Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination

Abstract

SummaryWe present a molecular dissection of pause site-dependent transcriptional termination for mammalian RNA polymerase II (Pol II)-transcribed genes. We show that nascent transcripts form RNA/DNA hybrid structures (R-loops) behind elongating Pol II and are especially prevalent over G-rich pause sites positioned downstream of gene poly(A) signals. Senataxin, a helicase protein associated with AOA2/ALS4 neurodegenerative disorders, acts to resolve these R-loop structures and by so doing allows access of the 5′–3′ exonuclease Xrn2 at 3′ cleavage poly(A) sites. This affords 3′ transcript degradation and consequent Pol II termination. In effect, R-loops formed over G-rich pause sites, followed by their resolution by senataxin, are key steps in the termination process.

Sen1 has unique structural features grafted on the architecture of the Upf1‐like helicase family

“…Analogously to S. cerevisiae Sen1, the human orthologue SETX has been proposed to play crucial roles in transcription termination and in the maintenance of genome integrity (Suraweera et al , 2009; Skourti‐Stathaki et al , 2011; Zhao et al , 2016). In line with its biological importance, mutations in SETX have been linked to two neurological disorders: ALS4 and AOA2.…”

“…Disease mutations cluster in the two most conserved regions of SETX, the N‐terminal domain and the helicase domain. Like its yeast orthologue, SETX has been assigned functions in transcription termination and in the control of R‐loop formation (Suraweera et al , 2009; Skourti‐Stathaki et al , 2011; Zhao et al , 2016). …”

LncRNAs: Bridging environmental sensing and gene expression

“…Resolution of R-loops in vivo would be accomplished by the activity of endogenous RNase H enzymes as well as RNA-DNA helicases such as Sen1/Senataxin. 70,76,77 It is also likely that these R-loops are cleared by transcription of another lncRNA molecule. The latter is supported by the fact that high levels of transcription correlate with the presence of R-loops in wild type cells, 78 which would be predicted to interfere with transcription if these structures were static.…”

An end in sight? Xrn2 and transcriptional termination by RNA polymerase II

“…The existence of auxiliary termination mechanisms would be reminiscent of fail-safe termination in budding yeast where, for example, compromising Rat1 leads to termination via the Nrd1 pathway [17]. Although the human equivalent of Nrd1 is not described, SETX is similar to the Nrd1-associating RNA:DNA helicase, Sen1, and is proposed to assist Xrn2 in termination [18]. …”