Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo

Žumer, Kristina; Maier, Kerstin; Farnung, Lucas; Jaeger, Martin G.; Rus, Petra; Ciulli, Alessio; Cramer, Patrick

doi:10.1016/j.molcel.2021.05.028

Cited by 72 publications

(65 citation statements)

References 103 publications

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“…As further evaluation of the role of upstream gene elongation in the accumulation of Pol2 in STIRs, we also examined the consequences of loss of Spt6 and Rtf1, two factors reported to separately control Pol2 progression. We used mNET‐seq data from K562 following Spt6 and Rtf1 depletion from (Žumer et al , 2021 ) and examined Pol2 distribution within STIRs (Fig EV4 ). Spt6 was shown to assist progression of elongating Pol2 through nucleosomes, and its depletion was shown to have little to no effect on Pol2 accumulated at promoters (Žumer et al , 2021 ).…”

Section: Resultsmentioning

confidence: 99%

“…We used mNET‐seq data from K562 following Spt6 and Rtf1 depletion from (Žumer et al , 2021 ) and examined Pol2 distribution within STIRs (Fig EV4 ). Spt6 was shown to assist progression of elongating Pol2 through nucleosomes, and its depletion was shown to have little to no effect on Pol2 accumulated at promoters (Žumer et al , 2021 ). Indeed, data in K562 recapitulated the pattern we observed in HeLa cells, showing strong accumulation of Pol2 in STIRs in control conditions (DMSO‐treated cells).…”

Section: Resultsmentioning

confidence: 99%

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Unique features of transcription termination and initiation at closely spaced tandem human genes

Nissani

Ulitsky

2022

Molecular Systems Biology

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The synthesis of RNA polymerase II (Pol2) products, which include messenger RNAs or long noncoding RNAs, culminates in transcription termination. How the transcriptional termination of a gene impacts the activity of promoters found immediately downstream of it, and which can be subject to potential transcriptional interference, remains largely unknown. We examined in an unbiased manner the features of the intergenic regions between pairs of ‘tandem genes’—closely spaced (< 2 kb) human genes found on the same strand. Intergenic regions separating tandem genes are enriched with guanines and are characterized by binding of several proteins, including AGO1 and AGO2 of the RNA interference pathway. Additionally, we found that Pol2 is particularly enriched in this region, and it is lost upon perturbations affecting splicing or transcriptional elongation. Perturbations of genes involved in Pol2 pausing and R loop biology preferentially affect expression of downstream genes in tandem gene pairs. Overall, we find that features associated with Pol2 pausing and accumulation rather than those associated with avoidance of transcriptional interference are the predominant driving force shaping short tandem intergenic regions.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Unique features of transcription termination and initiation at closely spaced tandem human genes

Nissani

Ulitsky

2022

Molecular Systems Biology

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“…However, transcription then rapidly attenuated within the CGI in a region ∼500-1500 bp downstream of the TSS, and this tended to be skewed towards the 3’ boundary of the CGI (Fig.4f-g). Given that we did not observe accumulation of RNA Pol II in the promoter region or the body of SET1-dependent genes in RNA Pol II cChIP-seq after SET1 protein depletion, the reduction in transcription does not appear to be due to increased promoter proximal pausing or reduced elongation rate in the gene body (Fig.4d) 86 . Therefore, we propose that the observed attenuation of transcription is likely caused by premature transcription termination (PTT), which would be consistent with largely unaffected promoter-proximal occupancy of RNA Pol II and a reduction of RNA Pol II in the body of SET1-dependent genes.…”

Section: Resultsmentioning

confidence: 75%

A CpG island-encoded mechanism protects genes from premature transcription termination

Hughes

Szczurek

Kelley

et al. 2022

Preprint

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Transcription must be highly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, we reveal that actively transcribed CpG island-associated gene promoters recruit SET1 chromatin modifying complexes to enable gene expression. Counterintuitively, this effect is independent of SET1 complex histone modifying activity, and instead relies on the capacity of these complexes to interact with the RNA Polymerase II-binding protein, WDR82. Unexpectedly, we discover that SET1 complexes sustain gene transcription by counteracting the activity of the ZC3H4/WDR82 protein complex, which we show can pervasively terminate both genic and extragenic transcription. Therefore, we discover a new gene regulatory mechanism whereby CpG island elements nucleate a protein complex that protects genic transcription from premature termination, effectively distinguishing genic from non-genic transcription to enable gene expression.

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“…Spt6 is an essential, conserved member of the Pol II elongation complex whose occupancy on chromatin correlates with that of Pol II (3,4,37,38). Spt6 promotes transcription elongation (17,87,88,97), interacts with histones and a co-regulatory protein Spn1 (98)(99)(100)(101), stimulates Set2-mediated H3K36me3 (102)(103)(104), and functions as a histone chaperone to maintain chromatin integrity on active genes (86,105,106). To our knowledge, our results are the first demonstration of a direct interaction between Cdc73 and Spt6, with the exception of a small number of chemically induced crosslinks between Spt6 and Cdc73 within the reconstituted human active elongation complex (4).…”

Section: Discussionmentioning

confidence: 99%

Spt6 directly interacts with Cdc73 and is required for Paf1C recruitment to active genes

Ellison

Blacksmith

Namjilsuren

et al. 2022

Preprint

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Paf1C is a conserved transcription elongation factor that regulates transcription elongation efficiency, facilitates co-transcriptional histone modifications, and impacts molecular processes linked to RNA synthesis, such as polyA site selection. Coupling of the activities of Paf1C to transcription elongation requires its association with RNA polymerase II (Pol II). Mutational studies in yeast identified Paf1C subunits Cdc73 and Rtf1 as important mediators of Paf1C recruitment to Pol II on active genes. While the interaction between Rtf1 and the general elongation factor Spt5 is relatively well-understood, the interactions involving Cdc73 remain to be elucidated. Using an in vivo site-specific protein cross-linking strategy, we identified direct interactions between Cdc73 and two components of the elongation complex, the elongation factor Spt6 and the largest subunit of Pol II. Through in vitro protein binding assays and crosslinking/mass spectrometry, we show that Cdc73 and Spt6 can interact in the absence of additional factors and propose a binding interface. Rapid depletion of Spt6 dissociated Paf1 from chromatin and altered patterns of Paf1C-dependent histone modifications genome-wide. These results reveal previously unrecognized interactions between Cdc73 and the Pol II elongation complex and identify Spt6 as a key factor contributing to Paf1C recruitment to active genes in Saccharomyces cerevisiae.

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Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo

Cited by 72 publications

References 103 publications

Unique features of transcription termination and initiation at closely spaced tandem human genes

Unique features of transcription termination and initiation at closely spaced tandem human genes

A CpG island-encoded mechanism protects genes from premature transcription termination

Spt6 directly interacts with Cdc73 and is required for Paf1C recruitment to active genes

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