ARS2 is a general suppressor of pervasive transcription

Abstract

Termination of transcription is important for establishing gene punctuation marks. It is also critical for suppressing many of the pervasive transcription events occurring throughout eukaryotic genomes and coupling their RNA products to efficient decay. In human cells, the ARS2 protein has been implicated in such function as its depletion causes transcriptional read-through of selected gene terminators and because it physically interacts with the ribonucleolytic nuclear RNA exosome. Here, we study the role of ARS2 on transcription and RNA metabolism genome wide. We show that ARS2 depletion negatively impacts levels of promoter-proximal RNA polymerase II at protein-coding (pc) genes. Moreover, our results reveal a general role of ARS2 in transcription termination-coupled RNA turnover at short transcription units like snRNA-, replication-dependent histone-, promoter upstream transcript- and enhancer RNA-loci. Depletion of the ARS2 interaction partner ZC3H18 mimics the ARS2 depletion, although to a milder extent, whereas depletion of the exosome core subunit RRP40 only impacts RNA abundance post-transcriptionally. Interestingly, ARS2 is also involved in transcription termination events within first introns of pc genes. Our work therefore establishes ARS2 as a general suppressor of pervasive transcription with the potential to regulate pc gene expression.

SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis

“…Another type of transcripts that we and other teams observed in hen2-2 and se-2 plants are truncated or misprocessed transcripts spanning the first intron (14,15,35,68). Similar 5′ transcript derived from protein coding genes have also been observed in human cells depleted from ARS2 and result from premature transcription termination rather than from compromised splicing of full-length pre-mRNAs (19,34,69). However, both SE and ARS2 do interact with splicing factors.…”

A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome

“…Using S. cerevisiae, we demonstrated previously that pA +,À 4sU RNA samples contain nascent RNA 3 0 ends (Schmid et al, 2018), which was likely to also be the case with the data analyzed here. Even so, signals within the pA +,À 4sU RNA 3 0 end fraction were specifically increased upon both siRRP40 and siZCCHC8 treatment ( Figures 2B and S2D; see also below), despite the fact that RRP40 depletion does not significantly alter Pol II recruitment to PROMPT regions (Iasillo et al, 2017). Hence, we interpreted such increased signals to be due to post-transcriptional transcript stabilization.…”

Transcriptional control by premature termination: a forgotten mechanism

“…PAS mediated cleavage within internal exons appears a small fraction compared to introns, and leads to transcripts without a stop codon, which typically get rapidly degraded through the non-stop decay pathway [30], although in rare cases can result in truncated proteins [31]. PTT frequently occurs in the beginning of the first intron [32][33][34], partially ~ 5 ~ coinciding with a second Pol II stalling event at stable nucleosomes downstream of CpG island promoters [35]. This typically leads to unstable transcripts that undergo rapid degradation (see below).…”

“…In the case of short sense transcripts, while PAS usage allows for transcript cleavage, this might not lead to efficient polyadenylation. Another explanation for the instability of short transcripts is that the 3' entry site for the nuclear exosome in such transcripts is physically close to the 5' capped end of the ~ 6 ~ transcript which is bound by the cap-binding complex (CBC), known to contribute to exosomal decay, especially of some classes of ncRNAs [34,47,48].…”