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
A conserved element in the leader mediates post-meiotic translation as well as cytoplasmic polyadenylation of a Drosophila spermatocyte mRNA.
TL;DR: Evidence is presented that the control for this additional polyadenylation also resides within the conserved element of the leader, which is crucial for this translational regulation of Mst87F.
Journal ArticleDOI
TAFII mutations disrupt Dorsal activation in the Drosophila embryo
TL;DR: It is suggested that TAFIIs contribute to the activation of transcription in vivo and support the hypothesis that subunits of TFIID may serve as targets of enhancer binding proteins.
Journal ArticleDOI
Two novel Drosophila TAF(II)s have homology with human TAF(II)30 and are differentially regulated during development.
Sofia G. Georgieva,Sofia G. Georgieva,Sofia G. Georgieva,Doris B. Kirschner,Tereza Jagla,Elena N. Nabirochkina,Elena N. Nabirochkina,Susanne Hanke,Heide Schenkel,Cécilia de Lorenzo,Pradip Sinha,Krysztof Jagla,Bernard Mechler,Laszlo Tora +13 more
TL;DR: Drosophila has not one but two hTAF II30 homologues, dTAFII16 and dTAfII24, which are encoded by two adjacent genes, and it is demonstrated that these novel dTAFIIs are expressed and that they are both associated with TBP and other bona fide dTA FIIs in dTFIID complexes.
Journal ArticleDOI
Differential Regulation of NF-κB by Elongation Factors Is Determined by Core Promoter Type
Liat Amir-Zilberstein,Elena Ainbinder,Leanne Toube,Yuki Yamaguchi,Hiroshi Handa,Rivka Dikstein +5 more
TL;DR: It is shown that upon induction of NF-κB, a subset of target genes is regulated differentially by either P-TEFb or DSIF, and the underlying mechanism for the dissociation of DSIF from TATA promoters involves the phosphorylation of RNA polymerase II by P- TEFb.
Journal ArticleDOI
Diversity of core promoter elements comprising human bidirectional promoters.
Mary Qu Yang,Laura Elnitski +1 more
TL;DR: CpG-islands dominate the regulatory landscape of this group of promoters, providing an explanation for the symmetrical co-expression patterns of many of these genes, and utilizing a variety of core promoter elements to initiate transcription.
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