ARS2 instructs early transcription termination-coupled RNA decay by recruiting ZC3H4 to nascent transcripts

The RNA-binding ARS2 protein is centrally involved in both early RNA polymerase II (RNAPII) transcription termination and transcript decay. Despite its essential nature, the mechanisms by which ARS2 enacts these functions have remained unclear. Here, we show that a conserved basic domain of ARS2 binds a corresponding acidic-rich, short linear motif in the transcription restriction factor ZC3H4. This interaction recruits ZC3H4 to chromatin to elicit Pol II termination, independent of other early termination pathways defined by the cleavage and polyadenylation (CPA) and Integrator (INT) complexes. ZC3H4, in turn, directly connects to the ZCCHC8 component of the nuclear exosome targeting (NEXT) complex, hereby facilitating rapid degradation of the nascent RNA. Hence, ARS2 instructs the coupled transcription termination and degradation of the transcript onto which it is bound. This contrasts with ARS2 function at CPA-instructed termination sites where the protein exclusively partakes in RNA suppression via post-transcriptional decay. Overall design: The ARS2 and ZC3H4 transcription termination factors were knocked down in HeLa cells using siRNA in presence or absence of ectopic expression of ARS2-WT or ZnF-mutant. The corresponding controls was the non-tageting EGFP siRNA knockdown. Two biological replicates were generated for each RNA-seq.