Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

Core, Leighton J.; Adelman, Karen

doi:10.1101/gad.325142.119

Cited by 408 publications

(453 citation statements)

References 228 publications

(354 reference statements)

Supporting

Mentioning

435

Contrasting

Unclassified

Order By: Relevance

“…During neuronal differentiation, poised Pol II primes neuronal transcription factors for activation whilst keeping non-neuronal genes silenced (Ferrai et al, 2017). Poised Pol II may experience high levels of backtracking due to increased GC content, specific promoter elements or chromatin configuration (Core and Adelman, 2019;Gomez-Herreros et al, 2012); PHF3 would prevent efficient TFIIS-mediated rescue from backtracking and induce premature termination. Reactivation of these genes would thus be highly dependent on TFIIS, which may be the reason for their marked de-repression in PHF3 KO cells where TFIIS would gain more access to Pol II.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

PHF3 regulates neuronal gene expression through the new Pol II CTD reader domain SPOC

Appel

Franke

Bruno

et al. 2020

Preprint

View full text Add to dashboard Cite

The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a new CTDbinding factor that negatively regulates transcription and mRNA stability. The PHF3 SPOC domain preferentially binds to CTD repeats phosphorylated on Serine-2 and PHF3 tracks with Pol II across the length of genes. PHF3 competes with TFIIS for Pol II binding through its TFIIS-like domain (TLD), thus inhibiting TFIIS-mediated rescue of backtracked Pol II. PHF3 knock-out or PHF3 SPOC deletion in human cells result in gene upregulation and a global increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 is a prominent effector of neuronal gene regulation at the interface of transcription elongation and mRNA decay.

show abstract

Section: Discussionmentioning

confidence: 99%

“…Transcription is a highly regulated process of RNA Polymerase II (Pol II) recruitment, initiation, pausing, elongation and termination (Chen et al, 2018;Core and Adelman, 2019;Kwak and Lis, 2013).…”

Section: Introductionmentioning

confidence: 99%

PHF3 regulates neuronal gene expression through the new Pol II CTD reader domain SPOC

Appel

Franke

Bruno

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Recent advances in the field of transcription regulation point to the fact that activation of paused genes is mediated through switching from a premature termination state of Pol II at PPP sites to a processive elongation state 13,16,17 , implying that continuous initiation is required for fast transcriptional induction 16 . Our results, showing that persistent initiation guarantees a prolonged transcription-coupled NER, are functionally linked to the fact that DNA damage-triggered widespread PPP release of a given Pol II is sufficient to drive immediate initiation of the next Pol II (see Fig.…”

Section: Discussionmentioning

confidence: 99%

“…After elongation of ∼30-60 nucleotides of initiation-associated RNAs (or TSS-associated RNAs), so-called start-RNAs 10,11 , Pol II is paused at PPP sites by negative elongation factors DSIF and NELF 2,12 . Signal-regulated phosphorylation of these factors and of serine 2 residue (S2P) of Pol II CTD by P-TEFb is required for productive elongation [13][14][15] . It recently emerged that, if this step does not occur rapidly, start-RNAs are terminated 14,16 , implying that Pol II turnover at PPP sites is high and that replenishment of Pol II engaged in early transcription is achieved by the continuous re-entry of pre-initiating Pol II into PICs 16,17 .…”

Section: Introductionmentioning

confidence: 99%

Continuous transcription initiation guarantees robust repair of transcribed genes and regulatory regions in response to DNA damage

Liakos

Konstantopoulos

Lavigne³

et al. 2019

Preprint

View full text Add to dashboard Cite

Inhibition of RNA synthesis caused by DNA damage-impaired RNA polymerase II (Pol II) elongation is found to conceal a local increase in de novo transcription, slowly progressing from Transcription Start Sites (TSSs) to gene ends. Although associated with accelerated repair of Pol II-encountered lesions and limited mutagenesis, it is still unclear how this mechanism is maintained during recovery from genotoxic stress. Here we uncover a surprising widespread gain in chromatin accessibility and preservation of the active histone mark H3K27ac after UV-irradiation. We show that the concomitant increase in Pol II release from promoter-proximal pause (PPP) sites of most active genes, PROMoter uPstream Transcripts (PROMPTs) and enhancer RNAs (eRNAs) favors unrestrained initiation, as demonstrated by the synthesis of short nascent RNAs, including TSSassociated RNAs (start-RNAs). In accordance, drug-inhibition of the transition into elongation replenished the post-UV reduced levels of pre-initiating pol II at TSSs. Continuous engagement of new Pol II thus ensures maximal transcription-driven DNA repair of active genes and non-coding regulatory loci. Together, our results reveal an unanticipated layer regulating the UV-triggered transcriptional-response and provide physiologically relevant traction to the emerging concept that transcription initiation rate is determined by pol II pauserelease dynamics.

show abstract

“…This is consistent with the CMV genome in vivo which displays pausing at all viral promoters but is not packaged into chromatin 40 . The positioning of a nucleosome downstream of the paused pol II never strongly supported that interpretation either 13 .…”

Section: Recapitulation Of Rna Pol II Pausingmentioning

confidence: 95%

Establishment of a Human RNA Pol II Pausing System and the Identification of O-GlcNAc Cycling Regulating Pol II Pausing and Elongation

Lewis

Levens

2020

Preprint

View full text Add to dashboard Cite

RNA polymerase II pausing is the major regulatory point in transcription in higher eukaryotes.Despite considerable knowledge of the general transcriptional machinery that are required to recruit RNA pol II to a promoter, much less is known how a paused RNA pol II is established and its release regulated, and the entirety of the machinery is likely not known. In part, this is due to the absence of an appropriate biochemical system that functionally recapitulates RNA pol II pausing and elongation and with which the pausing machinery can be identified. We describe herein a cell-free system (CFS) derived from HeLa cells that recapitulates pausing and elongation events known to occur in vivo. We have used this system to show that O-GlcNAc transferase (OGT) activity is required to establish a paused pol II, without which RNA pol II does not pause and instead enters productive elongation. Coupled with previous observations we show that both O-GlcNAc addition and removal are functionally required for pausing and elongation, respectively. Furthermore, the CFS offers significant inroads into understanding RNA pol II pausing and its regulation. technologies and genome-wide studies have shown that a significant majority of promoters, from Drosophila to humans, are regulated not at PIC formation but at the paused pol II step 4 . Thus, it is important to understand the nature and regulation of the paused pol II both as a fundamental problem and because many diseases are now considered "diseases of uncontrolled transcriptional elongation" 5 .A paused pol II is thought to be established by two factors, DSIF and NELF, that together bind to pol II and effectively misalign the active site of pol II from the DNA template preventing nucleotide incorporation and elongation 6-8 . Pol II release occurs via the phosphorylation of DSIF and NELF by P-TEFb, after which NELF is lost, and the polymerase moves into a productive elongation state 9 . More recently, another catalytic activity was found to participate in pol II release, poly-ADP ribose polymerase 1 (PARP-1) 10 .Nevertheless, our understanding of the establishment of a paused polymerase is incomplete. The addition of purified DSIF and NELF does not establish a paused pol II, but only slows its elongation rate 6,7,11,12 . We also do not understand mechanistically how pausing is established or released, now that PARP-1 and OGA are likely regulating these events along with CDK7 and CDK9. These data imply then that additional factors are required to establish a paused pol II. A human cell-free system that recapitulates pol II pausing would enable dissection of the pausing machinery and the sequence of reactions that regulate pause establishment and release 13 . Removal of the O-GlcNAc post-translational modification by the O-GlcNAc aminidase (OGA) is necessary for pol II elongation in a cell-free system 14 . For this to occur, an O-GlcNAcylated protein substrate(s) must have existed prior to OGA action. Additionally, O-GlcNAcylation by the O-GlcNAc transferase (OGT) is required for the...

show abstract

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

Cited by 408 publications

References 228 publications

PHF3 regulates neuronal gene expression through the new Pol II CTD reader domain SPOC

PHF3 regulates neuronal gene expression through the new Pol II CTD reader domain SPOC

Continuous transcription initiation guarantees robust repair of transcribed genes and regulatory regions in response to DNA damage

Establishment of a Human RNA Pol II Pausing System and the Identification of O-GlcNAc Cycling Regulating Pol II Pausing and Elongation

Contact Info

Product

Resources

About