Juven-Gershon T, Kadonaga JTRegulation of gene expression via the core promoter and the basal transcriptional machinery. Dev Biol 339:225-229

Section of Molecular Biology, 0347, University of California, San Diego, La Jolla, CA 92093-0347, USA.
Developmental Biology (Impact Factor: 3.55). 09/2009; 339(2):225-9. DOI: 10.1016/j.ydbio.2009.08.009
Source: PubMed


The RNA polymerase II core promoter is a structurally and functionally diverse transcriptional regulatory element. There are two main strategies for transcription initiation - focused and dispersed initiation. In focused initiation, transcription starts from a single nucleotide or within a cluster of several nucleotides, whereas in dispersed initiation, there are several weak transcription start sites over a broad region of about 50 to 100 nucleotides. Focused initiation is the predominant means of transcription in simpler organisms, whereas dispersed initiation is observed in approximately two-thirds of vertebrate genes. Regulated genes tend to have focused promoters, and constitutive genes typically have dispersed promoters. Hence, in vertebrates, focused promoters are used in a small but biologically important fraction of genes. The properties of focused core promoters are dependent upon the presence or absence of sequence motifs such as the TATA box and DPE. For example, Caudal, a key regulator of the homeotic gene network, preferentially activates transcription from DPE- versus TATA-dependent promoters. The basal transcription factors, which act in conjunction with the core promoter, are another important component in the regulation of gene expression. For instance, upon differentiation of myoblasts to myotubes, the cells undergo a switch from a TFIID-based transcription system to a TRF3-TAF3-based system. These findings suggest that the core promoter and basal transcription factors are important yet mostly unexplored components in the regulation of gene expression.

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    • "May 17, 2014; revised version accepted June 5, 2014. The signals that direct the initiation of transcription ultimately converge at the RNA polymerase II (Pol II) core promoter, which is sometimes referred to as the gateway to transcription (for reviews, see Smale and Kadonaga 2003; Goodrich and Tjian 2010; Juven-Gershon and Kadonaga 2010; Kadonaga 2012). The core promoter comprises the stretch of DNA that is typically from À40 to +40 nucleotides (nt) relative to the +1 start site, which is sufficient for accurate transcription initiation. "
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    ABSTRACT: The TCT core promoter element is present in most ribosomal protein (RP) genes in Drosophila and humans. Here we show that TBP (TATA box-binding protein)-related factor TRF2, but not TBP, is required for transcription of the TCT-dependent RP genes. In cells, TCT-dependent transcription, but not TATA-dependent transcription, increases or decreases upon overexpression or depletion of TRF2. In vitro, purified TRF2 activates TCT but not TATA promoters. ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing) experiments revealed the preferential localization of TRF2 at TCT versus TATA promoters. Hence, a specialized TRF2-based RNA polymerase II system functions in the synthesis of RPs and complements the RNA polymerase I and III systems.
    Genes & Development 06/2014; 28(14). DOI:10.1101/gad.245662.114 · 10.80 Impact Factor
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    • "The chromatin landscape around active gene promoters is characterized by the presence of several distinct features including the histone variant H2A.Z and acetylated histones H3 and H4 [37]. Additionally, distinct DNA-elements in the promoter region can contribute to PIC assembly. "
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    ABSTRACT: The process of eukaryotic transcription initiation involves the assembly of basal transcription factor complexes on the gene promoter. The recruitment of TFIID is an early and important step in this process. Gene promoters contain distinct DNA sequence elements and are marked by the presence of post-translationally modified nucleosomes. The contributions of these individual features for TFIID recruitment remain to be elucidated. Here, we use immobilized reconstituted promoter nucleosomes, conventional biochemistry and quantitative mass spectrometry to investigate the influence of distinct histone modifications and functional DNA-elements on the binding of TFIID. Our data reveal synergistic effects of H3K4me3, H3K14ac and a TATA box sequence on TFIID binding in vitro. Stoichiometry analyses of affinity purified human TFIID identified the presence of a stable dimeric core. Several peripheral TAFs, including those interacting with distinct promoter features, are substoichiometric yet present in substantial amounts. Finally, we find that the TAF3 subunit of TFIID binds to poised promoters in an H3K4me3-dependent manner. Moreover, the PHD-finger of TAF3 is important for rapid induction of target genes. Thus, fine-tuning of TFIID engagement on promoters is driven by synergistic contacts with both DNA-elements and histone modifications, eventually resulting in a high affinity interaction and activation of transcription.
    PLoS ONE 09/2013; 8(9):e73495. DOI:10.1371/journal.pone.0073495 · 3.23 Impact Factor
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    • "anticipated diversity of core promoter types and features, which suggests differential core promoter usage by subsets of genes (for reviews, see Müller et al. 2007; Goodrich and Tjian 2010; Juven-Gershon and Kadonaga 2010; Ohler and Wassarman 2010; Lenhard et al. 2012). The diversity of core promoters may reflect alternative integration points for developmental signals and plays a role in differential transcription regulation (D'Alessio et al. 2009; Müller et al. 2010). "
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    ABSTRACT: Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in different physiological and developmental contexts. Here, we provide a first and comprehensive description of the core promoter repertoire and its dynamic use during the development of a vertebrate embryo. By using cap analysis of gene expression (CAGE), we mapped transcription initiation events at single nucleotide resolution across 12 stages of zebrafish development. These CAGE-based transcriptome maps reveal genome-wide rules of core promoter usage, structure and dynamics, key to understanding the control of gene regulation during vertebrate ontogeny. They revealed the existence of multiple classes of pervasive intra- and intergenic post-transcriptionally processed RNA products and their developmental dynamics. Among these RNAs, we report splice donor site-associated intronic RNA (sRNA) to be specific to genes of the splicing machinery. For the identification of conserved features we compared the zebrafish datasets to the first CAGE promoter map of Tetraodon and the existing human CAGE data. We show that a number of features, such as promoter type, newly discovered promoter properties such as a specialised purine rich initiator motif, as well as sRNAs and the genes, in which they are detected, are conserved in mammalian and Tetraodon CAGE-defined promoter maps. The zebrafish developmental promoterome represents a powerful resource for studying developmental gene regulation and revealing promoter features shared across vertebrates.
    Genome Research 09/2013; 23(11). DOI:10.1101/gr.153692.112 · 14.63 Impact Factor
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