNA versus dsDNA binding and refutes single-stranded nucleosomes. In: Molecular Cell. 2021 ; Vol. 81, No. 8. pp. 1841-1853.e4.

Bibtex

@article{40f96b2da3ab4a509f05bb74bbff4522,
title = "Strand-specific ChIP-seq at DNA breaks distinguishes ssDNA versus dsDNA binding and refutes single-stranded nucleosomes",
abstract = "In a first step of DNA double-strand break (DSB) repair by homologous recombination, DNA ends are resected such that single-stranded DNA (ssDNA) overhangs are generated. ssDNA is specifically bound by RPA and other factors, which constitutes a ssDNA-domain on damaged chromatin. The molecular organization of this ssDNA and the adjacent dsDNA domain is crucial during DSB signaling and repair. However, data regarding the presence of nucleosomes, the most basic chromatin components, in the ssDNA domain have been contradictory. Here, we use site-specific induction of DSBs and chromatin immunoprecipitation followed by strand-specific sequencing to analyze in vivo binding of key DSB repair and signaling proteins to either the ssDNA or dsDNA domain. In the case of nucleosomes, we show that recently proposed ssDNA nucleosomes are not a major, persistent species, but that nucleosome eviction and DNA end resection are intrinsically coupled. These results support a model of separated dsDNA-nucleosome and ssDNA-RPA domains during DSB repair.",
keywords = "DNA binding, DNA double-stranded breaks, DNA end resection, histone, homologous recombination, nucleosome, nucleosome remodeller, single-stranded DNA",
author = "Martina Peritore and Reusswig, {Karl Uwe} and Bantele, {Susanne C.S.} and Tobias Straub and Boris Pfander",
note = "Publisher Copyright: {\textcopyright} 2021 Elsevier Inc.",
year = "2021",
doi = "10.1016/j.molcel.2021.02.005",
language = "English",
volume = "81",
pages = "1841--1853.e4",
journal = "Molecular Cell",
issn = "1097-2765",
publisher = "Cell Press",
number = "8",

}

RIS

TY - JOUR

T1 - Strand-specific ChIP-seq at DNA breaks distinguishes ssDNA versus dsDNA binding and refutes single-stranded nucleosomes

AU - Peritore, Martina

AU - Reusswig, Karl Uwe

AU - Bantele, Susanne C.S.

AU - Straub, Tobias

AU - Pfander, Boris

N1 - Publisher Copyright: © 2021 Elsevier Inc.

PY - 2021

Y1 - 2021

N2 - In a first step of DNA double-strand break (DSB) repair by homologous recombination, DNA ends are resected such that single-stranded DNA (ssDNA) overhangs are generated. ssDNA is specifically bound by RPA and other factors, which constitutes a ssDNA-domain on damaged chromatin. The molecular organization of this ssDNA and the adjacent dsDNA domain is crucial during DSB signaling and repair. However, data regarding the presence of nucleosomes, the most basic chromatin components, in the ssDNA domain have been contradictory. Here, we use site-specific induction of DSBs and chromatin immunoprecipitation followed by strand-specific sequencing to analyze in vivo binding of key DSB repair and signaling proteins to either the ssDNA or dsDNA domain. In the case of nucleosomes, we show that recently proposed ssDNA nucleosomes are not a major, persistent species, but that nucleosome eviction and DNA end resection are intrinsically coupled. These results support a model of separated dsDNA-nucleosome and ssDNA-RPA domains during DSB repair.

AB - In a first step of DNA double-strand break (DSB) repair by homologous recombination, DNA ends are resected such that single-stranded DNA (ssDNA) overhangs are generated. ssDNA is specifically bound by RPA and other factors, which constitutes a ssDNA-domain on damaged chromatin. The molecular organization of this ssDNA and the adjacent dsDNA domain is crucial during DSB signaling and repair. However, data regarding the presence of nucleosomes, the most basic chromatin components, in the ssDNA domain have been contradictory. Here, we use site-specific induction of DSBs and chromatin immunoprecipitation followed by strand-specific sequencing to analyze in vivo binding of key DSB repair and signaling proteins to either the ssDNA or dsDNA domain. In the case of nucleosomes, we show that recently proposed ssDNA nucleosomes are not a major, persistent species, but that nucleosome eviction and DNA end resection are intrinsically coupled. These results support a model of separated dsDNA-nucleosome and ssDNA-RPA domains during DSB repair.

KW - DNA binding

KW - DNA double-stranded breaks

KW - DNA end resection

KW - histone

KW - homologous recombination

KW - nucleosome

KW - nucleosome remodeller

KW - single-stranded DNA

U2 - 10.1016/j.molcel.2021.02.005

DO - 10.1016/j.molcel.2021.02.005

M3 - Journal article

C2 - 33651987

AN - SCOPUS:85103342333

VL - 81

SP - 1841-1853.e4

JO - Molecular Cell

JF - Molecular Cell

SN - 1097-2765

IS - 8

ER -

ID: 263017049