Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae

Éva Hegedüs, Endre Kókai, P. Nánási, László Imre, László Halász, Rozenn Jossé, Zsuzsa Antunovics, Martin R. Webb, Aziz El Hage, Yves Pommier, Lóránt Székvölgyi, V. Dombrádi, Gábor Szabó

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Molecular combing and gel electrophoretic studies revealed endogenous nicks with free 3'OH ends at ∼100 kb intervals in the genomic DNA (gDNA) of unperturbed and G1-synchronized Saccharomyces cerevisiae cells. Analysis of the distribution of endogenous nicks by Nick ChIP-chip indicated that these breaks accumulated at active RNA polymerase II (RNAP II) promoters, reminiscent of the promoter-proximal transient DNA breaks of higher eukaryotes. Similar periodicity of endogenous nicks was found within the ribosomal rDNA cluster, involving every ∼10th of the tandemly repeated 9.1 kb units of identical sequence. Nicks were mapped by Southern blotting to a few narrow regions within the affected units. Three of them were overlapping the RNAP II promoters, while the ARS-containing IGS2 region was spared of nicks. By using a highly sensitive reverse-Southwestern blot method to map free DNA ends with 3'OH, nicks were shown to be distinct from other known rDNA breaks and linked to the regulation of rDNA silencing. Nicks in rDNA and the rest of the genome were typically found at the ends of combed DNA molecules, occasionally together with R-loops, comprising a major pool of vulnerable sites that are connected with transcriptional regulation.

Original languageEnglish
Pages (from-to)10649-10668
Number of pages20
JournalNucleic Acids Research
Volume46
Issue number20
DOIs
Publication statusPublished - Nov 16 2018

Fingerprint

Single-Stranded DNA Breaks
RNA Polymerase II
Ribosomal DNA
Saccharomyces cerevisiae
DNA
Southwestern Blotting
DNA Breaks
Periodicity
Southern Blotting
Eukaryota
Gels
Genome

ASJC Scopus subject areas

  • Genetics

Cite this

Hegedüs, É., Kókai, E., Nánási, P., Imre, L., Halász, L., Jossé, R., ... Szabó, G. (2018). Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae. Nucleic Acids Research, 46(20), 10649-10668. https://doi.org/10.1093/nar/gky743

Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae. / Hegedüs, Éva; Kókai, Endre; Nánási, P.; Imre, László; Halász, László; Jossé, Rozenn; Antunovics, Zsuzsa; Webb, Martin R.; El Hage, Aziz; Pommier, Yves; Székvölgyi, Lóránt; Dombrádi, V.; Szabó, Gábor.

In: Nucleic Acids Research, Vol. 46, No. 20, 16.11.2018, p. 10649-10668.

Research output: Contribution to journalArticle

Hegedüs, É, Kókai, E, Nánási, P, Imre, L, Halász, L, Jossé, R, Antunovics, Z, Webb, MR, El Hage, A, Pommier, Y, Székvölgyi, L, Dombrádi, V & Szabó, G 2018, 'Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae', Nucleic Acids Research, vol. 46, no. 20, pp. 10649-10668. https://doi.org/10.1093/nar/gky743
Hegedüs, Éva ; Kókai, Endre ; Nánási, P. ; Imre, László ; Halász, László ; Jossé, Rozenn ; Antunovics, Zsuzsa ; Webb, Martin R. ; El Hage, Aziz ; Pommier, Yves ; Székvölgyi, Lóránt ; Dombrádi, V. ; Szabó, Gábor. / Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae. In: Nucleic Acids Research. 2018 ; Vol. 46, No. 20. pp. 10649-10668.
@article{cc274836340046d8826866b23ff37deb,
title = "Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae",
abstract = "Molecular combing and gel electrophoretic studies revealed endogenous nicks with free 3'OH ends at ∼100 kb intervals in the genomic DNA (gDNA) of unperturbed and G1-synchronized Saccharomyces cerevisiae cells. Analysis of the distribution of endogenous nicks by Nick ChIP-chip indicated that these breaks accumulated at active RNA polymerase II (RNAP II) promoters, reminiscent of the promoter-proximal transient DNA breaks of higher eukaryotes. Similar periodicity of endogenous nicks was found within the ribosomal rDNA cluster, involving every ∼10th of the tandemly repeated 9.1 kb units of identical sequence. Nicks were mapped by Southern blotting to a few narrow regions within the affected units. Three of them were overlapping the RNAP II promoters, while the ARS-containing IGS2 region was spared of nicks. By using a highly sensitive reverse-Southwestern blot method to map free DNA ends with 3'OH, nicks were shown to be distinct from other known rDNA breaks and linked to the regulation of rDNA silencing. Nicks in rDNA and the rest of the genome were typically found at the ends of combed DNA molecules, occasionally together with R-loops, comprising a major pool of vulnerable sites that are connected with transcriptional regulation.",
author = "{\'E}va Heged{\"u}s and Endre K{\'o}kai and P. N{\'a}n{\'a}si and L{\'a}szl{\'o} Imre and L{\'a}szl{\'o} Hal{\'a}sz and Rozenn Joss{\'e} and Zsuzsa Antunovics and Webb, {Martin R.} and {El Hage}, Aziz and Yves Pommier and L{\'o}r{\'a}nt Sz{\'e}kv{\"o}lgyi and V. Dombr{\'a}di and G{\'a}bor Szab{\'o}",
year = "2018",
month = "11",
day = "16",
doi = "10.1093/nar/gky743",
language = "English",
volume = "46",
pages = "10649--10668",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "20",

}

TY - JOUR

T1 - Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae

AU - Hegedüs, Éva

AU - Kókai, Endre

AU - Nánási, P.

AU - Imre, László

AU - Halász, László

AU - Jossé, Rozenn

AU - Antunovics, Zsuzsa

AU - Webb, Martin R.

AU - El Hage, Aziz

AU - Pommier, Yves

AU - Székvölgyi, Lóránt

AU - Dombrádi, V.

AU - Szabó, Gábor

PY - 2018/11/16

Y1 - 2018/11/16

N2 - Molecular combing and gel electrophoretic studies revealed endogenous nicks with free 3'OH ends at ∼100 kb intervals in the genomic DNA (gDNA) of unperturbed and G1-synchronized Saccharomyces cerevisiae cells. Analysis of the distribution of endogenous nicks by Nick ChIP-chip indicated that these breaks accumulated at active RNA polymerase II (RNAP II) promoters, reminiscent of the promoter-proximal transient DNA breaks of higher eukaryotes. Similar periodicity of endogenous nicks was found within the ribosomal rDNA cluster, involving every ∼10th of the tandemly repeated 9.1 kb units of identical sequence. Nicks were mapped by Southern blotting to a few narrow regions within the affected units. Three of them were overlapping the RNAP II promoters, while the ARS-containing IGS2 region was spared of nicks. By using a highly sensitive reverse-Southwestern blot method to map free DNA ends with 3'OH, nicks were shown to be distinct from other known rDNA breaks and linked to the regulation of rDNA silencing. Nicks in rDNA and the rest of the genome were typically found at the ends of combed DNA molecules, occasionally together with R-loops, comprising a major pool of vulnerable sites that are connected with transcriptional regulation.

AB - Molecular combing and gel electrophoretic studies revealed endogenous nicks with free 3'OH ends at ∼100 kb intervals in the genomic DNA (gDNA) of unperturbed and G1-synchronized Saccharomyces cerevisiae cells. Analysis of the distribution of endogenous nicks by Nick ChIP-chip indicated that these breaks accumulated at active RNA polymerase II (RNAP II) promoters, reminiscent of the promoter-proximal transient DNA breaks of higher eukaryotes. Similar periodicity of endogenous nicks was found within the ribosomal rDNA cluster, involving every ∼10th of the tandemly repeated 9.1 kb units of identical sequence. Nicks were mapped by Southern blotting to a few narrow regions within the affected units. Three of them were overlapping the RNAP II promoters, while the ARS-containing IGS2 region was spared of nicks. By using a highly sensitive reverse-Southwestern blot method to map free DNA ends with 3'OH, nicks were shown to be distinct from other known rDNA breaks and linked to the regulation of rDNA silencing. Nicks in rDNA and the rest of the genome were typically found at the ends of combed DNA molecules, occasionally together with R-loops, comprising a major pool of vulnerable sites that are connected with transcriptional regulation.

UR - http://www.scopus.com/inward/record.url?scp=85056716023&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85056716023&partnerID=8YFLogxK

U2 - 10.1093/nar/gky743

DO - 10.1093/nar/gky743

M3 - Article

VL - 46

SP - 10649

EP - 10668

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 20

ER -