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
TFIID sequence recognition of the initiator and sequences farther downstream in Drosophila class II genes.
TL;DR: Selecting the G/A/T C/TAT/GTG motif demonstrates that sequence-specific interactions downstream of the TATA element contribute to the interaction of TFIID on a wide spectrum of promoters.
Journal ArticleDOI
Unique TATA-binding protein-containing complexes and cofactors involved in transcription by RNA polymerases II and III
TL;DR: The results argue for a relationship between downstream interactions and overall promoter strength and the importance of TAFs in determining promoter specificity by different RNA polymerases.
Journal ArticleDOI
Testis-specific TAF homologs collaborate to control a tissue-specific transcription program.
Mark A. Hiller,Xin Chen,M. Jodeane Pringle,Martin Suchorolski,Yasemin Sancak,Sridhar Viswanathan,Benjamin Bolival,Ting-Yi Lin,Susan Marino,Margaret T. Fuller +9 more
TL;DR: It is proposed that the products of the five Drosophila genes encoding testis TAF homologs collaborate in an alternative TAF-containing protein complex to regulate a testis-specific gene expression program in primary spermatocytes required for terminal differentiation of male germ cells.
Journal ArticleDOI
A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation.
TL;DR: Observations indicate that yeast TFIID can stimulate transcription from TATA elements whose sequences differ from the consensus, and they suggest the possibility of alternative factors that may provide a related function for transcriptional activation.
Journal ArticleDOI
The basal initiation machinery: beyond the general transcription factors.
TL;DR: A simple model in which basal transcription factors sequentially assembled with RNA Polymerase II to generate a preinitiation complex (PIC) indicates that PIC composition is not universal, but promoter-dependent.
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