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
Genome-wide analysis of promoter architecture in Drosophila melanogaster
Roger A. Hoskins,Jane M. Landolin,James B. Brown,Jeremy E. Sandler,Hazuki Takahashi,Timo Lassmann,Charles Yu,Benjamin W. Booth,Dayu Zhang,Kenneth H. Wan,Li Yang,Nathan Boley,Justen Andrews,Thomas C. Kaufman,Brenton R. Graveley,Peter J. Bickel,Piero Carninci,Joseph W. Carlson,Susan E. Celniker +18 more
TL;DR: It is shown that TSS distributions form a complex continuum of shapes, and that promoters active in the embryo and adult have highly similar shapes in 95% of cases, which suggests that these distributions are generally determined by static elements such as local DNA sequence and are not modulated by dynamic signals such as histone modifications.
Journal ArticleDOI
Genome wide analysis of Arabidopsis core promoters
TL;DR: It is established that approximately 29% of all Arabidopsis promoters contain TATA motifs, clustered around position -32 with respect to the TSS, suggesting a distinct architecture of the core promoters of plant and animal genes.
Journal ArticleDOI
The MTE, a new core promoter element for transcription by RNA polymerase II
TL;DR: It is found that the loss of transcriptional activity upon mutation of a TATA-box or DPE can be compensated by the addition of an MTE, a novel downstream core promoter element that is important for transcription by RNA polymerase II.
Journal ArticleDOI
Functional consequences of bidirectional promoters
TL;DR: Increasing evidence indicates that non-coding transcription at promoters influences the expression of protein-c coding genes, revealing a new layer of transcriptional regulation.
Journal ArticleDOI
Different core promoters possess distinct regulatory activities in the Drosophila embryo
TL;DR: A transgenic embryo assay is employed to obtain evidence that promoter selection is influenced by the TATA element, providing in vivo evidence that different core promoters possess distinct regulatory activities.
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