Cryptic introns in lncRNAs recruit conserved Pir2/ARS2 protein to promote gene repression [RIP-seq]

Long non-coding RNAs (lncRNAs) dynamically regulate gene expression during development and in response to environmental conditions. In S. pombe, lncRNAs repress the expression of nearby genes via a mechanism involving silencing effector proteins. In this study, we find that invasion of a lncRNA into the neighboring gene results in inclusion of a cryptic intron that is required for its repressive activity. We show that cryptic introns are targeted by the conserved protein Pir2/ARS2 in association with splicing factors, which provide a scaffold for the recruitment of RNA degradation factors and chromatin modifying activities. RIP-seq of untagged WT cells and Pir2-GFP.