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
Non-coding RNAs as regulators of gene expression and epigenetics.
TL;DR: The characteristics and functions of regulatory ncRNAs in chromatin remodelling and at multiple levels of transcriptional and post-transcriptional regulation are reviewed.
Journal ArticleDOI
Computational analysis of core promoters in the Drosophila genome
TL;DR: This work identified TSS candidates for about 2,000 Drosophila genes by aligning 5' expressed sequence tags from cap-trapped cDNA libraries to the genome, while applying stringent criteria concerning coverage and 5'-end distribution and identified several new motifs enriched in promoter regions.
Journal ArticleDOI
Enhancer loops appear stable during development and are associated with paused polymerase
Yad Ghavi-Helm,Felix A. Klein,Tibor Pakozdi,Lucia Ciglar,Daan Noordermeer,Wolfgang Huber,Eileen E. M. Furlong +6 more
TL;DR: The results indicate that the general topology governing enhancer contacts is conserved from flies to humans and suggest that transcription initiates from preformed enhancer–promoter loops through release of paused polymerase.
Journal ArticleDOI
Enhancer RNAs and regulated transcriptional programs
TL;DR: Emerging evidence suggesting that at least some eRNAs contribute to enhancer function is reviewed, and potential mechanisms of action of e RNAs and other ncRNAs in regulated gene expression are discussed.
Journal ArticleDOI
Transcriptional Enhancers in Animal Development and Evolution
TL;DR: This review summarizes well-defined examples of enhancers controlling key processes in animal development and discusses the prospects for reconstructing transitions in animal evolution by introducing derived enhancers in basal ancestors.
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