Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast

Termination of RNA polymerase II (RNAPII) transcription is a fundamental step of gene expression that is critical for determining the borders between genes. In budding yeast, termination at protein-coding genes is initiated by the cleavage/polyadenylation machinery, whereas termination of most noncoding RNA (ncRNA) genes occurs via the Nrd1-Nab3-Sen1 (NNS) pathway. Unexpectedly, we show here that NNS-like transcription termination is not conserved in fission yeast. Instead, genome-wide location analyses show global recruitment of mRNA 3’ end processing factors at the end of ncRNA genes, including snoRNAs and snRNAs, and that this recruitment coincides with high levels of Ser2 and Tyr1 phosphorylation on the RNAPII C-terminal domain. We further show that termination of mRNA and ncRNA transcription requires the conserved Ysh1/CPSF-73 and Dhp1/XRN2 nucleases, supporting widespread cleavage-dependent transcription termination in fission yeast. Our findings thus reveal that a common mode of transcription termination can produce functionally and structurally distinct types of polyadenylated and non-polyadenylated RNAs. Exp1: Rpb1 ChIP-seq in WT and 4 NNS mutants. Exp2: ChIP-seq of Rpb1, RNApolII CTD modifications and 3' end processing factors in WT cells. Exp3: ChIP-seq of Rpb1 and Rpb3 in WT and dhp1-depleted cells using S. cerevisiae as spike-in. Exp4: ChIP-seq of RNApolII CTD modification in WT and dhp1-depleted cells using S. cerevisiae spike-in. Exp5: ChIP-seq of Rpb1 in WT and ysh1-depleted cells using S. cerevisiae as spike-in