Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity

Termination is a ubiquitous phase in every transcription cycle but is incompletely understood and a subject of debate. We have used gene editing as a new approach to address its mechanism through engineered conditional depletion of the 5’-3’ exonuclease, Xrn2, or the polyadenylation signal (PAS) endonuclease, CPSF73. The ability to rapidly control Xrn2 reveals a clear and general role for it in co-transcriptional degradation of 3’ flanking region RNA and transcriptional termination. This defect is characterised genome-wide, at high resolution, using native elongating transcript sequencing (mNET-seq). An Xrn2 effect on termination requires prior RNA cleavage and we provide evidence for this by showing that catalytically inactive CPSF73 cannot restore termination to cells lacking functional CPSF73. Notably, Xrn2 plays no significant role in either Histone or snRNA gene termination even though both RNA classes undergo 3’ end cleavage. In sum, efficient termination on most protein-coding genes involves CPSF73 mediated RNA cleavage and co-transcriptional degradation of polymerase-associated RNA by Xrn2. However, as CPSF73 loss caused more extensive read-through transcription than Xrn2 elimination, it likely plays a more underpinning role in termination. We performed total CTD mNET-seq and nuclear RNA-seq with auxin-inducible degron(AID) tagged cell lines treated with or without auxin to induce rapid depletion of XRN2. Cell lines ectopically express TIR1 from a sleeping beauty transposon inserted cassette. AID tagged proteins contain the inframe insertion of AID tag, P2A cleavage site, antibiotic resistance marker and SV40 polyA site. Two repair templates containing different antibiotic resistance markers (hygromycin and neomycin) were used to ensure biallelic insertion of the cassette by CRISPR/Cas9.