PT  - JOURNAL ARTICLE
AU  - Louis-Alexandre Fournier
AU  - Arun Kumar
AU  - Theodore Smith
AU  - Edmund Su
AU  - Michelle Moksa
AU  - Martin Hirst
AU  - Peter C. Stirling
TI  - Global prediction of candidate R-loop binding and R-loop regulatory proteins
AID  - 10.1101/2021.08.09.454968
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.08.09.454968
4099  - http://biorxiv.org/content/early/2021/08/09/2021.08.09.454968.short
4100  - http://biorxiv.org/content/early/2021/08/09/2021.08.09.454968.full
AB  - In the past decade there has been a growing appreciation for R-loop structures as important regulators of the epigenome, telomere maintenance, DNA repair and replication. Given these numerous functions, dozens, or potentially hundreds, of proteins could serve as direct or indirect regulators of R-loop writing, reading, and erasing. In order to understand common properties shared amongst potential R-loop binding proteins (RLBPs) we mined published proteomic studies and distilled 10 features that were enriched in RLBPs compared to the rest of the proteome. We used these RLBP-specific features along with their amino acid composition to create a random forest classifier which predicts the likelihood of a protein to bind to R-loops. In parallel, we employed a whole-genome CRISPR screen coupled with flow-cytometry using the S9.6 monoclonal antibody to sort guide RNAs associated with induction of high S9.6 staining. Known R-loop regulating pathways such as splicing and DNA damage repair are highly enriched in our datasets, and we validate two new R-loop modulating proteins. Together these resources provide a reference to pursue analyses of novel R-loop regulatory proteins.Competing Interest StatementThe authors have declared no competing interest.