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
Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex.
TL;DR: Evidence is provided for a third mechanism: promoter-proximal tethering elements that regulate enhancer–promoter interactions at other complex genetic loci.
Journal ArticleDOI
Synergy of human Pol II core promoter elements revealed by statistical sequence analysis
TL;DR: It is suggested that the BRE element is statistically more important than previously thought, and possible mechanisms of action of the core elements in the promoters with multiple transcription start sites are suggested.
Journal ArticleDOI
In search of the determinants of enhancer–promoter interaction specificity
TL;DR: A review of the current insights into the mechanisms that determine the specificity of enhancer-promoter interactions is assessed, and the functional genomic approaches that will lead the way towards better mechanistic understanding are highlighted.
Journal ArticleDOI
Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation
TL;DR: It is found that C. elegans equalizes X-chromosome expression between the sexes, to a level equivalent to autosomes, by reducing Pol II recruitment to promoters of hermaphrodite X-linked genes using a chromosome-restructuring condensin complex.
Journal ArticleDOI
Strange bedfellows: polyadenylation factors at the promoter.
Olga Calvo,James L. Manley +1 more
TL;DR: Evidence supporting the existence of a complex, evolutionarily conserved set of interactions that link even more tightly events that occur at the promoter to define the transcription start site and mRNA 5 end with those that occurred at the other end of the gene to produce the mRNA 3 end and ultimately the transcription stop site is discussed.
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