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
Strategies for gene disruption and expression in filamentous fungi
TL;DR: The newly discovered strategies of gene disruption, such as the CRISPR-Cas9 system, the site-specific recombination Cre/loxP system, and the I-SceI endonuclease-mediated system in filamentous fungi are reviewed.
Journal ArticleDOI
Advances in promoter engineering: Novel applications and predefined transcriptional control.
Andrew P Cazier,John Blazeck +1 more
TL;DR: Promoter engineering encompasses the development of new promoters that exhibit properties that don't exist in native sequences, such as improved strength or unique inducibility as mentioned in this paper, which can be created by following various design paradigms and applying tools like machine learning.
Journal ArticleDOI
Engineered Promoters for Potent Transient Overexpression.
Dan Y. Even,Adi Kedmi,Shani Basch-Barzilay,Diana Ideses,Ravid Tikotzki,Hila Shir-Shapira,Orit Shefi,Tamar Juven-Gershon +7 more
TL;DR: This is the first demonstration of long-term expression in transiently transfected mammalian cells, indicating that engineered core promoters can provide a novel non-viral strategy for biotechnological as well as gene-therapy-related applications that require potent expression for extended time periods.
Journal ArticleDOI
Conserved DNA sequence features underlie pervasive RNA polymerase pausing.
Martyna Gajos,Martyna Gajos,Olga Jasnovidova,Alena van Bömmel,Alena van Bömmel,Susanne Freier,Martin Vingron,Andreas Mayer +7 more
TL;DR: In this article, the authors developed a pause detecting algorithm (PDA) for nucleotide-resolution occupancy data and a new native elongating transcript sequencing approach, termed nested NET-seq, that strongly reduces artifactual peaks commonly misinterpreted as pausing sites.
Journal ArticleDOI
An intron-derived motif strongly increases gene expression from transcribed sequences through a splicing independent mechanism in Arabidopsis thaliana.
Jenna E. Gallegos,Alan B. Rose +1 more
TL;DR: The ability of this motif to substantially elevate expression from several hundred nucleotides downstream of the transcription start site reveals a novel type of eukaryotic gene regulation.
References
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Journal ArticleDOI
RNA-Seq: a revolutionary tool for transcriptomics
TL;DR: The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.
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Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer
TL;DR: The efficacy of this cDNA cloning strategy was demonstrated by isolating cDNA clones of mRNA from int-2, a mouse gene that expresses four different transcripts at low abundance, the longest of which is approximately 2.9 kilobases.
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The Role of Chromatin during Transcription
TL;DR: This Review highlights advances in the understanding of chromatin regulation and discusses how such regulation affects the binding of transcription factors as well as the initiation and elongation steps of transcription.
Journal ArticleDOI
The mechanism of eukaryotic translation initiation and principles of its regulation
TL;DR: This work has provided a solid foundation for studying the regulation of translation initiation by mechanisms that include the modulation of initiation factor activity and through sequence-specific RNA-binding proteins and microRNAs (which affect individual mRNAs).
Journal ArticleDOI
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
Philipp Kapranov,Jill Cheng,Sujit Dike,David A. Nix,Radharani Duttagupta,Aarron T. Willingham,Peter F. Stadler,Jana Hertel,Jörg Hackermüller,Ivo L. Hofacker,Ian Bell,Evelyn Cheung,Jorg Drenkow,Erica Dumais,Sandeep Patel,Gregg Helt,Madhavan Ganesh,Srinka Ghosh,Antonio Piccolboni,Victor Sementchenko,Hari Tammana,Thomas R. Gingeras +21 more
TL;DR: Three potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes and support a highly interleaved organization of the human transcriptome.
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