Loss of the yeast SR protein Npl3 alters gene expression due to transcription readthrough

Yeast Npl3 is a highly abundant RNA binding protein, related to metazoan SR proteins, with reported functions including transcription elongation, splicing and RNA 3’ end processing. To identify direct targets and functions for Npl3, we used UV crosslinking and analysis of cDNA (CRAC) to map precise RNA binding sites. Npl3 binds diverse RNA species, at sites indicative of roles in both early pre-mRNA processing and 3’ end formation on mRNAs and ncRNAs. Consistent with this, tiling array and RNAPII binding data revealed 3’ extended mRNA and snoRNA transcripts in the absence of Npl3. This reflected transcriptional readthrough by RNAPII, and extension and stabilization of cryptic unstable transcript (CUT) long noncoding RNAs. Transcription readthrough was widespread, often resulting in down-regulation of neighboring genes. We conclude that Npl3 is required for the formation of a termination-competent RNA, affecting both coding and noncoding RNAs. We assessed the role of Npl3 in transcription termination, by examining the RNA binding profile of Npl3, Nab3 and Rpo21in WT yeast, as well as Nab3 and Rpo21 in npl3∆ yeast. We have included replicates of each sample as well as an untagged 'BY' negative control