Two distinct transcription termination modes dictated by promoters

Transcription termination determines the ends of transcriptional units and thereby ensures integrity of gene regulation. Here we perform genome-wide investigation of RNA polymerase II (Pol II) transcription termination in Caenorhabditis elegans and observe two distinct modes of termination. Whereas a subset of genes requires the exoribonuclease XRN2, a known termination factor, termination of other genes appears independent of, and refractory to, XRN2. Unexpectedly, promoters instruct the choice of termination mode, but XRN2-independent termination additionally requires a compatible region downstream of the 3’ end cleavage site. Hence, different termination mechanisms may affect different configurations of Pol II complexes dictated by promoters. RNAi-treated, polyA-selected RNA-seq data: 3 replicates of mock and xrn-2 RNAi were analyzed, 2 of which can be found under series GSE79994 (1 included here). ChIP-seq: 2 replicates of ChIP and input samples for each factor/condition were analyzed, including untagged (control) strains for XRN2 ChIP. RNAi-treated, ribosomal RNA-depleted RNA-seq: 2 replicates of xrn-2 RNAi and one replicate of mock were analyzed. TS-mutant RNA-seq: one replicate of WT and xrn-2(xe31) RNA per timepoint (hours after temperature shift) were analyzed. Timepoints 06h and 10h were re-sequenced at approximately 4-fold deeper coverage. Catalytic-dead mutant RNA-seq: one replicate of WT and xrn-2cd;xrn-2(xe31) RNA per timepoint (06h and 10h after temperature shift) were analyzed.