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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Characterization of interleukin (IL)-1β regulatory elements and chromatin conformation in macrophage activation
TL;DR: It is suggested that within the context of a youth-services agency using a mobile application, using a tablet or computer to provide real-time information about an individual’s educational needs is a viable process.
Book ChapterDOI
RetroSpect, a New Method of Measuring Gene Regulatory Evolution Rates Using Co-mapping of Genomic Functional Features with Transposable Elements
Daniil Nikitin,Daniil Nikitin,Maxim Sorokin,Victor Tkachev,Andrew Garazha,Alexander V. Markov,Anton Buzdin +6 more
TL;DR: A method for measuring evolutionary rates of gene regulation based on relative quantitation of regulatory sites located within TEs next to gene transcriptional start sites is proposed, which allows interrogating regulatory evolution for organisms with TE-rich genomes.
Posted ContentDOI
Enhancer sharing promotes neighborhoods of transcriptional regulation across eukaryotes
TL;DR: Cross-organismic evidence is presented suggesting that most EP pairs are compatible, largely determined by physical proximity rather than specific interactions, and that EP distance is an important layer of information in gene regulation.
Posted ContentDOI
Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions
Christoph Sebastian Börlin,Nevena Cvetesic,Petter Holland,David Bergenholm,Verena Siewers,Boris Lenhard,Jens C. O. Nielsen +6 more
TL;DR: This analysis supplies a set of high quality TSS annotations useful for metabolic engineering and synthetic biology approaches in the industrially relevant laboratory strain CEN.PK113-7D, and provides novel insights into yeast TSS dynamics and gene regulation.
Journal ArticleDOI
DeePromClass: Delineator for Eukaryotic Core Promoters Employing Deep Neural Networks
TL;DR: This tool provides an insightful update on next-generation promoter prediction tools for promoter biologists and, unlike previous state-of-the-art tools, classify a chunk of 151mer sequence into a promoter along with the consensus signal type or a non-promoter.
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Related Papers (5)
Metazoan promoters: emerging characteristics and insights into transcriptional regulation
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Piero Carninci,Albin Sandelin,Boris Lenhard,Boris Lenhard,Shintaro Katayama,Kazuro Shimokawa,Jasmina Ponjavic,Colin A. Semple,Martin S. Taylor,Pär G. Engström,Martin C. Frith,Alistair R. R. Forrest,Wynand Alkema,Sin Lam Tan,Charles Plessy,Rimantas Kodzius,Timothy Ravasi,Timothy Ravasi,Takeya Kasukawa,Shiro Fukuda,Mutsumi Kanamori-Katayama,Yayoi Kitazume,Hideya Kawaji,Chikatoshi Kai,Mari M. Nakamura,Hideaki Konno,Kenji Nakano,Salim Mottagui-Tabar,Salim Mottagui-Tabar,Salim Mottagui-Tabar,Peter Arner,Alessandra Chesi,Stefano Gustincich,Francesca Persichetti,Harukazu Suzuki,Sean M. Grimmond,Christine A. Wells,Valerio Orlando,Claes Wahlestedt,Claes Wahlestedt,Edison T. Liu,Matthias Harbers,Jun Kawai,Vladimir B. Bajic,Vladimir B. Bajic,David A. Hume,Yoshihide Hayashizaki,Yoshihide Hayashizaki +47 more