Distinction and Relationship between Elongation Rate and Processivity of RNA Polymerase II In Vivo

Mason, Paul B.; Struhl, Kevin

doi:10.1016/j.molcel.2005.02.017

Cited by 359Genomics and Chromatin DynamicsRNA Research and SplicingNuclear Structure and Function

Distinction and Relationship between Elongation Rate and Processivity of RNA Polymerase II In Vivo

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Mason, Paul B., Struhl, Kevin·2005·Molecular Cell

DOI 10.1016/j.molcel.2005.02.017

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Abstract

A number of proteins and drugs have been implicated in the process of transcriptional elongation by RNA polymerase (Pol) II, but the factors that govern the elongation rate (nucleotide additions per min) and processivity (nucleotide additions per initiation event) in vivo are poorly understood. Here, we show that a mutation in the Rpb2 subunit of Pol II reduces both the elongation rate and processivity in vivo. In contrast, none of the putative elongation factors tested affect the elongation rate, although mutations in the THO complex and in Spt4 significantly reduce processivity. The drugs 6-azauracil and mycophenolic acid reduce both the elongation rate and processivity, and this processivity defect is aggravated by mutations in Spt4, TFIIS, and CTDK-1. Our results suggest that, in vivo, a reduced rate of Pol II elongation leads to premature dissociation along the chromatin template and that Pol II processivity can be uncoupled from elongation rate.

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In yeast, genes are quite short (around 1.5-2 kb long on average), although the gene YLR454W used for most experiments measuring RNA Pol II speed in budding yeast is exceptionally large with a size of around 8 kb.
“In yeast, genes are quite short (around 1.5–2 kb long on average, although the gene YLR454W, used for most of the experiments measuring RNA Pol II speed in budding yeast, is exceptionally large with a size of around 8 kb (Table 2) (Mason & Struhl, 2005; Quan & Hartzog, 2010; Kruk et al, 2011; García et al, 2012)).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Mason & Struhl, 2005
The paper’s discussion of biological significance says YLR454w is 8 kb, versus a typical yeast gene of 1–2 kb. Its description of the GAL1-YLR454 experiments confirms that it used this gene to measure Pol II elongation rate. It does not establish that YLR454w was used for most such experiments across budding-yeast research, or give an average of 1.5–2 kb. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Deletion of TFIIS has no effect on RNA Pol II velocity in budding yeast.
“Accordingly, TFIIS increases RNA Pol II speed in human cells (Sheridan et al, 2019; Zatreanu et al, 2019), while its deletion had no effect on RNA Pol II velocity in budding yeast (Mason & Struhl, 2005).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Mason & Struhl, 2005
Loss of Paf1C has no measurable effect on RNA Pol II velocity in budding yeast.
“Paf1C specifically increases RNA Pol II velocity within the first part of gene bodies in mice (Hou et al, 2019), although no effect of the loss of this factor could be measured in budding yeast (Mason & Struhl, 2005).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Mason & Struhl, 2005

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“Accordingly, TFIIS increases RNA Pol II speed in human cells (Sheridan et al , 2019; Zatreanu et al , 2019), while its deletion had no effect on RNA Pol II velocity in budding yeast (Mason & Struhl, 2005).”
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Authors: Mason, P. B., & Struhl, K.
Affiliations: Harvard University (US)
Corresponding author: Struhl, Kevin
ORCID: Struhl, Kevin
Venue: Molecular Cell
Publisher: Elsevier BV
Published: 2005-03
Volume: 17
Issue: 6
Pages: 831-840
ISSN: 1097-2765 (ISSN-L)
DOI: 10.1016/j.molcel.2005.02.017
OpenAlex: W2079493448
Cited by: 359
References: 62
Citations by year: 2026: 4 · 2025: 5 · 2024: 12 · 2023: 12 · 2022: 14 · 2021: 12 · 2020: 14 · 2019: 17 · 2018: 8 · 2017: 15 · 2016: 13 · 2015: 11 · 2014: 20 · 2013: 20 · 2012: 26
FWCI: 10.16
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 3060 d)
doi.org/10.15223/policy-017 (stm-asf)
doi.org/10.15223/policy-037 (stm-asf)
doi.org/10.15223/policy-012 (stm-asf)
doi.org/10.15223/policy-029 (stm-asf)
doi.org/10.15223/policy-004 (stm-asf)
Locations: Molecular Cell (publishedVersion)
PubMed (publishedVersion)
Funders: National Institutes of Health (GM30186)
National Institute of General Medical Sciences (GM30186)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Keywords: RNA polymerase II, transcription elongation, elongation rate, processivity, THO complex, Spt4, TFIIS, 6-azauracil, mycophenolic acid, elongation factors, chromatin templates
MeSH terms: Antibiotics, Antineoplastic, Antimetabolites, Chromatin, Mutation, Mycophenolic Acid, Nuclear Proteins, Peptide Chain Elongation, Translational, Protein Kinases, RNA Polymerase II, Saccharomyces cerevisiae, Transcription, Genetic, Uracil, Gene Expression Regulation, Fungal, Protein Subunits, Transcription Initiation Site, Saccharomyces cerevisiae Proteins, Transcriptional Elongation Factors

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Distinction and Relationship between Elongation Rate and Processivity of RNA Polymerase II In Vivo

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