Journal ArticleDOI
The core promoter: At the heart of gene expression.
TLDR
A broad spectrum of studies that highlight the importance of the core promoter and its pivotal role in the regulation of metazoan gene expression are reviewed and future research directions and challenges are suggested.About:
This article is published in Biochimica et Biophysica Acta.The article was published on 2015-08-01. It has received 140 citations till now. The article focuses on the topics: Enhancer RNAs & Transcription factor II D.read more
Citations
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Journal ArticleDOI
Nascent RNA sequencing reveals distinct features in plant transcription
Jonathan Hetzel,Sascha H. Duttke,Sascha H. Duttke,Christopher Benner,Joanne Chory,Joanne Chory +5 more
TL;DR: An extensive catalog of nascent and steady-state transcripts in Arabidopsis thaliana seedlings was generated using global nuclear run-on sequencing, 5′GRO-seq, and RNA-seq and published maize data to capture characteristics of plant transcription to provide insight into plant transcription and eukaryotic gene expression as a whole.
Journal ArticleDOI
The punctilious RNA polymerase II core promoter.
TL;DR: An expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure is described.
Journal ArticleDOI
Plant synthetic promoters and transcription factors.
TL;DR: The recent advances in synthetic promoters and TFs in plants are reviewed and a speculate on their future is speculated.
Journal ArticleDOI
Promoter analysis and prediction in the human genome using sequence-based deep learning models.
TL;DR: This work further develops the deep learning approach that was relatively successful to discriminate short promoter and non-promoter sequences and predicts the exact positions of the TSS inside the genomic sequences testing every possible location.
Journal ArticleDOI
ElemeNT: a computational tool for detecting core promoter elements.
Anna Sloutskin,Yehuda M. Danino,Yaron Orenstein,Yonathan Zehavi,Tirza Doniger,Ron Shamir,Tamar Juven-Gershon +6 more
TL;DR: The Elements Navigation Tool (ElemeNT) is a user-friendly web-based, interactive tool for prediction and display of putative core promoter elements and their biologically-relevant combinations, and the CORE database summarizes ElemeNT-predicted core promoter Elements near CAGE and RNA-seq-defined Drosophila melanogaster transcription start sites (TSSs).
References
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Journal ArticleDOI
Activator-mediated disruption of sequence-specific DNA contacts by the general transcription factor TFIIB.
TL;DR: The results reveal a novel function for activators in the modulation of core promoter recognition by TFIIB, which suppresses the basal level of transcription elicited by a core promoter, and increases the amplitude of transcriptional stimulation in the presence of an activator protein.
Journal ArticleDOI
Novel Cofactors and TFIIA Mediate Functional Core Promoter Selectivity by the Human TAFII150-Containing TFIID Complex
TL;DR: It is demonstrated that the human TAFII150-containing TFIID complex is not sufficient, in the context of all purified GTFs and RNA polymerase II, to mediate transcription synergism between TATA and initiator elements and initiate-directed transcription from a TAF II-dependent TATA-less promoter.
Journal ArticleDOI
Functional Characterization of Core Promoter Elements: DPE-Specific Transcription Requires the Protein Kinase CK2 and the PC4 Coactivator
TL;DR: This work finds that the protein kinase CK2 and the coactivator PC4 establish DPE-specific transcription in an in vitro transcription system containing TFIID, Mediator, and the GTFs, and establishes that CK2 acts as a switch, converting the transcriptional machinery from functioning on one type of downstream element to another.
Journal ArticleDOI
Chromatin and DNA sequences in defining promoters for transcription initiation
TL;DR: This review attempts to summarise these promoter features and discusses the available evidence pointing at their interactions in defining transcription initiation in developmental contexts.
Journal ArticleDOI
The complex transcription regulatory landscape of our genome: control in three dimensions
Erik Splinter,Wouter de Laat +1 more
TL;DR: Functional genomics studies that uncover and characterize sequence motifs that can control gene transcription over distance are discussed, and it is argued transcriptional control over distance can be understood when considering action in the context of the folded genome.
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