scholarly journals RNA Polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation

Nucleus ◽  
2014 ◽  
Vol 5 (3) ◽  
pp. 224-236 ◽  
Author(s):  
Elizabeth A Bowman ◽  
William G Kelly
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Pol Ii ◽  
Rna Polymerase Ii Transcription

scholarly journals CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

2020 ◽  
Vol 48 (14) ◽  
pp. 7712-7727
Author(s):  
Michael Tellier ◽  
Justyna Zaborowska ◽  
Livia Caizzi ◽  
Eusra Mohammad ◽  
Taras Velychko ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Pol Ii ◽  
Terminal Domain ◽  
Carboxyl Terminal Domain ◽  
Genome Wide ◽  
A Genome ◽  
Carboxyl Terminal ◽  
Rna Polymerase Ii Transcription

Abstract Cyclin-dependent kinase 12 (CDK12) phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II) but its roles in transcription beyond the expression of DNA damage response genes remain unclear. Here, we have used TT-seq and mNET-seq to monitor the direct effects of rapid CDK12 inhibition on transcription activity and CTD phosphorylation in human cells. CDK12 inhibition causes a genome-wide defect in transcription elongation and a global reduction of CTD Ser2 and Ser5 phosphorylation. The elongation defect is explained by the loss of the elongation factors LEO1 and CDC73, part of PAF1 complex, and SPT6 from the newly-elongating pol II. Our results indicate that CDK12 is a general activator of pol II transcription elongation and indicate that it targets both Ser2 and Ser5 residues of the pol II CTD.

Structural Biology of RNA Polymerase II Transcription: 20 Years On

2020 ◽  
Vol 36 (1) ◽  
pp. 1-34 ◽  
Author(s):  
Sara Osman ◽  
Patrick Cramer
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Focal Point ◽  
Dna Lesions ◽  
Cellular Regulation ◽  
Pol Ii ◽  
Associated Proteins ◽  
Rna Polymerase Ii Transcription

Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.

scholarly journals A Role for SSU72 in Balancing RNA Polymerase II Transcription Elongation and Termination

2002 ◽  
Vol 10 (5) ◽  
pp. 1139-1150 ◽  
Author(s):  
Bernhard Dichtl ◽  
Diana Blank ◽  
Martin Ohnacker ◽  
Arno Friedlein ◽  
Daniel Roeder ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Rna Polymerase Ii Transcription

scholarly journals Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

2016 ◽  
Vol 428 (12) ◽  
pp. 2623-2635 ◽  
Author(s):  
Tassa Saldi ◽  
Michael A. Cortazar ◽  
Ryan M. Sheridan ◽  
David L. Bentley
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Mrna Splicing ◽  
Rna Polymerase Ii Transcription

scholarly journals Mitotic repression of RNA polymerase II transcription is accompanied by release of transcription elongation complexes.

1997 ◽  
Vol 17 (10) ◽  
pp. 5791-5802 ◽  
Author(s):  
G G Parsons ◽  
C A Spencer
Keyword(s):  
Cell Cycle ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Synthesis ◽  
Transcription Elongation ◽  
Control Cell ◽  
Specific Gene ◽  
Mitotic Chromosomes ◽  
Transcription Repression ◽  
Rna Polymerase Ii Transcription

Nuclear RNA synthesis is repressed during the mitotic phase of each cell cycle. Although total RNA synthesis remains low throughout mitosis, the degree of RNA polymerase II transcription repression on specific genes has not been examined. In addition, it is not known whether mitotic repression of RNA polymerase II transcription is due to polymerase pausing or ejection of transcription elongation complexes from mitotic chromosomes. In this study, we show that RNA polymerase II transcription is repressed in mammalian cells on a number of specific gene regions during mitosis. We also show that the majority of RNA polymerase II transcription elongation complexes are physically excluded from mitotic chromosomes between late prophase and late telophase. Despite generalized transcription repression and stripping of RNA polymerase II complexes from DNA, arrested RNA polymerase II ternary complexes appear to remain on some gene regions during mitosis. The cyclic repression of transcription and ejection of RNA polymerase II transcription elongation complexes may help regulate the transcriptional events that control cell cycle progression and differentiation.

Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models

2018 ◽  
Vol 49 ◽  
pp. 54-62 ◽  
Author(s):  
Ilona Christy Unarta ◽  
Lizhe Zhu ◽  
Carmen Ka Man Tse ◽  
Peter Pak-Hang Cheung ◽  
Jin Yu ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Molecular Mechanisms ◽  
Transcription Elongation ◽  
Network Models ◽  
Rna Polymerase Ii Transcription

scholarly journals Histone H2B Ubiquitylation Is Associated with Elongating RNA Polymerase II

2005 ◽  
Vol 25 (2) ◽  
pp. 637-651 ◽  
Author(s):  
Tiaojiang Xiao ◽  
Cheng-Fu Kao ◽  
Nevan J. Krogan ◽  
Zu-Wen Sun ◽  
Jack F. Greenblatt ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Transcription Elongation ◽  
Lysine Methylation ◽  
Coding Region ◽  
Elongation Complex ◽  
Histone H2b ◽  
Pol Ii ◽  
Paf1 Complex

ABSTRACT Rad6-mediated ubiquitylation of histone H2B at lysine 123 has been linked to transcriptional activation and the regulation of lysine methylation on histone H3. However, how Rad6 and H2B ubiquitylation contribute to the transcription and histone methylation processes is poorly understood. Here, we show that the Paf1 transcription elongation complex and the E3 ligase for Rad6, Bre1, mediate an association of Rad6 with the hyperphosphorylated (elongating) form of RNA polymerase II (Pol II). This association appears to be necessary for the transcriptional activities of Rad6, as deletion of various Paf1 complex members or Bre1 abolishes H2B ubiquitylation (ubH2B) and reduces the recruitment of Rad6 to the promoters and transcribed regions of active genes. Using the inducible GAL1 gene as a model, we find that the recruitment of Rad6 upon activation occurs rapidly and transiently across the gene and coincides precisely with the appearance of Pol II. Significantly, during GAL1 activation in an rtf1 deletion mutant, Rad6 accumulates at the promoter but is absent from the transcribed region. This fact suggests that Rad6 is recruited to promoters independently of the Paf1 complex but then requires this complex for entrance into the coding region of genes in a Pol II-associated manner. In support of a role for Rad6-dependent H2B ubiquitylation in transcription elongation, we find that ubH2B levels are dramatically reduced in strains bearing mutations of the Pol II C-terminal domain (CTD) and abolished by inactivation of Kin28, the serine 5 CTD kinase that promotes the transition from initiation to elongation. Furthermore, synthetic genetic array analysis reveals that the Rad6 complex interacts genetically with a number of known or suspected transcription elongation factors. Finally, we show that Saccharomyces cerevisiae mutants bearing defects in the pathway to H2B ubiquitylation display transcription elongation defects as assayed by 6-azauracil sensitivity. Collectively, our results indicate a role for Rad6 and H2B ubiquitylation during the elongation cycle of transcription and suggest a mechanism by which H3 methylation may be regulated.

scholarly journals Structural visualization of de novo initiation of RNA polymerase II transcription

2021 ◽  
Author(s):  
Chun Yang ◽  
Rina Fujiwara ◽  
Hee Jong Kim ◽  
Jose J Gorbea Col&oacuten ◽  
Stefan Steimle ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
De Novo ◽  
Base Pairs ◽  
Pol Ii ◽  
Promoter Escape ◽  
General Transcription Factor ◽  
Short Transcript ◽  
Transition To Elongation ◽  
Rna Polymerase Ii Transcription

Structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription were previously facilitated by the use of synthetic oligonucleotides. Here we report structures of initiation complexes de novo converted from pre-initiation complex (PIC) through catalytic activities and stalled at different template positions. Contrary to previous models, the closed-to-open promoter transition was accompanied by a large positional change of the general transcription factor TFIIH which became in closer proximity to TFIIE for the active delivery of the downstream DNA to the pol II active center. The initially-transcribing complex (ITC) reeled over 80 base pairs of the downstream DNA by scrunching, while retaining the fixed upstream contact, and underwent the transition to elongation when it encountered promoter-proximal pol II from a preceding round of transcription. TFIIH is therefore conducive to promoter melting, TSS scanning, and promoter escape, extending far beyond synthesis of a short transcript.

scholarly journals RNA polymerase II senses obstruction in the DNA minor groove via a conserved sensor motif

2016 ◽  
Vol 113 (44) ◽  
pp. 12426-12431 ◽  
Author(s):  
Liang Xu ◽  
Wei Wang ◽  
Deanna Gotte ◽  
Fei Yang ◽  
Alissa A. Hare ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Minor Groove ◽  
Dna Lesions ◽  
Pol Ii ◽  
Dna Minor Groove ◽  
Minor Groove Binders ◽  
Groove Binders

RNA polymerase II (pol II) encounters numerous barriers during transcription elongation, including DNA strand breaks, DNA lesions, and nucleosomes. Pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA with programmable sequence specificity and high affinity. Previous studies suggest that Py-Im polyamides can prevent transcription factor binding, as well as interfere with pol II transcription elongation. However, the mechanism of pol II inhibition by Py-Im polyamides is unclear. Here we investigate the mechanism of how these minor-groove binders affect pol II transcription elongation. In the presence of site-specifically bound Py-Im polyamides, we find that the pol II elongation complex becomes arrested immediately upstream of the targeted DNA sequence, and is not rescued by transcription factor IIS, which is in contrast to pol II blockage by a nucleosome barrier. Further analysis reveals that two conserved pol II residues in the Switch 1 region contribute to pol II stalling. Our study suggests this motif in pol II can sense the structural changes of the DNA minor groove and can be considered a “minor groove sensor.” Prolonged interference of transcription elongation by sequence-specific minor groove binders may present opportunities to target transcription addiction for cancer therapy.

Sign in / Sign up

Export Citation Format

Share Document