Program in Gene Function and Expression; Program in Molecular Medicine; Program in Bioinformatics and Integrative Biology
Medical Subject Headings
TATA-Box Binding Protein; TATA-Binding Protein Associated Factors; Transcription Factors; Transcription Factors, General; Embryonic Stem Cells
Genetics and Genomics
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.
Supplementary file 1. List of antibodies, primer sequences and siRNA/shRNAs used in this study. (A) List of antibodies used in this study. (B) Primers sequences for qRT-PCR, ChIP and ChIP-chip validation experiments. (C) Sequences of synthesized siRNAs, and clone ID numbers for shRNAs obtained from Open Biosystems (the luciferase siRNA sequence was previously reported (Elbashir et al., 2001)).