The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery

Parry, Trevor J.; Theisen, Joshua W. M.; Hsu, Jer-Yuan; Wang, Yuanliang; Corcoran, David L.; Eustice, Moriah; Ohler, Uwe; Kadonaga, James T.

doi:10.1101/gad.1951110

Cited by 115 publications

(163 citation statements)

References 33 publications

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“…71 The core promoters of most ribosomal protein genes in Drosophila and humans contain a functional TCT motif, which is not recognized by the TBP/TFIID complex. 21 Remarkably, TRF2, but not TBP, has recently been shown to mediate the transcription of ribosomal protein genes that lack a TATA box and have functional TCT motifs. 73 In vitro transcription analysis using Drosophila TRF2-depleted embryonic nuclear extracts demonstrated that transcription of 4 TCT-dependent ribosomal genes (RpL30, RpLP1, RpS12 and RpS15) was reduced, while no effect on transcription of TATA-dependent genes was observed.…”

Section: Tbp-related Factorsmentioning

confidence: 99%

“…The TCT motif is a polypyrimidine initiator located from ¡2 to C6 relative to the TSS, which has been identified in genes encoding ribosomal proteins as well as other proteins involved in translation. 21 Both the MTE and DPE motifs are located at a specific position relative to the Inr (with strict spacing requirements from the A C1 of the Inr) and their function depends on the Inr. The MTE is located from C18 to C27 relative to the A C1 of the Inr, and its consensus sequence is CSARCSSAAC.…”

Section: Introductionmentioning

confidence: 99%

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TRF2: TRansForming the view of general transcription factors

et al. 2015

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These authors contributed equally to this work.Keywords: core promoter elements/motifs, DPE, embryonic development, histone gene cluster, RNAP II transcription, ribosomal protein genes, spermiogenesis, TBP-related factors, TRF2, TCT Transcriptional regulation is pivotal for development and differentiation of organisms. Transcription of eukaryotic protein-coding genes by RNA polymerase II (RNAP II) initiates at the core promoter. Core promoters, which encompass the transcription start site, may contain functional core promoter elements, such as the TATA box, initiator, TCT and downstream core promoter element. TRF2 (TATA-box-binding protein-related factor 2) does not bind TATA box-containing promoters. Rather, it is recruited to core promoters via sequences other than the TATA box. We review the recent findings implicating TRF2 as a basal transcription factor in the regulation of diverse biological processes and specialized transcriptional programs.

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Section: Tbp-related Factorsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

TRF2: TRansForming the view of general transcription factors

et al. 2015

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“…Two dinucleotides, CC and TC, are part of a broader TC/ CT motif (Fig. 3C), similar to the TCT initiator, specific to highly expressed protein translation-associated genes (Parry et al 2010). Indeed, the genes that carry these motifs are also protein translation-associated genes in zebrafish (Supplemental Fig.…”

Section: Evolutionary Conservation Of Sequence Characteristics Suggesmentioning

confidence: 99%

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

et al. 2013

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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 data sets 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 specialized 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.

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“…This initiator motif is common to this functional category of genes in both Drosophila and mammalian genomes. It is characterised by a "sharp" transcription initiation pattern and, in Drosophila, it does not seem to contain a TATA box or any other known fixed-spacing motifs [6]. It has recently been reported that the PIC at this type of promoters lacks TBP, whose place is taken by the structurally related TRF2 [82].…”

Section: Promoter Classes and Modes Of Regulationmentioning

confidence: 99%

Promoter architectures and developmental gene regulation

Haberle

Lenhard

2016

Seminars in Cell & Developmental Biology

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Core promoters are minimal regions sufficient to direct accurate initiation of transcription and are crucial for regulation of gene expression. They are highly diverse in terms of associated core promoter motifs, underlying sequence composition and patterns of transcription initiation.Distinctive features of promoters are also seen at the chromatin level, including nucleosome positioning patterns and presence of specific histone modifications. Recent advances in identifying and characterizing promoters using next-generation sequencing-based technologies have provided the basis for their classification into functional groups and have shed light on their modes of regulation, with important implications for transcriptional regulation in development.This review discusses the methodology and the results of genome-wide studies that provided insight into the diversity of RNA polymerase II promoter architectures in vertebrates and other Metazoa, and the association of these architectures with distinct modes of regulation in embryonic development and differentiation.

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The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery

Cited by 115 publications

References 33 publications

TRF2: TRansForming the view of general transcription factors

TRF2: TRansForming the view of general transcription factors

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

Promoter architectures and developmental gene regulation

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