Cited by 79Genomics and Chromatin DynamicsChromatin Remodeling and CancerEpigenetics and DNA Methylation

Histone H3K4 and K36 Methylation, Chd1 and Rpd3S Oppose the Functions of Saccharomyces cerevisiae Spt4–Spt5 in Transcription

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Quan, Tiffani Kiyoko, Hartzog, Grant Ashley·2010·Genetics

Abstract

Spt4–Spt5, a general transcription elongation factor for RNA polymerase II, also has roles in chromatin regulation. However, the relationships between these functions are not clear. Previously, we isolated suppressors of a Saccharomyces cerevisiae spt5 mutation in genes encoding members of the Paf1 complex, which regulates several cotranscriptional histone modifications, and Chd1, a chromatin remodeling enzyme. Here, we show that this suppression of spt5 can result from loss of histone H3 lysines 4 or 36 methylation, or reduced recruitment of Chd1 or the Rpd3S complex. These spt5 suppressors also rescue the synthetic growth defects observed in spt5 mutants that also lack elongation factor TFIIS. Using a FLO8 reporter gene, we found that a chd1 mutation caused cryptic initiation of transcription. We further observed enhancement of cryptic initiation in chd1 isw1 mutants and increased histone acetylation in a chd1 mutant. We suggest that, as previously proposed for H3 lysine 36 methylation and the Rpd3S complex, H3 lysine 4 methylation and Chd1 function to maintain normal chromatin structures over transcribed genes, and that one function of Spt4–Spt5 is to help RNA polymerase II overcome the repressive effects of these histone modifications and chromatin regulators on transcription.

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Crossref · 10.1534/genetics.109.111526

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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 Quan & Hartzog, 2010

    The Results (page not provided) identify YLR454W as a 7.9-kb gene and describe its use to measure RNA polymerase II elongation rate. The paper does not give an average yeast gene length of 1.5–2 kb or establish that YLR454W was used in most budding-yeast speed experiments. (LLM, conf=0.88)

    Experimental — accuracy not yet measured
  • In budding yeast, Spt5 increases transcription speed.

    “In budding yeast, Spt5 increases transcription speed (Quan & Hartzog, 2010).”

    From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Quan & Hartzog, 2010

    The Results report that the spt5-242 mutation decreases transcription elongation rate relative to wild-type budding yeast. That supports a role for Spt5 in maintaining elongation speed, but the study does not show that Spt5 generally increases transcription speed; its direct rate measurement concerns this specific mutation and assay. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

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1 of the 95 references couldn’t be matched to a known paper.

Research works printed but not linked: 1

  1. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman et al., 1991 Current Protocols in Molecular Biology. Greene Publishing Associates and Wiley-Interscience, New York.

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Authors
Quan, T. K., & Hartzog, G. A.
Affiliations
University of California, Santa Cruz (US)
Corresponding author
Hartzog, Grant Ashley
Venue
Genetics
Published
2010-02-01
Volume
184
Issue
2
Pages
321-334
ISSN
  • 0016-6731 (ISSN-L)
  • 1943-2631
OpenAlex
W2153154881
Cited by
79
References
95
Citations by year
2026: 2 · 2025: 1 · 2024: 3 · 2023: 4 · 2022: 1 · 2021: 5 · 2020: 1 · 2019: 4 · 2018: 3 · 2017: 5 · 2016: 4 · 2015: 2 · 2014: 9 · 2013: 8 · 2012: 16
FWCI
3.62
Type
journal article
Language
en
Open access
Locations
  • Genetics (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
National Institute of General Medical Sciences (T32GM008646, T32-GM08646, R01GM060479, GM060479)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
histone H3 lysine 4 methylation, CHD1, histone acetylation, Paf1 complex, chromatin remodeling, transcriptional repression, synthetic growth defect, TFIIS, Saccharomyces cerevisiae
MeSH terms
Acetylation, Chromatin, Chromosomal Proteins, Non-Histone, DNA-Binding Proteins, Histone Deacetylases, Histones, Kinetics, Lysine, Methylation, Mutation, Nuclear Proteins, Nucleosomes, Saccharomyces cerevisiae, Transcription, Genetic, Conserved Sequence, Protein Structure, Tertiary, Saccharomyces cerevisiae Proteins, Transcriptional Elongation Factors

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