CRISPR-Cas13d screens identifyKILR, a breast cancer risk-associated lncRNA that regulates DNA replication and repair

Abstract

Long noncoding RNAs (lncRNAs) have surpassed the number of protein-coding genes, yet the majority have no known function. We previously discovered >800 lncRNAs at regions identified by breast cancer genome-wide association studies (GWAS). Here, we performed a pooled CRISPR-Cas13d RNA knockdown screen to identify which of these lncRNAs altered cell proliferation. We found thatKILR,a lncRNA that functions as a tumor suppressor, safeguards breast cells against uncontrolled proliferation. The half-life ofKILRis significantly reduced by the risk haplotype, revealing an alternative mechanism by which variants alter cancer risk. We showed thatKILRsequesters RPA1, a subunit of the RPA complex, required for DNA replication and repair. ReducedKILRexpression promotes cell proliferation by increasing the available pool of RPA1 and the speed of DNA replication. Our findings confirm lncRNAs as mediators of breast cancer risk, emphasize the need to annotate noncoding transcripts in relevant cell types when investigating GWAS variants and provide a scalable platform for mapping phenotypes associated with lncRNAs.