RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons.

ABSTRACT: While RNA-seq has enabled comprehensive quantification of alternative splicing, no correspondingly high-throughput assay exists for functionally interrogating individual isoforms. We describe pgFARM (paired guide RNAs for alternative exon removal), a CRISPR-Cas9-based method to manipulate isoforms independent of gene inactivation. This approach enabled rapid suppression of exon recognition in polyclonal settings to identify functional roles for individual exons, such as an SMNDC1 cassette exon that regulates pan-cancer intron retention. We generalized this method to a pooled screen to measure the functional relevance of 'poison' cassette exons, which disrupt their host genes' reading frames yet are frequently ultraconserved. Many poison exons were essential for the growth of both cultured

SUBMITTER: Thomas JD 

PROVIDER: S-EPMC6962552 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature