Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID

Linda Warfield; Srinivas Ramachandran; Tiago Baptista; Didier Devys; Laszlo Tora; Steven Hahn

doi:10.1016/j.molcel.2017.08.014

Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID

Mol Cell. 2017 Oct 5;68(1):118-129.e5. doi: 10.1016/j.molcel.2017.08.014. Epub 2017 Sep 14.

Authors

Linda Warfield¹, Srinivas Ramachandran², Tiago Baptista³, Didier Devys³, Laszlo Tora³, Steven Hahn⁴

Affiliations

¹ Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
² Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
³ Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France; U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, Cedex, France.
⁴ Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Electronic address: shahn@fredhutch.org.

Abstract

Previous studies suggested that expression of most yeast mRNAs is dominated by either transcription factor TFIID or SAGA. We re-examined the role of TFIID by rapid depletion of S. cerevisiae TFIID subunits and measurement of changes in nascent transcription. We find that transcription of nearly all mRNAs is strongly dependent on TFIID function. Degron-dependent depletion of Taf1, Taf2, Taf7, Taf11, and Taf13 showed similar transcription decreases for genes in the Taf1-depleted, Taf1-enriched, TATA-containing, and TATA-less gene classes. The magnitude of TFIID dependence varies with growth conditions, although this variation is similar genome-wide. Many studies have suggested differences in gene-regulatory mechanisms between TATA and TATA-less genes, and these differences have been attributed in part to differential dependence on SAGA or TFIID. Our work indicates that TFIID participates in expression of nearly all yeast mRNAs and that differences in regulation between these two gene categories is due to other properties.

MeSH terms

Gene Deletion
Gene Expression Regulation, Fungal*
Genome, Fungal*
Promoter Regions, Genetic
Protein Subunits / genetics
Protein Subunits / metabolism
RNA Polymerase II / genetics*
RNA Polymerase II / metabolism
RNA, Fungal / genetics
RNA, Fungal / metabolism
RNA, Messenger / genetics
RNA, Messenger / metabolism
Saccharomyces cerevisiae / genetics*
Saccharomyces cerevisiae / metabolism
Saccharomyces cerevisiae Proteins / chemistry*
Saccharomyces cerevisiae Proteins / genetics*
Saccharomyces cerevisiae Proteins / metabolism
TATA-Binding Protein Associated Factors / deficiency
TATA-Binding Protein Associated Factors / genetics
TATA-Box Binding Protein / genetics*
TATA-Box Binding Protein / metabolism
Trans-Activators / chemistry*
Trans-Activators / genetics
Trans-Activators / metabolism
Transcription Factor TFIID / deficiency
Transcription Factor TFIID / genetics
Transcription, Genetic*

Substances

Protein Subunits
RNA, Fungal
RNA, Messenger
SAGA complex, S cerevisiae
SPT15 protein, S cerevisiae
Saccharomyces cerevisiae Proteins
TAF1 protein, S cerevisiae
TAF11 protein, S cerevisiae
TAF2 protein, S cerevisiae
TATA-Binding Protein Associated Factors
TATA-Box Binding Protein
Trans-Activators
Transcription Factor TFIID
RNA Polymerase II

Abstract

MeSH terms

Substances

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