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

• Published in: Molecular cell Vol. 72; no. 2; pp. 222 - 238.e11
• Main Authors: Shastri, Nishita, Tsai, Yu-Chen, Hile, Suzanne, Jordan, Deondre, Powell, Barrett, Chen, Jessica, Maloney, Dillon, Dose, Marei, Lo, Yancy, Anastassiadis, Theonie, Rivera, Osvaldo, Kim, Taehyong, Shah, Sharvin, Borole, Piyush, Asija, Kanika, Wang, Xiang, Smith, Kevin D., Finn, Darren, Schug, Jonathan, Casellas, Rafael, Yatsunyk, Liliya A., Eckert, Kristin A., Brown, Eric J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 18.10.2018
• Subjects: Animals; AT-rich; Ataxia Telangiectasia Mutated Proteins - antagonists & inhibitors; Ataxia Telangiectasia Mutated Proteins - genetics; ATR; Cell Cycle Proteins - genetics; Chromatin - genetics; Chromatin Immunoprecipitation - methods; DNA Breaks, Double-Stranded; DNA damage; DNA Damage - genetics; DNA double-strand breaks; DNA Replication - genetics; Female; Genomic Instability - genetics; hairpin; Humans; inverted repeats; Mice; microsatellite; Microsatellite Repeats - genetics; replication fork collapse; Replication Protein A - genetics; RPA; short tandem repeats; RPA; short tandem repeats; inverted repeats; DNA damage; microsatellite; hairpin; replication fork collapse; DNA double-strand breaks; AT-rich; ATR
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2018.08.047

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. [Display omitted] •>500 ATR-dependent sites were identified in the mouse and human genomes•ATR-inhibitor-driven fork collapse occurs primarily at structure-forming repeats•Repeat structures include non-B form DNA and hairpins (AT-rich and inverted repeats)•Discrete repeat types accumulate RPA differentially upon fork collapse Shastri et al. have identified new classes of difficult-to-replicate sequences in the mouse and human genomes that are highly dependent on ATR function for stability during DNA replication. Structure-forming short tandem repeats, inverted retroelements, and quasi-palindromic AT-rich repeats characterize the sites for fork collapse caused by ATR inhibition.