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.
Embryonic stem cells have two characteristic properties: they are able to differentiate into any type of cell, a property known as pluripotency, and they are able to replicate themselves indefinitely to produce an endless supply of new stem cells. Different genes code for the various proteins associated with these two properties, and understanding the behaviour and properties of stem cells in detail is a major challenge in developmental biology. In human embryonic stem cells that have not yet differentiated, the genes that code for the transcription factors involved in the self-renewal process are expressed, whereas the genes associated with differentiation are not active. However, if the expression of the genes for self-renewal is reduced, the process of differentiation will begin, and the embryonic stem cells will be able to produce any one of the 200 or so different types of cell found in the human body.
All of this activity is orchestrated by proteins that oversee the transcription of specific regions of DNA into messenger RNA. Transcription is the first step in the process by which genes are expressed as proteins, and it cannot start until the relevant transcription factor binds to a stretch of DNA near the gene called the promoter. These transcription factors are complex structures that contain a central protein called TBP, which binds to the promoter, and 14 or so other proteins called TAFs.
Maston et al. now report that the transcription machinery that regulates gene expression and self-renewal in human embryonic stem cells is different from that found in other types of cells, including embryonic stem cells taken from mice. In particular, they found that undifferentiated human embryonic stem cells contain only 6 of the 14 TAFs observed in other cells, although all 14 are present after differentiation. Moreover, for many active genes the transcription factors contained only two of these TAFs. There was also evidence for a new complex that contained the other four TAFs plus TBP.
Maston et al. also demonstrated that the removal of just one of the six TAFs, or the addition of just one extra TAF, caused the process of differentiation to begin. This shows, they argue, that the unusual transcription machinery they have discovered is essential for the proper workings of human embryonic stem cells.