Non-canonical TAF complexes regulate active promoters in human embryonic stem cells

Glenn A Maston,Michael R Green,Lynn Chamberlain,Lihua Julie Zhu,Minggang Fang,Ling Lin

doi:10.7554/elife.00068

Glenn A Maston, Michael R Green + Show 4 more

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https://doi.org/10.7554/elife.00068

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Abstract

The general transcription factor TFIID comprises the TATA-box-binding protein (TBP) and approximately 14 TBP-associated factors (TAFs). Here we find, unexpectedly, that undifferentiated human embryonic stem cells (hESCs) contain only six TAFs (TAFs 2, 3, 5, 6, 7 and 11), whereas following differentiation all TAFs are expressed. Directed and global chromatin immunoprecipitation analyses reveal an unprecedented promoter occupancy pattern: most active genes are bound by only TAFs 3 and 5 along with TBP, whereas the remaining active genes are bound by TBP and all six hESC TAFs. Consistent with these results, hESCs contain a previously undescribed complex comprising TAFs 2, 6, 7, 11 and TBP. Altering the composition of hESC TAFs, either by depleting TAFs that are present or ectopically expressing TAFs that are absent, results in misregulated expression of pluripotency genes and induction of differentiation. Thus, the selective expression and use of TAFs underlies the ability of hESCs to self-renew.DOI:http://dx.doi.org/10.7554/eLife.00068.001.

Highlights

The specification of tissues and organs in development depends upon the spatially and temporally accurate execution of gene expression programs, much of which is regulated at the level of transcription
In a search of published expression datasets (Abeyta et al, 2004), we found that several TBP-associated factors (TAFs) of the canonical TFIID complex were apparently not expressed in human embryonic stem cells (hESCs)
Based upon these results we conclude that only six of the canonical TFIID TAFs are present in hESCs

Summary

Introduction

The specification of tissues and organs in development depends upon the spatially and temporally accurate execution of gene expression programs, much of which is regulated at the level of transcription. The factors involved in the accurate transcription of eukaryotic structural genes by RNA polymerase II can be classified into two groups. General (or basic) transcription factors (GTFs) are necessary and can be sufficient for accurate transcription initiation in vitro (for review, see Thomas and Chiang, 2006). These basic factors include RNA polymerase II itself and at least six GTFs: TFIID, TFIIA, TFIIB, TFIIE, TFIIF and TFIIH. Transcriptional activity is greatly stimulated by the second class of factors, promoter-specific activator proteins (activators). Activators are sequence-specific DNA-binding proteins whose recognition sites are typically present upstream of the core promoter. Activators work in large part by increasing PIC formation but can act through other mechanisms, such as accelerating the rate of transcriptional elongation, promoting multiple rounds of transcription and directing chromatin modifications (reviewed in Green, 2005; Fuda et al, 2009; Weake and Workman, 2010)

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