Transcriptional regulation by coactivators in embryonic stem cells

Abstract

Embryonic stem (ES) cells, like all cell types, are defined by their unique transcriptional signatures. The ability of ES cells to self-renew or exit the pluripotent state and enter differentiation requires extensive changes in their transcriptome and epigenome. Remarkably, transcriptional programs governing each cell fate must remain sufficiently malleable so that expression of only a handful of transcriptional activators can override the pre-existing state by collaborating with an unexpectedly elaborate collection of coactivators to specify, restrict and stabilize the new state. Here, we discuss recent advances in our understanding of how the same coactivator can interpret multiple lines of information encoded by different activators and integrate signals from diverse regulators into stem cell-specific transcriptional outputs.

Figure 1

Multi-step activation model of an Oct4/Sox2-target gene in embryonic stem cells. The transcription apparatus is assembled on an Oct4/Sox2-target gene promoter in a spatially and temporally regulated manner to initiate gene expression. The stepwise assembly is depicted here in the order proposed in [68]. (1) ‘Orchestration’: sequence-specific transcription factors, Oct4 and Sox2, bind to both the proximal (PE) and distal (DE) enhancers. (2) ‘Access’: Chromatin remodelers and histone modifying enzymes such as histone acetyltransferases (HATs) and histone methyltransferases (HMTs) act coordinately to remodel chromatin around the gene loci by altering nucleosome positioning and histone modifications. This allows access of other transcription factors and cofactors to the gene promoter. (3) ‘Initiation’: Preinitiation complex (PIC) and various coactivators (e.g. TAFs/TFIID, Mediator and SCC) are assembled onto the core promoter via interaction with activators bound on PE and DE (e.g. TAFs-Oct4/Sox2 or SCC-Oct4/Sox2), promoter DNA elements (e.g. TBP-TATA), and modified nucleosomes (e.g. TAF3-H3K4me3). DNA looping by cohesin and Mediator can further stabilize the long range enhancer-promoter DNA interaction. (4) ‘Elongation’: phosphorylation of the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) by TFIIH facilitates promoter escape while subsequent phosphorylation by P-TEFb stimulates the transition of Pol II into productive elongation.

Figure 2

Mechanisms of cell type-specific transcriptional activation by coactivators. (a) Prototypic TFIID purified from HeLa cells is composed of the TATA-binding protein (TBP) and 13–14 TBP-associated factors (TAFs). Canonical TAFs are replaced with gonad-selective TAFs in both male and female germ cells. TAF7 is substituted with its paralog TAF7L in spermatocytes while TAF4 is replaced with TAF4B in granulosa cells of the ovary. Genetic inactivation of TAF7L and TAF4B in mice led to sterility. Incorporation of non-canonical TAFs like TAF7L and TAF4B in TFIID may provide unique contact surfaces for germ cell-specific transcription factors to mediate transcriptional activation [9]. (b) In mouse embryonic stem (ES) cells, the combinatorial assembly of TAF3, CTCF (CCCTC-binding factor), cohesin and presumably an endoderm lineage-specific TF (yellow) permits selective long distance enhancer-promoter DNA interaction (via DE1 but not DE2) that leads to activation of the Mapk3 (mitogen-activated kinase 3) locus and endoderm commitment during ES cell differentiation. (c) Binding of transcription factors (TFs) to Mediator induces conformational changes that convert Mediator from an inactive, closed conformation to an open, transcriptionally competent one, which in turns, facilitates additional contacts with other TFs occupied at the proximal (PE) or distal (DE) enhancers as well as the general transcription machinery (general transcription factors, GTFs, and RNA polymerase II, Pol II) assembled on a gene promoter (TATA). The modular nature of Mediator provides unique contact surfaces for diverse TFs. In the hypothetical example depicted above, recruitment of Mediator to the DE of Gene A by TF1 via the middle module causes a conformational change in Mediator that exposes unique, TF1-dependent interacting surfaces for Pol II and PE-bound TF3. On the other hand, activation of Gene B involves the binding of TF2 to Mediator tail at PE. TF2-induced conformation change in Mediator exposes new docking sites for another coactivator (“4”) and the general transcription machinery [69]. (d) In ES cells, the Xpc-Rad23b-Cetn2 complex (SCC) functions both as a coactivator for Oct4 and Sox2 at the Nanog gene, and as an initiator of global genome-nucleotide excision repair (GG-NER) by binding to specific DNA lesion and recruiting other NER factors (Xpa, Rpa, TFIIH, Xpg and Xpf-Ercc1). SCC may function to couple stem cell-specific transcription with genome surveillance.