Core Promoter Recognition Complex Research Articles

Core promoter factor TAF9B regulates neuronal gene expression.

Emerging evidence points to an unexpected diversification of core promoter recognition complexes that serve as important regulators of cell-type specific gene transcription. Here, we report that the orphan TBP-associated factor TAF9B is selectively up-regulated upon in vitro motor neuron differentiation, and is required for the transcriptional induction of specific neuronal genes, while dispensable for global gene expression in murine ES cells. TAF9B binds to both promoters and distal enhancers of neuronal genes, partially co-localizing at binding sites of OLIG2, a key activator of motor neuron differentiation. Surprisingly, in this neuronal context TAF9B becomes preferentially associated with PCAF rather than the canonical TFIID complex. Analysis of dissected spinal column from Taf9b KO mice confirmed that TAF9B also regulates neuronal gene transcription in vivo. Our findings suggest that alternative core promoter complexes may provide a key mechanism to lock in and maintain specific transcriptional programs in terminally differentiated cell types.DOI: http://dx.doi.org/10.7554/eLife.02559.001.

Genome Wide Association Analysis of a Founder Population Identified TAF3 as a Gene for MCHC in Humans

The red blood cell related traits are highly heritable but their genetics are poorly defined. Only 5–10% of the total observed variance is explained by the genetic loci found to date, suggesting that additional loci should be searched using approaches alternative to large meta analysis. GWAS (Genome Wide Association Study) for red blood cell traits in a founder population cohort from Northern Italy identified a new locus for mean corpuscular hemoglobin concentration (MCHC) in the TAF3 gene. The association was replicated in two cohorts (rs1887582, P = 4.25E–09). TAF3 encodes a transcription cofactor that participates in core promoter recognition complex, and is involved in zebrafish and mouse erythropoiesis. We show here that TAF3 is required for transcription of the SPTA1 gene, encoding alpha spectrin, one of the proteins that link the plasma membrane to the actin cytoskeleton. Mutations in SPTA1 are responsible for hereditary spherocytosis, a monogenic disorder of MCHC, as well as for the normal MCHC level. Based on our results, we propose that TAF3 is required for normal erythropoiesis in human and that it might have a role in controlling the ratio between hemoglobin (Hb) and cell volume and in the dynamics of RBC maturation in healthy individuals. Finally, TAF3 represents a potential candidate or a modifier gene for disorders of red cell membrane.

Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3

Deciphering the molecular basis of pluripotency is fundamental to our understanding of development and embryonic stem cell function. Here, we report that TAF3, a TBP-associated core promoter factor, is highly enriched in ES cells. In this context, TAF3 is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. In addition to its role in the core promoter recognition complex TFIID, genome-wide binding studies reveal that TAF3 localizes to a subset of chromosomal regions bound by CTCF/cohesin that are selectively associated with genes upregulated by TAF3. Notably, CTCF directly recruits TAF3 to promoter distal sites and TAF3-dependent DNA looping is observed between the promoter distal sites and core promoters occupied by TAF3/CTCF/cohesin. Together, our findings support a new role of TAF3 in mediating long-range chromatin regulatory interactions that safeguard the finely-balanced transcriptional programs underlying pluripotency.

Subnuclear segregation of genes and core promoter factors in myogenesis

Recent findings implicate alternate core promoter recognition complexes in regulating cellular differentiation. Here we report a spatial segregation of the alternative core factor TAF3, but not canonical TFIID subunits, away from the nuclear periphery, where the key myogenic gene MyoD is preferentially localized in myoblasts. This segregation is correlated with the differential occupancy of TAF3 versus TFIID at the MyoD promoter. Loss of this segregation by modulating either the intranuclear location of the MyoD gene or TAF3 protein leads to altered TAF3 occupancy at the MyoD promoter. Intriguingly, in differentiated myotubes, the MyoD gene is repositioned to the nuclear interior, where TAF3 resides. The specific high-affinity recognition of H3K4Me3 by the TAF3 PHD (plant homeodomain) finger appears to be required for the sequestration of TAF3 to the nuclear interior. We suggest that intranuclear sequestration of core transcription components and their target genes provides an additional mechanism for promoter selectivity during differentiation.

Core promoter recognition complex changes accompany liver development

Recent studies of several key developmental transitions have brought into question the long held view of the basal transcriptional apparatus as ubiquitous and invariant. In an effort to better understand the role of core promoter recognition and coactivator complex switching in cellular differentiation, we have examined changes in transcription factor IID (TFIID) and cofactor required for Sp1 activation/Mediator during mouse liver development. Here we show that the differentiation of fetal liver progenitors to adult hepatocytes involves a wholesale depletion of canonical cofactor required for Sp1 activation/Mediator and TFIID complexes at both the RNA and protein level, and that this alteration likely involves silencing of transcription factor promoters as well as protein degradation. It will be intriguing for future studies to determine if a novel and as yet unknown core promoter recognition complex takes the place of TFIID in adult hepatocytes and to uncover the mechanisms that down-regulate TFIID during this critical developmental transition.

Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation

The eukaryotic core promoter recognition complex was generally thought to play an essential but passive role in the regulation of gene expression. However, recent evidence now indicates that core promoter recognition complexes together with 'non-prototypical' subunits may have a vital regulatory function in driving cell-specific programmes of transcription during development. Furthermore, new roles for components of these complexes have been identified beyond development; for example, in mediating interactions with chromatin and in maintaining active gene expression across cell divisions.

Wnt signaling targets ETO coactivation domain of TAF4/TFIID in vivo

Understanding the diverse activities of the multisubunit core promoter recognition complex TFIID in vivo requires knowledge of how individual subunits contribute to overall functions of this TATA box-binding protein (TBP)/TBP-associated factor (TAF) complex. By generating altered holo-TFIID complexes in Drosophila we identify the ETO domain of TAF4 as a coactivator domain likely targeted by Pygopus, a protein that is required for Wingless-induced transcription of naked cuticle. These results establish a coactivator function of TAF4 and provide a strategy to dissect mechanisms of TFIID function in vivo.

MyoD Targets TAF3/TRF3 to Activate Myogenin Transcription

Skeletal muscle differentiation requires a cascade of transcriptional events to control the spatial and temporal expression of muscle-specific genes. Until recently, muscle-specific transcription was primarily attributed to prototypic enhancer-binding factors, while the role of core promoter recognition complexes in directing myogenesis remained unknown. Here, we report the development of a purified reconstituted system to analyze the properties of a TAF3/TRF3 complex in directing transcription initiation at the Myogenin promoter. Importantly, this new complex is required to replace the canonical TFIID to recapitulate MyoD-dependent activation of Myogenin. In vitro and cell-based assays identify a domain of TAF3 that mediates coactivator functions targeted by MyoD. Our findings also suggest changes to CRSP/Mediator in terminally differentiated myotubes. This switching of the core promoter recognition complex during myogenesis allows a more balanced division of labor between activators and TAF coactivators, thus providing another strategy to accommodate cell-specific regulation during metazoan development.

Structural Changes in TAF4b-TFIID Correlate with Promoter Selectivity

Proper ovarian development requires the cell type-specific transcription factor TAF4b, a subunit of the core promoter recognition complex TFIID. We present the 35 A structure of a cell type-specific core promoter recognition complex containing TAF4b and TAF4 (4b/4-IID), which is responsible for directing transcriptional synergy between c-Jun and Sp1 at a TAF4b target promoter. As a first step toward correlating potential structure/function relationships of the prototypic TFIID versus 4b/4-IID, we have compared their 3D structures by electron microscopy and single-particle reconstruction. These studies reveal that TAF4b incorporation into TFIID induces an open conformation at the lobe involved in TFIIA and putative activator interactions. Importantly, this open conformation correlates with differential activator-dependent transcription and promoter recognition by 4b/4-IID. By combining functional and structural analysis, we find that distinct localized structural changes in a megadalton macromolecular assembly can significantly alter its activity and lead to a TAF4b-induced reprogramming of promoter specificity.

An Unexpected Role of TAFs and TRFs in Skeletal Muscle Differentiation: Switching Core Promoter Complexes

Sequence-specific enhancer-binding transcription factors and chromatin-modifying proteins are well recognized for their potential contributions to cell-type-specific gene regulation. In contrast, the role of core promoter recognition factors, such as TFIID in modulating gene- and cell-type-specific programs of transcription has been less understood. In general, the so-called basal factors have largely been relegated to a supporting role as invariant components of the preinitiation complex. To dissect the potential contributions of TFIID to cell-type-specific transcription, we have studied the developmental process of skeletal myogenesis. Terminal differentiation during myogenesis involves an intricate reprogramming of transcription that is thought to be directed by cell-type-specific transcription regulatory factors. Here, we summarize our findings that the canonical TFIID complex must first be dismantled as a requisite step during the differentiation of myoblasts into myotubes and subsequently substituted by a novel core transcription complex composed of TAF3 and TRF3. Although this remarkable mechanism of completely switching core promoter recognition complexes to drive terminal differentiation has not been previously documented, it may eventually prove to be the rule rather than the exception as we learn more about cell-type-specific gene regulation.

Transcription strategies in terminally differentiated cells: shaken to the core

The formation of mature tissues and cell types in eukaryotic organisms requires that cells undergo a regulated series of steps leading to terminal cell differentiation, which includes a permanent withdrawal from the cell cycle and the eventual cessation of all cell proliferation. Concomitant with this process is the stable repression of many genes involved in normal cell growth and cell cycle control, accompanied by profound changes in nuclear chromatin structure that arise as previously active genes gradually become silenced and are modified epigenetically to form facultative heterochromatin (Grigoryev et al. 2006). At the same time, newly activated signaling pathways must induce the de novo expression, function, or nuclear localization of the various tissue-specific enhancer-binding proteins needed to regulate the genes responsible for creating and maintaining the differentiated cell phenotype. A powerful system used to identify the fundamental principles of cell fate specification is the process of skeletal muscle differentation, or myogenesis, in which multipotential mesodermal precursor cells commit and differentiate to a muscle cell fate (Sartorelli and Caretti 2005). This process can be studied in defined sequential stages, wherein the precursor cells first commit to form undifferentiated myoblasts, then differentiate and fuse to form multinucleated myotubes, and subsequently mature into functional myofibers. Key upstream activators in this process include members of the MyoD family of basic helix–loop–helix (bHLH) regulators (MyoD, myogenin, MRF4, and Myf5), as well as the MEF2 family of MADS-box factors (MEF2-A, MEF2-B, MEF2-C, MEF2D). In this system, the myogenic bHLH factors form heterodimers with E-box factors (E12, E47), and function cooperatively with the MEF2 proteins to activate skeletal muscle-specific genes, while also creating strong autoregulatory feedback loops that ensure their own sustained expression (Bassel-Duby and Olson 2006; Baugh and Hunter 2006). MEF2 can also act independently of MyoD through its ability to associate with myocardin and MASTR/SAP domain protein in cardiac and skeletal muscle cells, respectively (Creemers et al. 2006). Moreover, MEF2C also interacts directly with the Notch coactivator, Mastermind (MamL1), the targeted deletion of which causes a severe muscular dystrophy in mice (Shen et al. 2006). These factors assemble large muscle-specific enhancer complexes and cooperate with other DNAbound activators, such as the serum response factor (SRF), to displace repressors and recruit the coactivators needed to up-regulate transcription (Pipes et al. 2006). In this issue of Genes & Development, Deato and Tjian (2007) describe a remarkable new mode of transcriptional regulation in differentiated cells that is centered on the core transcriptional machinery. Detailed analysis of core promoter factor expression in these cells reveals that myotube differentiation is accompanied by a dramatic loss of the TATA-binding protein (TBP) as well as many of the RNA polymerase II (RNAPII) TATA-associated factor (TAF) subunits (TAF1, TAF4, TAF9, TAF10), suggestive of a wholesale extinction of the TFIID complex. The loss of TFIID components, which was detected at both the RNA and protein level, may provide an effective mechanism for large-scale silencing of genes whose functions are needed only in undifferentiated cells, including those that control cell proliferation and progression through the cell cycle. These findings confirm and extend an earlier report from Perletti et al. (2001) that both TBP and TAF4 are down-regulated by targeted proteolysis in C2C12-derived myotubes and differentiated F9 cells. Deato and Tjian (2007) further discovered that the loss of core factors in differentiated myotubes is highly selective and that the expression of certain other core factors, namely the TATA-related factor TRF3 and the TAF3 protein, persists in differentiated cells. Interestingly, TRF3 and TAF3 were found to interact directly to form a minimal core promoter recognition complex that binds to the Myogenin core promoter and cooperates with the myogenic upstream activators to activate transcription in differentiated myotubes. Further analyses in stable small interfering RNA (siRNA)-expressing cell lines established that TRF3 and TAF3 are both necessary for myogenesis, and have no effect on TFIID function or stability in dividing myoblasts. Taken together, these findings support a model in which core promoter switching mediates the global repression of TFIID-dependent genes and simultaneously allows for selective activation of myogenic genes that deCorrespondence. E-MAIL jones@salk.edu; FAX (858) 535-8194. Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.1598007.

Switching of the core transcription machinery during myogenesis.

Transcriptional mechanisms that govern cellular differentiation typically include sequence-specific DNA-binding proteins and chromatin-modifying activities. These regulatory factors are assumed necessary and sufficient to drive both divergent programs of proliferation and terminal differentiation. By contrast, potential contributions of the basal transcriptional apparatus to orchestrate cell-specific gene expression have been poorly explored. In order to probe alternative mechanisms that control differentiation, we have assessed the fate of the core promoter recognition complex, TFIID, during skeletal myogenesis. Here we report that differentiation of myoblast to myotubes involves the disruption of the canonical holo-TFIID and replacement by a novel TRF3/TAF3 (TBP-related factor 3/TATA-binding protein-associated factor 3) complex. This required switching of core promoter complexes provides organisms a simple yet effective means to selectively turn on one transcriptional program while silencing many others. Although this drastic but parsimonious transcriptional switch had previously escaped our attention, it may represent a more general mechanism for regulating cell type-specific terminal differentiation.

Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1

Downstream elements are a newly appreciated class of core promoter elements of RNA polymerase II-transcribed genes. The downstream core element (DCE) was discovered in the human beta-globin promoter, and its sequence composition is distinct from that of the downstream promoter element (DPE). We show here that the DCE is a bona fide core promoter element present in a large number of promoters and with high incidence in promoters containing a TATA motif. Database analysis indicates that the DCE is found in diverse promoters, supporting its functional relevance in a variety of promoter contexts. The DCE consists of three subelements, and DCE function is recapitulated in a TFIID-dependent manner. Subelement 3 can function independently of the other two and shows a TFIID requirement as well. UV photo-cross-linking results demonstrate that TAF1/TAF(II)250 interacts with the DCE subelement DNA in a sequence-dependent manner. These data show that downstream elements consist of at least two types, those of the DPE class and those of the DCE class; they function via different DNA sequences and interact with different transcription activation factors. Finally, these data argue that TFIID is, in fact, a core promoter recognition complex.