New insights into the role of TFIIB in transcription initiation

Wang, Yuming; Roberts, Stefan G. E.

doi:10.4161/trns.1.3.12900

Cited by 11 publications

(5 citation statements)

References 34 publications

(50 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This element might thus rather be conducive to constitutive basal levels of TFIIB binding to promoters, especially in the scaffold scenario. TFIIB has been implicated in stimulating release of paused Pol II in via interactions with TFIIF [ 82 – 84 ], and constitutive TFIIB presence at the promoter may thus also dampen rhythms in release of paused Pol II. TFIIB binding might, in fact, be linked to high H3K4me3 levels [ 85 ].…”

Section: Discussionmentioning

confidence: 99%

Linking Core Promoter Classes to Circadian Transcription

Westermark

2016

PLoS Genet

View full text Add to dashboard Cite

Circadian rhythms in transcription are generated by rhythmic abundances and DNA binding activities of transcription factors. Propagation of rhythms to transcriptional initiation involves the core promoter, its chromatin state, and the basal transcription machinery. Here, I characterize core promoters and chromatin states of genes transcribed in a circadian manner in mouse liver and in Drosophila. It is shown that the core promoter is a critical determinant of circadian mRNA expression in both species. A distinct core promoter class, strong circadian promoters (SCPs), is identified in mouse liver but not Drosophila. SCPs are defined by specific core promoter features, and are shown to drive circadian transcriptional activities with both high averages and high amplitudes. Data analysis and mathematical modeling further provided evidence for rhythmic regulation of both polymerase II recruitment and pause release at SCPs. The analysis provides a comprehensive and systematic view of core promoters and their link to circadian mRNA expression in mouse and Drosophila, and thus reveals a crucial role for the core promoter in regulated, dynamic transcription.

show abstract

Section: Discussionmentioning

confidence: 99%

Linking Core Promoter Classes to Circadian Transcription

Westermark

2016

PLoS Genet

View full text Add to dashboard Cite

show abstract

“…Consistent with this, some initiation factors are required for transcription termination. Conversely, some termination factors have been found to associate with the 5' end of a gene as well as with the initiation factors, and in fact have been shown to influence transcription reinitiation [44, [53][54][55][56][57].…”

Section: Rpb4 Plays An Indirect Role In the Termination Of Transcriptionmentioning

confidence: 99%

RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit

Allepuz-Fuster

O’Brien

González-Polo

et al. 2019

Preprint

View full text Add to dashboard Cite

words)Gene loops are formed by the interaction of initiation and termination factors occupying the distal ends of a gene during transcription. RNAPII is believed to affect gene looping indirectly owing to its essential role in transcription. The results presented here, however, demonstrate a direct role of RNAPII in gene looping through the Rpb4 subunit. 3C analysis revealed that gene looping is abolished in the rpb4∆ mutant. In contrast to the other looping-defective mutants, rpb4∆ cells do not exhibit a transcription termination defect. RPB4 overexpression, however, rescued the transcription termination and gene looping defect of sua7-1, a mutant of TFIIB. Furthermore, RPB4 overexpression rescued the ssu72-2 gene looping defect, while SSU72 overexpression restored the formation of gene loops in rpb4∆ cells. Interestingly, the interaction of TFIIB with Ssu72 is compromised in rpb4∆ cells. These results suggest that the TFIIB-Ssu72 interaction, which is critical for gene loop formation, is facilitated by Rpb4. We propose that Rpb4 is promoting the transfer of RNAPII from the terminator to the promoter for reinitiation of transcription through TFIIB-Ssu72 mediated gene looping.[14]. Besides activators and TFIIB, TFIIH and Mediator complex also play a critical role in gene loop formation by directly interacting with the CF1 and CPF 3'-end processing/termination factors [12,16]. It is generally believed that RNAPII is not directly involved in formation of gene loops, but is a rather passive player in the process. Since gene looping is a transcription-dependent process, it has been presumed that all mutations that affect transcription will also alter gene looping. Accordingly, gene looping was completely abolished in the rpb1-1 mutant [17].The structure of RNAPII is highly conserved among eukaryotes. In all eukaryotes from yeast to humans, RNAPII is composed of 12 subunits. Only Saccharomyces cerevisiae RNAPII exists in a 10-subunit core and a dissociable subcomplex formed by Rpb4 and Rpb7 [18,19].The 12 subunits of RNAPII have been implicated in different functions during the process of transcription. The two largest subunits, Rpb1 and Rpb2, are required for binding to the DNA template. Rpb1 contains a groove for the entry of deoxyribonucleotides. Rpb7 has two RNA binding domains and plays a pivotal role in mRNA decay [20]. Rpb9 has been implicated in start-site selection, but is dispensable for assembly of the 10-subunit enzyme (Hull et al., 1995). While the two largest subunits, Rpb1 and Rpb2, have well-established roles in the initiation of transcription, a few published reports suggest that some of the RNAPII subunits function in the termination of transcription. The CTD of the largest subunit Rpb1 consists of multiple repeats of the heptapeptide sequence (YSPTSPS). The phosphorylation of Ser2 of the CTD is critical for the recruitment of 3'-end processing factors and for termination of transcription [21,22]. In the crystal structure, the Rpb3/Rpb11 heterodimer lies in close proximity of the RNA exit channel [...

show abstract

“…By far the most attention has been placed on the founding family member TFIIB. During the transcription cycle, TFIIB is directly involved in numerous roles including facilitating Pol II recruitment to the promoter, TSS recognition, open-complex formation, abortive initiation, promoter clearance, and roles in termination and gene looping [47, 71, 79, 80]. A subset of these transcriptional functions have also been described for TFB and Brf1 [11, 66–68].…”

Section: General Functions Of Tfiib and Brf1mentioning

confidence: 99%

TFIIB-related factors in RNA polymerase I transcription

Knutson

Hahn

2013

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

View full text Add to dashboard Cite

Eukaryotic RNA polymerases (Pol) I, II, III and archaeal Pol use a related set of general transcription factors to recognize promoter sequences, recruit Pol to promoters and to function at key points in the transcription initiation mechanism. The TFIIB-like general transcription factors (GTFs) function during several important and conserved steps in the initiation pathway for Pol II, III, and archaeal Pol. Until recently, the mechanism of Pol I initiation seemed unique, since it appeared to lack a GTF paralogous to the TFIIB-like proteins. The surprising recent discovery of TFIIB-related Pol I general factors in yeast and humans highlights the evolutionary conservation of transcription initiation mechanisms for all eukaryotic and archaeal Pols. These findings reveal new roles for the function of the Pol I GTFs and insight into the function of TFIIB-related factors. Models for Pol I transcription initiation are reexamined in light of these recent findings.

show abstract

New insights into the role of TFIIB in transcription initiation

Cited by 11 publications

References 34 publications

Linking Core Promoter Classes to Circadian Transcription

Linking Core Promoter Classes to Circadian Transcription

RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit

TFIIB-related factors in RNA polymerase I transcription

Contact Info

Product

Resources

About