The core promoter: At the heart of gene expression

Danino, Yehuda M.; Even, Dan; Ideses, Diana; Juven‐Gershon, Tamar

doi:10.1016/j.bbagrm.2015.04.003

Cited by 143 publications

(122 citation statements)

References 259 publications

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“…The process is dependent on the assembly of regulatory multiprotein complexes at promoter sequences, which include TFs responsible for cell type-specific or stimulusresponsive gene expression. These complexes direct the transcriptional machinery, composed of RNA polymerase II and many additional factors, to the start site of gene transcription [2]. Although factors that do not contain a DBD are sometimes regarded as TFs, the standard TF consists of a domain that is responsible for sequence-specific binding to regulatory cis-acting elements in promoters, and additional domains with regulatory functions.…”

Section: Introductionmentioning

confidence: 99%

The AtMYB12 activation domain maps to a short C-terminal region of the transcription factor

Stracke

Turgut-Kara

Weißhaar

2017

Zeitschrift Für Naturforschung C

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Abstract:The Arabidopsis thaliana R2R3-MYB transcription factor MYB12 is a light-inducible, flavonolspecific activator of flavonoid biosynthesis. The transactivation activity of the AtMYB12 protein was analyzed using a C-terminal deletion series in a transient A. thaliana protoplast assay with the goal of mapping the activation domain (AD). Although the deletion of the last 46 C-terminal amino acids did not affect the activation capacity, the deletion of the last 98 amino acids almost totally abolished transactivation of two different target promoters. A domain swap experiment using the yeast GAL4 DNA-binding domain revealed that the region from positions 282 to 328 of AtMYB12 was sufficient for transactivation. In contrast to the R2R3-MYB ADs known thus far, that of AtMYB12 is not located at the rearmost C-terminal end of the protein. The AtMYB12 AD is conserved in other experimentally proven R2R3-MYB flavonol regulators from different species.

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Section: Introductionmentioning

confidence: 99%

The AtMYB12 activation domain maps to a short C-terminal region of the transcription factor

Stracke

Turgut-Kara

Weißhaar

2017

Zeitschrift Für Naturforschung C

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“…At the core promoter, located approximately ±50 bp relative to the TSS, basal TFs cooperate with conserved DNA sequence motifs to orchestrate recruitment of the RNA polymerase (RNAP) (1,3). Transcription has been studied extensively in a number of species (1)(2)(3) but not in plant model systems. Studies focusing on promoterenriched sequences were hindered by the lack of precise TSSs (4, 5) but have improved dramatically through techniques such as paired end analysis of transcription start sites (3PEAT) (6) and cap analysis gene expression (CAGE) (7), but both methods are affected by RNA processing and transcript stability.…”

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confidence: 99%

“…Sequence-specific transcription factors (TFs) commonly bind the proximal promoter around −150 to −50 bp upstream of the transcriptional start site (TSS) (1,2). At the core promoter, located approximately ±50 bp relative to the TSS, basal TFs cooperate with conserved DNA sequence motifs to orchestrate recruitment of the RNA polymerase (RNAP) (1,3). Transcription has been studied extensively in a number of species (1)(2)(3) but not in plant model systems.…”

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confidence: 99%

Nascent RNA sequencing reveals distinct features in plant transcription

Hetzel

Duttke

Benner

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

146

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Transcriptional regulation of gene expression is a major mechanism used by plants to confer phenotypic plasticity, and yet compared with other eukaryotes or bacteria, little is known about the design principles. We generated an extensive catalog of nascent and steadystate transcripts in Arabidopsis thaliana seedlings using global nuclear run-on sequencing (GRO-seq), 5′GRO-seq, and RNA-seq and reanalyzed published maize data to capture characteristics of plant transcription. De novo annotation of nascent transcripts accurately mapped start sites and unstable transcripts. Examining the promoters of coding and noncoding transcripts identified comparable chromatin signatures, a conserved "TGT" core promoter motif and unreported transcription factor-binding sites. Mapping of engaged RNA polymerases showed a lack of enhancer RNAs, promoter-proximal pausing, and divergent transcription in Arabidopsis seedlings and maize, which are commonly present in yeast and humans. In contrast, Arabidopsis and maize genes accumulate RNA polymerases in proximity of the polyadenylation site, a trend that coincided with longer genes and CpG hypomethylation. Lack of promoter-proximal pausing and a higher correlation of nascent and steady-state transcripts indicate Arabidopsis may regulate transcription predominantly at the level of initiation. Our findings provide insight into plant transcription and eukaryotic gene expression as a whole.plant transcription | nascent transcripts | RNA polymerase pausing | 5′GRO-seq | GRO-seq G ene expression is a hallmark of life and subject to adaptation in changing environments. Steady-state transcript levels are a result of transcription initiation, elongation, and termination, followed by maturation and decay. Much has been learned about transcriptional mechanisms using yeast and animal models. In contrast, owing to technical difficulties created by plant cell extracts, there remains a large gap in knowledge in plant transcription. Plants and animals diverged more than 1.6 billion years ago. Studying plant transcription therefore not only contributes to a better understanding of the world's largest food source but also the evolution of eukaryotic gene expression.The signals initiating transcription are ultimately integrated at the promoter. Sequence-specific transcription factors (TFs) commonly bind the proximal promoter around −150 to −50 bp upstream of the transcriptional start site (TSS) (1, 2). At the core promoter, located approximately ±50 bp relative to the TSS, basal TFs cooperate with conserved DNA sequence motifs to orchestrate recruitment of the RNA polymerase (RNAP) (1, 3). Transcription has been studied extensively in a number of species (1-3) but not in plant model systems. Studies focusing on promoterenriched sequences were hindered by the lack of precise TSSs (4, 5) but have improved dramatically through techniques such as paired end analysis of transcription start sites (3PEAT) (6) and cap analysis gene expression (CAGE) (7), but both methods are affected by RNA processing and trans...

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“…The multifarious signals that lead to the initiation of transcription ultimately converge at the core promoter, which is sometimes referred to as the gateway to transcription (for reviews, see Smale and Kadonaga 2003;Goodrich and Tjian 2010;Kadonaga 2012;Danino et al 2015). The core promoter is the stretch of DNA-which typically is from about −40 to +40 nucleotides (nt) relative to the +1 transcription start site (TSS)-that directs the initiation of transcription.…”

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confidence: 99%

The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters

et al. 2017

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DNA sequence signals in the core promoter, such as the initiator (Inr), direct transcription initiation by RNA polymerase II. Here we show that the human Inr has the consensus of BBCA +1 BW at focused promoters in which transcription initiates at a single site or a narrow cluster of sites. The analysis of 7678 focused transcription start sites revealed 40% with a perfect match to the Inr and 16% with a single mismatch outside of the CA +1 core. TATA-like sequences are underrepresented in Inr promoters. This consensus is a key component of the DNA sequence rules that specify transcription initiation in humans.Supplemental material is available for this article.Received November 14, 2016; revised version accepted December 19, 2016. The multifarious signals that lead to the initiation of transcription ultimately converge at the core promoter, which is sometimes referred to as the gateway to transcription (for reviews, see Smale and Kadonaga 2003;Goodrich and Tjian 2010;Kadonaga 2012;Danino et al. 2015). The core promoter is the stretch of DNA-which typically is from about −40 to +40 nucleotides (nt) relative to the +1 transcription start site (TSS)-that directs the initiation of transcription. Core promoters are diverse in terms of their composition and function, and their activities are driven by the presence or absence of DNA sequence motifs such as the TATA box, initiator (Inr), TFIIB recognition elements (BRE u and BRE d ), polypyrimidine initiator (TCT), motif ten element (MTE), and downstream core promoter element (DPE). There are no universal core promoter motifs. Specific core promoter elements can be important for enhancer-promoter specificity (for example, see Butler and Kadonaga 2001; Juven-Gershon et al. 2008) as well as the regulation of gene networks (for example, see Juven-Gershon et al. 2008;Parry et al. 2010;Duttke et al. 2014;Wang et al. 2014).The long-term goal of this study is to gain a more specific understanding of the human core promoter. It has been estimated, for instance, that <25% of human core promoters contain the well-known TATA box or a TATA-like sequence (Gershenzon and Ioshikhes 2005;Carninci et al. 2006;Yang et al. 2007). In fact, it appears that the Inr is the most common core promoter element in humans. For example, ∼48%-49% of human promoters were found to have a sequence in the TSS region (from −5 to +6 relative to the +1 TSS) that is related to the 8-nt "cap signal" (i.e., Inr) position-weight matrix (based on 502 eukaryotic promoters) (Bucher 1990;Gershenzon and Ioshikhes 2005). In addition, it has been found that ∼46% of human promoters contain the YYA +1 NWYY Inr consensus within −80 to +80 nt relative to the TSS (Yang et al. 2007). These observations were interesting, but the precise sequence, abundance, and positioning of the human Inr remained to be determined.The Inr is an extensively studied core promoter element. The presence of a distinct sequence motif that encompasses the TSS was initially described by Corden et al. (1980), and the function of this sequence, w...

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The core promoter: At the heart of gene expression

Cited by 143 publications

References 259 publications

The AtMYB12 activation domain maps to a short C-terminal region of the transcription factor

The AtMYB12 activation domain maps to a short C-terminal region of the transcription factor

Nascent RNA sequencing reveals distinct features in plant transcription

The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters

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