Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes

Baejen, Carlo; Andréani, Jessica; Torkler, Phillipp; Battaglia, Sofia; Schwalb, Björn; Lidschreiber, Michael; Maier, Kerstin; Boltendahl, Andrea; Rus, Petra; Esslinger, Stephanie; Söding, Johannes; Cramer, Patrick

doi:10.1016/j.molcel.2017.02.009

Cited by 108 publications

(151 citation statements)

References 86 publications

(129 reference statements)

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“…At the same time, because XRN2 inactivation does not fully prevent but only delays termination in human cells and because Rat1p depletion in yeast caused globally less severe termination defects than depletion of CPFs, alternative termination mechanisms have been speculated to compensate partially for loss of XRN2 (Fong et al 2015;Baejen et al 2017). Here, we provide direct evidence for the operation of an XRN2-independent pathway of transcriptional termination in Caenorhabditis elegans.…”

mentioning

confidence: 71%

“…Since recent studies revealed that loss of XRN2/Rat1p activities caused global termination defects in yeast and human cells (Fong et al 2015;Baejen et al 2017), it seems possible that termination in C. elegans might differ from that in previously studied systems. For instance, termination on genes with fast elongation rates requires distances of several kilobases past pA signal in human cells (Fong et al 2015).…”

Section: Discussionmentioning

confidence: 99%

“…Although transcription termination can occur in vitro without transcript cleavage at the pA site (Zhang et al 2015), recent transcriptomics studies led to the conclusion that XRN2/Rat1p are broadly important for efficient transcription termination in human cells (Fong et al 2015) and budding yeast (Baejen et al 2017). At the same time, because XRN2 inactivation does not fully prevent but only delays termination in human cells and because Rat1p depletion in yeast caused globally less severe termination defects than depletion of CPFs, alternative termination mechanisms have been speculated to compensate partially for loss of XRN2 (Fong et al 2015;Baejen et al 2017).…”

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confidence: 99%

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Two distinct transcription termination modes dictated by promoters

2017

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Transcription termination determines the ends of transcriptional units and thereby ensures the integrity of the transcriptome and faithful gene regulation. Studies in yeast and human cells have identified the exoribonuclease XRN2 as a key termination factor for protein-coding genes. Here we performed a genome-wide investigation of RNA polymerase II (Pol II) transcription termination in XRN2-deficient Caenorhabditis elegans and observed two distinct modes of termination. Although a subset of genes requires XRN2, termination of other genes appears both independent of, and refractory to, XRN2. XRN2 independence is not merely a consequence of failure to recruit XRN2, since XRN2 is present on-and promotes Pol II accumulation near the polyadenylation sites of-both gene classes. Unexpectedly, promoters instruct the choice of termination mode, but XRN2-independent termination additionally requires a compatible region downstream from the 3 ′ end cleavage site. Hence, different termination mechanisms may work with different configurations of Pol II complexes dictated by promoters.

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confidence: 71%

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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Two distinct transcription termination modes dictated by promoters

2017

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“…Its homolog, Rat1, was simultaneously found to promote termination more widely in budding yeast (Kim et al 2004), with recent transcriptome-wide analysis supporting this finding (Baejen et al 2017). The broader role of Xrn2 in human cells has been less clear.…”

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confidence: 99%

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

et al. 2018

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Termination is a ubiquitous phase in every transcription cycle but is incompletely understood and a subject of debate. We 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 (cleavage and polyadenylation specificity factor 73). The ability to rapidly control Xrn2 reveals a clear and general role for it in cotranscriptional degradation of 3 ′ flanking region RNA and transcriptional termination. This defect is characterized genome-wide at high resolution using mammalian 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 small nuclear RNA (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 cotranscriptional degradation of polymerase-associated RNA by Xrn2. However, as CPSF73 loss caused more extensive readthrough transcription than Xrn2 elimination, it likely plays a more underpinning role in termination.

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“…RNA interference (RNAi) of the human 5ʹ-3ʹ exonuclease, Xrn2, or mutation of its budding yeast equivalent, Rat1, was originally shown to disrupt termination on transfected plasmids and endogenous genes respectively [6,7]. Although the role of Rat1 was recently re-affirmed [8], RNAi of Xrn2 did not reveal a general termination defect at the 3ʹ end of protein-coding genes [9]. However, termination was subsequently shown to be affected when a catalytically inactive version of Xrn2 is expressed in an RNAi background [10].…”

Section: Overviewmentioning

confidence: 99%