A whole genome RNAi screen identifies replication stress response genes

Abstract

Proper DNA replication is critical to maintain genome stability. When the DNA replication machinery encounters obstacles to replication, replication forks stall and the replication stress response is activated. This response includes activation of cell cycle checkpoints, stabilization of the replication fork, and DNA damage repair and tolerance mechanisms. Defects in the replication stress response can result in alterations to the DNA sequence causing changes in protein function and expression, ultimately leading to disease states such as cancer. To identify additional genes that control the replication stress response, we performed a three-parameter, high content, whole genome siRNA screen measuring DNA replication before and after a challenge with replication stress as well as a marker of checkpoint kinase signalling. We identified over 200 replication stress response genes and subsequently analysed how they influence cellular viability in response to replication stress. These data will serve as a useful resource for understanding the replication stress response.

Efficient Pre-mRNA Cleavage Prevents Replication-Stress-Associated Genome Instability

“…Reassuringly, when ranked according to a Z score of cells in RC, the checkpoint kinase ATR, whose inhibition or partial depletion primes cells to undergo RC (Toledo et al., 2013) and which was used as positive control, scored highly with three out of three siRNAs (Figure 1D; Table S2). Gene ontology (GO) analysis of replication stress resilience modulators revealed that they were enriched for genes involved in DNA and RNA metabolism (Figure 1E), consistent with previous work (Kavanaugh et al., 2015, Paulsen et al., 2009). Interestingly, our data indicate that deregulated RNA metabolism can have both protective and sensitizing functions in the context of acute replication stress (Figures 1F and S1C), calling for detailed and gene-specific analyses of RNA processing factors and their roles in genome integrity maintenance.…”

Phosphoproteomics reveals novel modes of function and inter‐relationships among PIKKs in response to genotoxic stress

“…The wealth of information obtained through these screens can be further amplified if the data of these screens are collated, allowing prioritization of candidate DDR factors for in‐depth functional studies in view of their repeated appearance in screens. We constructed a database that contains manually curated information provided by the data of 34 such screens (Kolas et al , 2007; Matsuoka et al , 2007; Stokes et al , 2007; Lovejoy et al , 2009; Paulsen et al , 2009; Bennetzen et al , 2010; Bensimon et al , 2010; Chou et al , 2010; Hurov et al , 2010; O'Connell et al , 2010; O'Donnell et al , 2010; Piwko et al , 2010; Smogorzewska et al , 2010; Cotta‐Ramusino et al , 2011; Kondo & Perrimon, 2011; Menzel et al , 2011; Stirling et al , 2011; Adamson et al , 2012; Beli et al , 2012; Floyd et al , 2013; Jungmichel et al , 2013; Sirbu et al , 2013; Benzina et al , 2015; Boucas et al , 2015; Elia et al , 2015; Herr et al , 2015; Izhar et al , 2015; Kavanaugh et al , 2015; Raschle et al , 2015; Boeing et al , 2016; Kozlov et al , 2016; Lopez‐Saavedra et al , 2016; Baranes‐Bachar et al , 2018; Olivieri et al , 2020). Queries to this database provide a “profile” for a candidate protein according to the screens in which it was identified.…”

Chromosome instability caused by mutations in the genes involved in transcription and splicing

“…Interestingly, according to these results, the most significantly enriched pathway mediating genome instability includes proteins operating at different stages of mRNA processing, such as RNA splicing and spliceosome assembly [32]. In addition, genes important for transcription and RNA processing appear to be enriched among those genes responding to replication stress [33] (For comprehensive reviews, see [34]).…”