scholarly journals RNA polymerase II dynamics and mRNA stability feedback determine mRNA scaling with cell size

2021 ◽  
Author(s):  
Matthew P Swaffer ◽  
Georgi K Marinov ◽  
Huan Zheng ◽  
Andrew W Jones ◽  
Anshul Kundaje ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Cell Size ◽  
Mrna Stability ◽  
Dynamic Equilibrium ◽  
Reaction Rates ◽  
Cellular Growth ◽  
Limiting Factor ◽  
Similar Reaction ◽  
Dna Template

A defining feature of cellular growth is that protein and mRNA amounts scale with cell size so that concentrations remain approximately constant, thereby ensuring similar reaction rates and efficient biosynthesis. A key component of this biosynthetic scaling is the scaling of mRNA amounts with cell size, which occurs even among cells with the same DNA template copy number. Here, we identify RNA polymerase II as a major limiting factor increasing transcription with cell size. Other components of the transcriptional machinery are only minimally limiting and the chromatin environment is largely invariant with size. However, RNA polymerase II activity does not increase in direct proportion to cell size, inconsistent with previously proposed DNA-titration models. Instead, our data support a dynamic equilibrium model where the rate of polymerase loading is proportional to the unengaged nucleoplasmic polymerase concentration. This sublinear transcriptional increase is then balanced by a compensatory increase in mRNA stability as cells get larger. Taken together, our results show how limiting RNA polymerase II and feedback on mRNA stability work in concert to ensure the precise scaling of mRNA amounts across the physiological cell size range.

Assembly of RNA polymerase II preinitiation complexes before assembly of nucleosomes allows efficient initiation of transcription on nucleosomal templates

1988 ◽  
Vol 8 (8) ◽  
pp. 3114-3121
Author(s):  
J A Knezetic ◽  
G A Jacob ◽  
D S Luse
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Chromatin Assembly ◽  
Nucleosome Assembly ◽  
Preinitiation Complex ◽  
Naked Dna ◽  
Initiation Of Transcription ◽  
Dna Template

We have previously shown that assembly of nucleosomes on the DNA template blocks transcription initiation by RNA polymerase II in vitro. In the studies reported here, we demonstrate that assembly of a complete RNA polymerase II preinitiation complex before nucleosome assembly results in nucleosomal templates which support initiation in vitro as efficiently as naked DNA. Control experiments prove that our observations are not the result of slow displacement of nucleosomes by the transcription machinery during chromatin assembly, nor are they an artifact of inefficient nucleosome deposition on templates already bearing an RNA polymerase. Thus, the RNA polymerase II preinitiation complex appears to be resistant to disruption by subsequent nucleosome assembly.

scholarly journals Assembly of RNA polymerase II preinitiation complexes before assembly of nucleosomes allows efficient initiation of transcription on nucleosomal templates.

1988 ◽  
Vol 8 (8) ◽  
pp. 3114-3121 ◽  
Author(s):  
J A Knezetic ◽  
G A Jacob ◽  
D S Luse
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Chromatin Assembly ◽  
Nucleosome Assembly ◽  
Preinitiation Complex ◽  
Naked Dna ◽  
Initiation Of Transcription ◽  
Dna Template

We have previously shown that assembly of nucleosomes on the DNA template blocks transcription initiation by RNA polymerase II in vitro. In the studies reported here, we demonstrate that assembly of a complete RNA polymerase II preinitiation complex before nucleosome assembly results in nucleosomal templates which support initiation in vitro as efficiently as naked DNA. Control experiments prove that our observations are not the result of slow displacement of nucleosomes by the transcription machinery during chromatin assembly, nor are they an artifact of inefficient nucleosome deposition on templates already bearing an RNA polymerase. Thus, the RNA polymerase II preinitiation complex appears to be resistant to disruption by subsequent nucleosome assembly.

scholarly journals Evidence for Eviction and Rapid Deposition of Histones upon Transcriptional Elongation by RNA Polymerase II

2004 ◽  
Vol 24 (23) ◽  
pp. 10111-10117 ◽  
Author(s):  
Marc A. Schwabish ◽  
Kevin Struhl
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Dynamic Equilibrium ◽  
Yeast Genome ◽  
Transcriptional Elongation ◽  
Coding Region ◽  
Pol Ii ◽  
Core Histones ◽  
Histone Exchange

ABSTRACT Biochemical experiments indicate that transcriptional elongation by RNA polymerase II (Pol II) is inhibited by nucleosomes and hence requires chromatin-modifying activities. Here, we examine the fate of histones upon passage of elongating Pol II in vivo. Histone density throughout the entire Saccharomyces cerevisiae GAL10 coding region is inversely correlated with Pol II association and transcriptional activity, suggesting that the elongating Pol II machinery efficiently evicts core histones from the DNA. Furthermore, new histones appear to be deposited onto DNA less than 1 min after passage of Pol II. Transcription-dependent deposition of histones requires the FACT complex that travels with elongating Pol II. Our results suggest that Pol II transcription generates a highly dynamic equilibrium of histone eviction and histone deposition and that there is significant histone exchange throughout most of the yeast genome within a single cell cycle.

scholarly journals CDK13 cooperates with CDK12 to control global RNA polymerase II processivity

2020 ◽  
Vol 6 (18) ◽  
pp. eaaz5041 ◽  
Author(s):  
Zheng Fan ◽  
Jennifer R. Devlin ◽  
Simon J. Hogg ◽  
Maria A. Doyle ◽  
Paul F. Harrison ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Cellular Growth ◽  
Transcriptional Elongation ◽  
Transcriptional Responses ◽  
Kinase Inhibition ◽  
Homology Directed Repair ◽  
Molecular Events ◽  
Genome Wide ◽  
Transcriptional Changes

The RNA polymerase II (POLII)–driven transcription cycle is tightly regulated at distinct checkpoints by cyclin-dependent kinases (CDKs) and their cognate cyclins. The molecular events underpinning transcriptional elongation, processivity, and the CDK-cyclin pair(s) involved remain poorly understood. Using CRISPR-Cas9 homology-directed repair, we generated analog-sensitive kinase variants of CDK12 and CDK13 to probe their individual and shared biological and molecular roles. Single inhibition of CDK12 or CDK13 induced transcriptional responses associated with cellular growth signaling pathways and/or DNA damage, with minimal effects on cell viability. In contrast, dual kinase inhibition potently induced cell death, which was associated with extensive genome-wide transcriptional changes including widespread use of alternative 3′ polyadenylation sites. At the molecular level, dual kinase inhibition resulted in the loss of POLII CTD phosphorylation and greatly reduced POLII elongation rates and processivity. These data define substantial redundancy between CDK12 and CDK13 and identify both as fundamental regulators of global POLII processivity and transcription elongation.

scholarly journals RNAs nonspecifically inhibit RNA polymerase II by preventing binding to the DNA template

RNA ◽  
2014 ◽  
Vol 20 (5) ◽  
pp. 644-655 ◽  
Author(s):  
Dave A. Pai ◽  
Craig D. Kaplan ◽  
Hye Kyong Kweon ◽  
Kenji Murakami ◽  
Philip C. Andrews ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Dna Template

scholarly journals Effect of Sarkosyl and heparin on single-step addition reactions catalysed by wheat-germ RNA polymerase II–poly[d(A–T)]transcription complexes

1989 ◽  
Vol 260 (3) ◽  
pp. 795-801 ◽  
Author(s):  
L De Mercoyrol ◽  
C Job ◽  
D Job
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Wheat Germ ◽  
Single Step ◽  
Addition Reactions ◽  
Phosphodiester Bond ◽  
Sizeable Fraction ◽  
Transcription Complexes ◽  
Enzyme Molecules ◽  
Dna Template

Incubation of purified wheat-germ RNA polymerase II with poly[d(A-T)] template, Mn2+, U-A dinucleoside monophosphate primer and UTP substrate resulted in catalytic formation of the trinucleoside diphosphate U-A-U, in accordance with the results of previous studies. Both Sarkosyl and heparin inhibited completely and immediately (within less than 1 min) U-A-U synthesis, if either of these compounds was added to the assays during the progress of the reaction. This behaviour is in marked contrast to that reported for single-step addition reactions catalysed by Escherichia coli RNA polymerase on the same template [Sylvester & Cashel (1980) Biochemistry 19, 1069-1074]. However, treatment of the transcription complexes with Sarkosyl or heparin for periods sufficient to abolish U-A-U formation completely did not suppress completely the ability of such complexes to elongate RNA chains. Hence, the effect of Sarkosyl or heparin on the rate of U-A-U synthesis was predominantly due to change in the rate (or in the mechanism) of trinucleotide product release by the transcription complexes. Furthermore, once U-A-U synthesis has begun on the poly[d(A-T)] template, the transcription complexes became resistant to the action of a competitor DNA such as poly[d(G-C)]. The results are consistent with a model where at least a sizeable fraction of the enzyme molecules remains associated with the DNA template upon formation of a single phosphodiester bond.

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