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
Divergent Transcription from Active Promoters
Amy C. Seila,J. Mauro Calabrese,Stuart S. Levine,Gene W. Yeo,Peter B. Rahl,Ryan A. Flynn,Richard A. Young,Phillip A. Sharp +7 more
TL;DR: Evidence of widespread divergent transcription at protein-encoding gene promoters is presented and it is suggested that Divergent transcription over short distances is common for active promoters and may help promoter regions maintain a state poised for subsequent regulation.
Journal ArticleDOI
Enhancer function: new insights into the regulation of tissue-specific gene expression.
Chin-Tong Ong,Victor G. Corces +1 more
TL;DR: Surprisingly, cohesin and non-coding RNAs are emerging as crucial players responsible for facilitating enhancer–promoter interactions at some genes and may be required not only to facilitate initiation of transcription but also to activate the release of RNA polymerase II from promoter-proximal pausing.
Journal ArticleDOI
Promoter sequences of eukaryotic protein-coding genes
Jeffry L. Corden,Bohdan Wasylyk,A. Buchwalder,Paolo Sassone-Corsi,Claude Kedinger,Pierre Chambon +5 more
TL;DR: Sequences which are essential for the initiation of specific transcription in vitro were shown to be located between 12 and 32 base pairs upstream from the 5' end of these genes.
Journal ArticleDOI
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.
Julia Zeitlinger,Alexander Stark,Manolis Kellis,Joung-Woo Hong,Sergei Nechaev,Karen Adelman,Michael Levine,Richard A. Young +7 more
TL;DR: It is proposed that Pol II stalling facilitates rapid temporal and spatial changes in gene activity during development and is highly enriched for developmental control genes, which are either repressed or poised for activation during later stages of embryogenesis.
Journal ArticleDOI
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
Toshiyuki Shiraki,Shinji Kondo,Shintaro Katayama,Kazunori Waki,Takeya Kasukawa,Hideya Kawaji,Rimantas Kodzius,Akira Watahiki,Mari M. Nakamura,Takahiro Arakawa,Shiro Fukuda,Daisuke Sasaki,Anna J. Podhajska,Matthias Harbers,Jun Kawai,Piero Carninci,Yoshihide Hayashizaki +16 more
TL;DR: By analyzing four libraries (brain, cortex, hippocampus, and cerebellum), this work redefined more accurately the TSPs of 11-27% of the analyzed transcriptional units that were hit.
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