scholarly journals Impaired Core Promoter Recognition Caused by Novel Yeast TAF145 Mutations Can Be Restored by Creating a Canonical TATA Element within the Promoter Region of the TUB2Gene

2000 ◽  
Vol 20 (7) ◽  
pp. 2385-2399 ◽  
Author(s):  
Yoshihiro Tsukihashi ◽  
Tsuyoshi Miyake ◽  
Masashi Kawaichi ◽  
Tetsuro Kokubo
Keyword(s):  
Core Promoter ◽  
Temperature Sensitive ◽  
Reporter System ◽  
Core Promoters ◽  
The Core ◽  
General Transcription Factor ◽  
Eukaryotic Genes ◽  
Specific Subset ◽  
Tata Element ◽  
Promoter Recognition

ABSTRACT The general transcription factor TFIID, which is composed of TATA-binding protein (TBP) and an array of TBP-associated factors (TAFs), has been shown to play a crucial role in recognition of the core promoters of eukaryotic genes. We isolated Saccharomyces cerevisiae yeast TAF145 (yTAF145) temperature-sensitive mutants in which transcription of a specific subset of genes was impaired at restrictive temperatures. The set of genes affected in these mutants overlapped with but was not identical to the set of genes affected by a previously reportedyTAF145 mutant (W.-C. Shen and M. R. Green, Cell 90:615–624, 1997). To identify sequences which rendered transcription yTAF145 dependent, we conducted deletion analysis of theTUB2 promoter using a novel mini-CLN2 hybrid gene reporter system. The results showed that the yTAF145mutations we isolated impaired core promoter recognition but did not affect activation by any of the transcriptional activators we tested. These observations are consistent with the reported yTAF145 dependence of the CLN2 core promoter in the mutant isolated by Shen and Green, although the CLN2 core promoter functioned normally in the mutants we report here. These results suggest that different promoters require different yTAF145 functions for efficient transcription. Interestingly, insertion of a canonical TATA element into the TATA-less TUB2 promoter rescued impaired transcription in the yTAF145 mutants we studied. It therefore appears that strong binding of TBP to the core promoter can alleviate the requirement for at least one yTAF145 function.

Predicting Polymerase II Core Promoters by Cooperating Transcription Factor Binding Sites in Eukaryotic Genes

2004 ◽  
Vol 36 (4) ◽  
pp. 250-258 ◽  
Author(s):  
Xiao-Tu Ma ◽  
Min-Ping Qian ◽  
Hai-Xu Tang
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Core Promoter ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Upstream Gene ◽  
Core Promoters ◽  
Factor Binding ◽  
The Core ◽  
Eukaryotic Genes

Abstract Several discriminate functions for predicting core promoters that based on the potential cooperation between transcription factor binding sites (TFBSs) are discussed. It is demonstrated that the promoter predicting accuracy is improved when the cooperation among TFBSs is taken into consideration. The core promoter region of a newly discovered gene CKLFSF1 is predicted to locate more than 1.5 kb far away from the 5′ end of the transcript and in the last intron of its upstream gene, which is experimentally confirmed later. The core promoters of 3402 human RefSeq sequences, obtained by extending the mRNAs in human genome sequences, are predicted by our algorithm, and there are about 60% of the predicted core promoters locating within the ± 500 bp region relative to the annotated transcription start site.

scholarly journals Evidence that Mediator is essential for Pol II transcription, but is not a required component of the preinitiation complex in vivo

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Natalia Petrenko ◽  
Yi Jin ◽  
Koon Ho Wong ◽  
Kevin Struhl
Keyword(s):  
Core Promoter ◽  
Mediator Complex ◽  
Preinitiation Complex ◽  
Pol Ii ◽  
Core Promoters ◽  
The Core ◽  
Promoter Escape ◽  
General Transcription Factor ◽  
Occupancy Profile

The Mediator complex has been described as a general transcription factor, but it is unclear if it is essential for Pol II transcription and/or is a required component of the preinitiation complex (PIC) in vivo. Here, we show that depletion of individual subunits, even those essential for cell growth, causes a general but only modest decrease in transcription. In contrast, simultaneous depletion of all Mediator modules causes a drastic decrease in transcription. Depletion of head or middle subunits, but not tail subunits, causes a downstream shift in the Pol II occupancy profile, suggesting that Mediator at the core promoter inhibits promoter escape. Interestingly, a functional PIC and Pol II transcription can occur when Mediator is not detected at core promoters. These results provide strong evidence that Mediator is essential for Pol II transcription and stimulates PIC formation, but it is not a required component of the PIC in vivo.

scholarly journals Computational identification and experimental characterization of preferred downstream positions in human core promoters

2021 ◽  
Author(s):  
René Dreos ◽  
Nati Malachi ◽  
Anna Sloutskin ◽  
Philipp Bucher ◽  
Tamar Juven-Gershon
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Motif Discovery ◽  
Core Promoter ◽  
Sequence Motifs ◽  
Promoter Element ◽  
Pol Ii ◽  
Core Promoters ◽  
The Core

AbstractMetazoan core promoters, which direct the initiation of transcription by RNA polymerase II (Pol II), may contain short sequence motifs termed core promoter elements/motifs (e.g. the TATA box, initiator (Inr) and downstream core promoter element (DPE)), which recruit Pol II via the general transcription machinery. The DPE was discovered and extensively characterized in Drosophila, where it is strictly dependent on both the presence of an Inr and the precise spacing from it. Since the Drosophila DPE is recognized by the human transcription machinery, it is most likely that some human promoters contain a downstream element that is similar, though not necessarily identical, to the Drosophila DPE. However, only a couple of human promoters were shown to contain a functional DPE, and attempts to computationally detect human DPE-containing promoters have mostly been unsuccessful. Using a newly-designed motif discovery strategy based on Expectation-Maximization probabilistic partitioning algorithms, we discovered preferred downstream positions (PDP) in human promoters that resemble the Drosophila DPE. Available chromatin accessibility footprints revealed that Drosophila and human Inr+DPE promoter classes are not only highly structured, but also similar to each other, particularly in the proximal downstream region. Clustering of the corresponding sequence motifs using a neighbor-joining algorithm strongly suggests that canonical Inr+DPE promoters could be common to metazoan species. Using reporter assays we demonstrate the contribution of the identified downstream positions to the function of multiple human promoters. Furthermore, we show that alteration of the spacing between the Inr and PDP by two nucleotides results in reduced promoter activity, suggesting a strict spacing dependency of the newly discovered human PDP on the Inr. Taken together, our strategy identified novel functional downstream positions within human core promoters, supporting the existence of DPE-like motifs in human promoters.Author summaryTranscription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properties to it. Interestingly, core promoter motifs can be located both upstream and downstream of the transcription start site. Variable compositions of core promoter elements have been identified. The initiator (Inr) motif and the downstream core promoter element (DPE) is a combination of elements that has been identified and extensively characterized in fruit flies. Although a few Inr+DPE - containing human promoters have been identified, the presence of transcriptionally important downstream core promoter positions within human promoters has been a matter of controversy in the literature. Here, using a newly-designed motif discovery strategy, we discovered preferred downstream positions in human promoters that resemble fruit fly DPE. Clustering of the corresponding sequence motifs in eight additional species indicated that such promoters could be common to multicellular non-plant organisms. Importantly, functional characterization of the newly discovered preferred downstream positions supports the existence of Inr+DPE-containing promoters in human genes.

scholarly journals Identification and characterization of cis-regulatory elements for photoreceptor type-specific transcription in zebrafish

2019 ◽  
Author(s):  
Wei Fang ◽  
Yi Wen ◽  
Xiangyun Wei
Keyword(s):  
Core Promoter ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Protein Coding ◽  
Core Promoters ◽  
Protein Coding Genes ◽  
The Core ◽  
Cell Type Specific ◽  
Identification And Characterization

AbstractTissue-specific or cell type-specific transcription of protein-coding genes is controlled by both trans-regulatory elements (TREs) and cis-regulatory elements (CREs). However, it is challenging to identify TREs and CREs, which are unknown for most genes. Here, we describe a protocol for identifying two types of transcription-activating CREs—core promoters and enhancers—of zebrafish photoreceptor type-specific genes. This protocol is composed of three phases: bioinformatic prediction, experimental validation, and characterization of the CREs. To better illustrate the principles and logic of this protocol, we exemplify it with the discovery of the core promoter and enhancer of the mpp5b apical polarity gene (also known as ponli), whose red, green, and blue (RGB) cone-specific transcription requires its enhancer, a member of the rainbow enhancer family. While exemplified with an RGB cone-specific gene, this protocol is general and can be used to identify the core promoters and enhancers of other protein-coding genes.

scholarly journals A Role for Gcn5-Mediated Global Histone Acetylation in Transcriptional Regulation

2006 ◽  
Vol 26 (5) ◽  
pp. 1610-1616 ◽  
Author(s):  
Rachel Maria Imoberdorf ◽  
Irini Topalidou ◽  
Michel Strubin
Keyword(s):  
Histone Acetylation ◽  
Core Promoter ◽  
Histone Acetyltransferases ◽  
Gene Promoters ◽  
Core Promoters ◽  
The Core ◽  
Strength Of Interaction ◽  
Genome Wide ◽  
The Common

ABSTRACT Transcriptional activators often require histone acetyltransferases (HATs) for full activity. The common explanation is that activators directly recruit HATs to gene promoters to locally hyperacetylate histones and thereby facilitate transcription complex formation. However, in addition to being targeted to specific loci, HATs such as Gcn5 also modify histones genome-wide. Here we provide evidence for a role of this global HAT activity in regulated transcription. We show that activation by direct recruitment of the transcriptional machinery neither recruits Gcn5 nor induces changes in histone acetylation yet can strongly depend on Gcn5 at promoters showing a high basal state of Gcn5-mediated histone acetylation. We also show that Gcn5 dependency varies among core promoters and is influenced by the strength of interaction used to recruit the machinery and by the affinity of the latter for the core promoter. These data support a role for global Gcn5 HAT activity in modulating transcription independently of its known coactivator function.

scholarly journals Highly diversified core promoters in the human genome and their effects on gene expression and disease predisposition

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Hemant Gupta ◽  
Khyati Chandratre ◽  
Siddharth Sinha ◽  
Teng Huang ◽  
Xiaobing Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Genome ◽  
Transcription Initiation ◽  
Gene Expression Regulation ◽  
Core Promoter ◽  
Genome Project ◽  
Human Populations ◽  
Core Promoters ◽  
The Core ◽  
Disease Predisposition

Abstract Background Core promoter controls transcription initiation. However, little is known for core promoter diversity in the human genome and its relationship with diseases. We hypothesized that as a functional important component in the genome, the core promoter in the human genome could be under evolutionary selection, as reflected by its highly diversification in order to adjust gene expression for better adaptation to the different environment. Results Applying the “Exome-based Variant Detection in Core-promoters” method, we analyzed human core-promoter diversity by using the 2682 exome data sets of 25 worldwide human populations sequenced by the 1000 Genome Project. Collectively, we identified 31,996 variants in the core promoter region (− 100 to + 100) of 12,509 human genes (https://dbhcpd.fhs.um.edu.mo). Analyzing the rich variation data identified highly ethnic-specific patterns of core promoter variation between different ethnic populations, the genes with highly variable core promoters, the motifs affected by the variants, and their involved functional pathways. eQTL test revealed that 12% of core promoter variants can significantly alter gene expression level. Comparison with GWAS data we located 163 variants as the GWAS identified traits associated with multiple diseases, half of these variants can alter gene expression. Conclusion Data from our study reals the highly diversified nature of core promoter in the human genome, and highlights that core promoter variation could play important roles not only in gene expression regulation but also in disease predisposition.

scholarly journals Selective Promoter Recognition by Chlamydial σ28 Holoenzyme

2006 ◽  
Vol 188 (21) ◽  
pp. 7364-7377 ◽  
Author(s):  
Li Shen ◽  
Xiaogeng Feng ◽  
Yuan Yuan ◽  
Xudong Luo ◽  
Thomas P. Hatch ◽  
...  
Keyword(s):  
Core Promoter ◽  
Sigma Factors ◽  
Promoter Sequences ◽  
E Coli ◽  
The Core ◽  
Recognition Specificity ◽  
Promoter Recognition ◽  
Transcription In Vitro

ABSTRACT The σ transcription factor confers the promoter recognition specificity of RNA polymerase (RNAP) in eubacteria. Chlamydia trachomatis has three known sigma factors, σ66, σ54, and σ28. We developed two methods to facilitate the characterization of promoter sequences recognized by C. trachomatis σ28 (σ28 Ct). One involved the arabinose-induced expression of plasmid-encoded σ28 Ct in a strain of Escherichia coli defective in the σ28 structural gene, fliA. The second was an analysis of transcription in vitro with a hybrid holoenzyme reconstituted with E. coli RNAP core and recombinant σ28 Ct. These approaches were used to investigate the interactions of σ28 Ct with the σ28 Ct-dependent hctB promoter and selected E. coli σ28 (σ28 Ec)-dependent promoters, in parallel, compared with the promoter recognition properties of σ28 EC. Our results indicate that RNAP containing σ28 Ct has at least three characteristics: (i) it is capable of recognizing some but not all σ28 EC-dependent promoters; (ii) it can distinguish different promoter structures, preferentially activating promoters with upstream AT-rich sequences; and (iii) it possesses a greater flexibility than σ28 EC in recognizing variants with different spacing lengths separating the −35 and −10 elements of the core promoter.

scholarly journals Escherichia coli Promoters with UP Elements of Different Strengths: Modular Structure of Bacterial Promoters

1998 ◽  
Vol 180 (20) ◽  
pp. 5375-5383 ◽  
Author(s):  
Wilma Ross ◽  
Sarah E. Aiyar ◽  
Julia Salomon ◽  
Richard L. Gourse
Keyword(s):  
Escherichia Coli ◽  
Core Promoter ◽  
Consensus Sequence ◽  
Α Subunit ◽  
Core Promoters ◽  
E Coli ◽  
Promoter Recognition ◽  
Transcription In Vitro ◽  
Up Elements

ABSTRACT The α subunit of Escherichia coli RNA polymerase (RNAP) participates in promoter recognition through specific interactions with UP element DNA, a region upstream of the recognition hexamers for the ς subunit (the −10 and −35 hexamers). UP elements have been described in only a small number of promoters, including the rRNA promoter rrnB P1, where the sequence has a very large (30- to 70-fold) effect on promoter activity. Here, we analyzed the effects of upstream sequences from several additional E. coli promoters (rrnD P1, rrnB P2, λp R, lac, merT, and RNA II). The relative effects of different upstream sequences were compared in the context of their own core promoters or as hybrids to thelac core promoter. Different upstream sequences had different effects, increasing transcription from 1.5- to ∼90-fold, and several had the properties of UP elements: they increased transcription in vitro in the absence of accessory protein factors, and transcription stimulation required the C-terminal domain of the RNAP α subunit. The effects of the upstream sequences correlated generally with their degree of similarity to an UP element consensus sequence derived previously. Protection of upstream sequences by RNAP in footprinting experiments occurred in all cases and was thus not a reliable indicator of UP element strength. These data support a modular view of bacterial promoters in which activity reflects the composite effects of RNAP interactions with appropriately spaced recognition elements (−10, −35, and UP elements), each of which contributes to activity depending on its similarity to the consensus.

scholarly journals Analysis of a Ubiquitous Promoter Element in a Primitive Eukaryote: Early Evolution of the Initiator Element

1999 ◽  
Vol 19 (3) ◽  
pp. 2380-2388 ◽  
Author(s):  
David R. Liston ◽  
Patricia J. Johnson
Keyword(s):  
Trichomonas Vaginalis ◽  
Core Promoter ◽  
Start Site ◽  
Promoter Element ◽  
Core Promoters ◽  
Core Promoter Element ◽  
Tata Element ◽  
Protein Encoding ◽  
Parasitic Protist ◽  
Encoding Genes

ABSTRACTTypical metazoan core promoter elements, such as TATA boxes and Inr motifs, have yet to be identified in early-evolving eukaryotes, underscoring the extensive divergence of these organisms. Towards the identification of core promoters in protists, we have studied transcription of protein-encoding genes in one of the earliest-diverging lineages of Eukaryota, that represented by the parasitic protistTrichomonas vaginalis. A highly conserved element, comprised of a motif similar to a metazoan initiator (Inr) element, surrounds the start site of transcription in all examinedT. vaginalisgenes. In contrast, a metazoan-like TATA element appears to be absent in trichomonad promoters. We demonstrate that the conserved motif found inT. vaginalisprotein-encoding genes is an Inr promoter element. This trichomonad Inr is essential for transcription, responsible for accurate start site selection, and interchangeable between genes, demonstrating its role as a core promoter element. The sequence requirements of the trichomonad Inr are similar to metazoan Inrs and can be replaced by a mammalian Inr. These studies show that the Inr is a ubiquitous, core promoter element for protein-encoding genes in an early-evolving eukaryote. Functional and structural similarities between this protist Inr and the metazoan Inr strongly indicate that the Inr promoter element evolved early in eukaryotic evolution.

scholarly journals Genomic environments scale the activities of diverse core promoters

2021 ◽  
Author(s):  
Clarice KY Hong ◽  
Barak A Cohen
Keyword(s):  
Core Promoter ◽  
Massively Parallel ◽  
Reporter Assay ◽  
Core Promoters ◽  
The Core ◽  
Genomic Location ◽  
Promoter Class ◽  
A Genome ◽  
Genomic Locations ◽  
Massively Parallel Reporter Assay

AbstractOne model for how cells integrate cis-regulatory information is that different classes of core promoters respond specifically to certain genomic environments. We tested this model using a genome-integrated massively parallel reporter assay (MPRA) to measure the activity of hundreds of diverse core promoters at four genomic locations and, in a complementary experiment, six core promoters at thousands of genomic locations. While genomic locations had large effects on expression, the relative strengths of core promoters were preserved across locations regardless of promoter class, suggesting that their intrinsic activities are scaled by diverse genomic environments. The extent of scaling depends on the genomic location and the strength of the core promoter, but not on its class. Our results support a modular genome in which genomic environments scale the activities of core promoters.One Sentence SummaryGenomic environments have consistent effects on gene expression that depend on the strength, but not the class of core promoter.

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