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 elements associated with RNA Pol II stalling in the Drosophila embryo.
David A. Hendrix,Joung-Woo Hong,Julia Zeitlinger,Daniel S. Rokhsar,Daniel S. Rokhsar,Michael Levine +5 more
TL;DR: A combined computational and experimental analysis of stalled promoters to determine how they come to bind Pol II in the early Drosophila embryo reveals a shared sequence motif, the “pause button” (PB): KCGRWCG.
Journal ArticleDOI
Crosstalk between mRNA 3′ End Processing and Transcription Initiation
Christophe K. Mapendano,Søren Lykke-Andersen,Jørgen Kjems,Edouard Bertrand,Torben Heick Jensen +4 more
TL;DR: It is demonstrated that 3' end formation stimulates transcription initiation and suggested that coordinated recycling of factors from a gene terminator back to the promoter is essential for sustaining continued transcription.
Journal ArticleDOI
Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo
Mounia Lagha,Jacques P. Bothma,Emilia Esposito,Samuel Ng,Laura Stefanik,Chiahao Tsui,Jeff Johnston,Kai Chen,David S. Gilmour,Julia Zeitlinger,Michael Levine +10 more
TL;DR: It is concluded that paused Pol II and transcriptional synchrony are essential for coordinating cell behavior during morphogenesis and computational modeling of the dorsal-ventral patterning network recapitulates these variable and bistable gastrulation profiles and emphasizes the importance of timing of gene activation in development.
Journal ArticleDOI
A paired-end sequencing strategy to map the complex landscape of transcription initiation.
Ting Ni,David L. Corcoran,Elizabeth A. Rach,Shen Song,Eric P. Spana,Yuan Gao,Uwe Ohler,Jun Zhu,Jun Zhu +8 more
TL;DR: A paired- end sequencing strategy is described, which enables more robust mapping and characterization of capped transcripts and demonstrated paired-end TSS analysis to be a powerful method to uncover the transcriptional complexity of eukaryotic genomes.
Journal ArticleDOI
Human TAFII105 Is a Cell Type–Specific TFIID Subunit Related to hTAFII130
TL;DR: It is reported that differentiated B cells contain a novel substoichiometric TAF of 105 kDa not found associated with TFIID isolated from other cell types, suggesting that TAFII105 is a cell type-specific subunit of TFIIDs that may be responsible for mediating transcription by a subset of activators in B cells.
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