Human snRNA genes use polyadenylation factors to promote efficient transcription termination

Abstract

RNA polymerase II transcribes both protein coding and non-coding RNA genes and, in yeast, different mechanisms terminate transcription of the two gene types. Transcription termination of mRNA genes is intricately coupled to cleavage and polyadenylation, whereas transcription of small nucleolar (sno)/small nuclear (sn)RNA genes is terminated by the RNA-binding proteins Nrd1, Nab3 and Sen1. The existence of an Nrd1-like pathway in humans has not yet been demonstrated. Using the U1 and U2 genes as models, we show that human snRNA genes are more similar to mRNA genes than yeast snRNA genes with respect to termination. The Integrator complex substitutes for the mRNA cleavage and polyadenylation specificity factor complex to promote cleavage and couple snRNA 3′-end processing with termination. Moreover, members of the associated with Pta1 (APT) and cleavage factor I/II complexes function as transcription terminators for human snRNA genes with little, if any, role in snRNA 3′-end processing. The gene-specific factor, proximal sequence element-binding transcription factor (PTF), helps clear the U1 and U2 genes of nucleosomes, which provides an easy passage for pol II, and the negative elongation factor facilitates termination at the end of the genes where nucleosome levels increase. Thus, human snRNA genes may use chromatin structure as an additional mechanism to promote efficient transcription termination in vivo.

DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes

“…Since inhibition of NELF, Integrator and P-TEFb all resulted in defective 3 0 processing and termination of the U1 gene (Figs 2 and 3), it is likely that these processes occur in a coordinated manner by a mechanism similar to that of protein-coding genes. This view is consistent with a recent study that suggested the coupling of transcription termination and 3 0 processing of U1 snRNA 39 .…”

Transcription termination and the control of the transcriptome: why, where and how to stop

“…No clear homologues or analogues of the Nrd1 and Nab3 components of the NNS complex have been described in metazoans. SETX is unlikely to be involved in transcription termination of genes encoding snRNAs because termination defects have not been seen in SETX-knockdown experiments 86,89 . Genes encoding snRNAs contain a conserved 13-16-nucleotide sequence element (termed the 3ʹ box) that is required both for 3ʹ end processing and for transcription termination.…”

“…As the INT complex is recruited through its interaction with the Ser7P CTD and recognizes the nascent RNA, the pattern of concurrent recognition of signals on the nascent RNA and the CTD is conserved for snRNA 3ʹ processing and termination. However, termination is unlikely to be triggered by cleavage of the nascent transcript through an XRN2-dependent torpedo mechanism 89 . Rather, release of the polymerase has been linked to the particular structure of these genes, with a nucleosome-depleted region that spans the whole transcription unit, and to the action of negative elongation factor (NELF), which is involved in promoter-proximal pausing for mRNA transcription 89,92 .…”

“…However, termination is unlikely to be triggered by cleavage of the nascent transcript through an XRN2-dependent torpedo mechanism 89 . Rather, release of the polymerase has been linked to the particular structure of these genes, with a nucleosome-depleted region that spans the whole transcription unit, and to the action of negative elongation factor (NELF), which is involved in promoter-proximal pausing for mRNA transcription 89,92 . A role for the cap-binding complex (CBC) and the associated factor ARS2 (also known as SRRT) has also been described in the termination of genes encoding snRNAs, which possibly involves the CFII factors CLP1 and PCF11 (REFS 89,93).…”

Termination of Transcription of Short Noncoding RNAs by RNA Polymerase II

“…Mutation of the human version is implicated in the neurodegenerative diseases ataxia oculomotor apraxia 2 (AOA2) and amyotrophic lateral sclerosis 4 (ALS4) (164, 165). The role of senataxin in the termination of small RNAs in mammals is unclear, especially given that the full NNS system seems poorly conserved and short noncoding transcripts tend to be carved out of larger precursor transcripts terminated by the conventional polyadenylation-coupled machinery (166). More recently, a role for senataxin in the unwinding of RNA hybridized to duplex DNA (R-loop) suggested a function for this protein in polyadenylation-coupled mRNA termination in mammalian cells (167).…”