scholarly journals Structural Motifs for CTD Kinase Specificity on RNA Polymerase II during Eukaryotic Transcription

2020 ◽  
Vol 15 (8) ◽  
pp. 2259-2272
Author(s):  
Mukesh Kumar Venkat Ramani ◽  
Edwin E. Escobar ◽  
Seema Irani ◽  
Joshua E. Mayfield ◽  
Rosamaria Y. Moreno ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Structural Motifs ◽  
Eukaryotic Transcription ◽  
Kinase Specificity

scholarly journals Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

Science ◽  
2009 ◽  
Vol 325 (5940) ◽  
pp. 626-628 ◽  
Author(s):  
Courtney Hodges ◽  
Lacramioara Bintu ◽  
Lucyna Lubkowska ◽  
Mikhail Kashlev ◽  
Carlos Bustamante
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Optical Tweezers ◽  
Direct Evidence ◽  
Eukaryotic Transcription ◽  
Pol Ii ◽  
The Core ◽  
Nucleosomal Dna ◽  
Dna Loop ◽  
Core Histones

RNA polymerase II (Pol II) must overcome the barriers imposed by nucleosomes during transcription elongation. We have developed an optical tweezers assay to follow individual Pol II complexes as they transcribe nucleosomal DNA. Our results indicate that the nucleosome behaves as a fluctuating barrier that locally increases pause density, slows pause recovery, and reduces the apparent pause-free velocity of Pol II. The polymerase, rather than actively separating DNA from histones, functions instead as a ratchet that rectifies nucleosomal fluctuations. We also obtained direct evidence that transcription through a nucleosome involves transfer of the core histones behind the transcribing polymerase via a transient DNA loop. The interplay between polymerase dynamics and nucleosome fluctuations provides a physical basis for the regulation of eukaryotic transcription.

scholarly journals Characterization of the mouse beta maj globin transcription termination region: a spacing sequence is required between the poly(A) signal sequence and multiple downstream termination elements.

1993 ◽  
Vol 13 (1) ◽  
pp. 578-587 ◽  
Author(s):  
J Tantravahi ◽  
M Alvira ◽  
E Falck-Pedersen
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Element ◽  
Recombinant Adenovirus ◽  
Signal Sequence ◽  
Transcription Termination ◽  
Eukaryotic Transcription ◽  
Sequence Elements

For the majority of mRNA encoding eukaryotic transcription units, there is little or no knowledge of the elements responsible for transcription termination or how they may interact with RNA polymerase. In this report, we have used recombinant adenovirus reporter vectors to characterize the mouse beta maj globin sequence elements that cause transcription termination. Within the globin 3' termination region, we have identified at least three sequence elements which induce significant levels of transcription termination (> 50%). The smallest functionally active element (64% termination) is 69 bp in length. The natural arrangement of these elements results in a cumulative termination which is greater than 90%. Recognition of the termination elements by RNA polymerase II depends on the presence of a functional poly(A) signal sequence. We demonstrate that efficient transcription termination depends on appropriate spacing between the poly(A) signal sequence and the termination element.

scholarly journals Bending DNA can repress a eukaryotic basal promoter and inhibit TFIID binding.

1995 ◽  
Vol 15 (10) ◽  
pp. 5492-5498 ◽  
Author(s):  
A TenHarmsel ◽  
M D Biggin
Keyword(s):  
Transcription Factors ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Dna Sequences ◽  
Promoter Sequence ◽  
Eukaryotic Transcription ◽  
Transcription System ◽  
General Transcription Factors ◽  
Dna Loop ◽  
Reduced Rate

Previous studies indicated that repression by eve involves cooperative DNA binding and leads to the formation of a DNA loop which encompasses the DNA sequences normally bound by the RNA polymerase II general transcription factors. To test the general principle of whether bending of a basal promoter sequence can contribute directly to repression of transcription, a minicircle template of 245 bp was used. In a purified transcription system, transcription from the minicircular DNA is greatly reduced compared with that from the identical DNA fragment in linear form. Transcription is also reduced when the minicircle contains a single-stranded nick, indicating that transcription is reduced because of DNA bending, rather than any constraint on supercoiling. We show that the reduced transcription from the minicircle in these experiments is not due to a reduced rate of elongation by RNA polymerase II. Rather, repression occurs, at least in part, because binding of the general transcription factor TFIID to the minicircle is strongly inhibited compared with binding to the linear DNA. We suggest that bending DNA may be a mechanism by which eukaryotic transcription may be regulated, by modulating the activity of the general transcription factors.

scholarly journals A SUMO-dependent pathway controls elongating RNA Polymerase II upon UV-induced damage

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Irina Heckmann ◽  
Maximilian J. Kern ◽  
Boris Pfander ◽  
Stefan Jentsch
Keyword(s):  
Dna Damage ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Ubiquitin Ligase ◽  
Rna Polymerase Iii ◽  
Messenger Rnas ◽  
Eukaryotic Transcription ◽  
Small Nuclear Rnas ◽  
Defective Rna ◽  
Dependent Pathway

AbstractRNA polymerase II (RNAPII) is the workhorse of eukaryotic transcription and produces messenger RNAs and small nuclear RNAs. Stalling of RNAPII caused by transcription obstacles such as DNA damage threatens functional gene expression and is linked to transcription-coupled DNA repair. To restore transcription, persistently stalled RNAPII can be disassembled and removed from chromatin. This process involves several ubiquitin ligases that have been implicated in RNAPII ubiquitylation and proteasomal degradation. Transcription by RNAPII is heavily controlled by phosphorylation of the C-terminal domain of its largest subunit Rpb1. Here, we show that the elongating form of Rpb1, marked by S2 phosphorylation, is specifically controlled upon UV-induced DNA damage. Regulation of S2-phosphorylated Rpb1 is mediated by SUMOylation, the SUMO-targeted ubiquitin ligase Slx5-Slx8, the Cdc48 segregase as well as the proteasome. Our data suggest an RNAPII control pathway with striking parallels to known disassembly mechanisms acting on defective RNA polymerase III.

Characterization of the mouse beta maj globin transcription termination region: a spacing sequence is required between the poly(A) signal sequence and multiple downstream termination elements

1993 ◽  
Vol 13 (1) ◽  
pp. 578-587
Author(s):  
J Tantravahi ◽  
M Alvira ◽  
E Falck-Pedersen
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Element ◽  
Recombinant Adenovirus ◽  
Signal Sequence ◽  
Transcription Termination ◽  
Eukaryotic Transcription ◽  
Sequence Elements

For the majority of mRNA encoding eukaryotic transcription units, there is little or no knowledge of the elements responsible for transcription termination or how they may interact with RNA polymerase. In this report, we have used recombinant adenovirus reporter vectors to characterize the mouse beta maj globin sequence elements that cause transcription termination. Within the globin 3' termination region, we have identified at least three sequence elements which induce significant levels of transcription termination (> 50%). The smallest functionally active element (64% termination) is 69 bp in length. The natural arrangement of these elements results in a cumulative termination which is greater than 90%. Recognition of the termination elements by RNA polymerase II depends on the presence of a functional poly(A) signal sequence. We demonstrate that efficient transcription termination depends on appropriate spacing between the poly(A) signal sequence and the termination element.

scholarly journals Cdk9 regulates a promoter-proximal checkpoint to modulate RNA Polymerase II elongation rate

2017 ◽  
Author(s):  
Gregory T. Booth ◽  
Pabitra K. Parua ◽  
Miriam Sansó ◽  
Robert P. Fisher ◽  
John T. Lis
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Time Course ◽  
Kinase Activity ◽  
Elongation Rate ◽  
Transcription Start ◽  
Eukaryotic Transcription ◽  
Pol Ii ◽  
Cdk9 Kinase Activity

Multiple kinases modify RNA Polymerase II (Pol II) and its associated pausing and elongation factors to regulate Pol II transcription and transcription-coupled mRNA processing1,2. The conserved Cdk9 kinase is essential for regulated eukaryotic transcription3, but its mechanistic role remains incompletely understood. Here, we use altered-specificity kinase mutations and highly-specific inhibitors in fission yeast, Schizosaccharomyces pombe to examine the role of Cdk9, and related Cdk7 and Cdk12 kinases, on transcription at base-pair resolution using Precision Run-On sequencing (PRO-seq). Within a minute, Cdk9 inhibition causes a dramatic reduction in the phosphorylation of Pol II-associated factor, Spt5. The effects of Cdk9 inhibition on transcription are the more severe than inhibition of Cdk7 and Cdk12 and result in a shift of Pol II towards the transcription start site (TSS). A kinetic time course of Cdk9 inhibition reveals that early transcribing Pol II is the most compromised, with a measured rate of only ~400 bp/min, while Pol II that is already well into the gene continues rapidly to the end of genes with a rate > 1 kb/min. Our results indicate that while Pol II in S. pombe can escape promoter-proximal pausing in the absence of Cdk9 activity, it is impaired in elongation, suggesting the existence of a conserved global regulatory checkpoint that requires Cdk9 kinase activity.

Sign in / Sign up

Export Citation Format

Share Document