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Mol Cell. 2018 Oct 18;72(2):222-238.e11. doi: 10.1016/j.molcel.2018.08.047. Epub 2018 Oct 4.

Genome-wide Identification of Structure-Forming Repeats as Principal Sites of Fork Collapse upon ATR Inhibition.

Author information

1
Abramson Family Cancer Research Institute and Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
2
Department of Pathology and Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA.
3
Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA.
4
Lymphocyte Nuclear Biology, NIAMS, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
5
Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
6
Functional Genomics Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
7
Abramson Family Cancer Research Institute and Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: brownej@upenn.edu.

Abstract

DNA polymerase stalling activates the ATR checkpoint kinase, which in turn suppresses fork collapse and breakage. Herein, we describe use of ATR inhibition (ATRi) as a means to identify genomic sites of problematic DNA replication in murine and human cells. Over 500 high-resolution ATR-dependent sites were ascertained using two distinct methods: replication protein A (RPA)-chromatin immunoprecipitation (ChIP) and breaks identified by TdT labeling (BrITL). The genomic feature most strongly associated with ATR dependence was repetitive DNA that exhibited high structure-forming potential. Repeats most reliant on ATR for stability included structure-forming microsatellites, inverted retroelement repeats, and quasi-palindromic AT-rich repeats. Notably, these distinct categories of repeats differed in the structures they formed and their ability to stimulate RPA accumulation and breakage, implying that the causes and character of replication fork collapse under ATR inhibition can vary in a DNA-structure-specific manner. Collectively, these studies identify key sources of endogenous replication stress that rely on ATR for stability.

KEYWORDS:

AT-rich; ATR; DNA damage; DNA double-strand breaks; RPA; hairpin; inverted repeats; microsatellite; replication fork collapse; short tandem repeats

PMID:
30293786
PMCID:
PMC6407864
DOI:
10.1016/j.molcel.2018.08.047
[Indexed for MEDLINE]
Free PMC Article

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