Transcription Regulation Through Nascent RNA Folding.
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TLDR
In this paper, the authors discuss recent studies in both prokaryotes and eukaryotes showing that structure formation may carry a more widespread regulatory logic during RNA synthesis, showing that local structures forming close to the catalytic center of RNA polymerases have the potential to regulate transcription.About:
This article is published in Journal of Molecular Biology.The article was published on 2021-07-09 and is currently open access. It has received 5 citations till now. The article focuses on the topics: RNA & Riboswitch.read more
Citations
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Journal ArticleDOI
Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription
TL;DR: In this article, the authors describe the conventional and condensate-dependent models of RNA polymerase II (pol II) and highlight the central role of RNA in these processes, and discuss mutations that disrupt normal partitioning of transcription factors.
Transcription complexes as RNA chaperones.
TL;DR: In this article, the authors discuss the role of transcription complexes as RNA chaperones based on recent examples from bacterial transcription, and show that RNA polymerase and associated transcription factors play a role in co-transcriptional RNA folding by fostering or preventing strategic contacts to the nascent transcripts.
Posted ContentDOI
Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch
TL;DR: In this article, the authors studied the structure and function of the Bacillus subtilis yxjA purine riboswitch, a transcriptional RNA downregulator that downregulates a nucleoside transporter in response to binding guanine.
Posted ContentDOI
R-loops between nascent pri-miRNAs and the encoding loci promote co-transcriptional processing of miRNAs in plants
Lucia Gonzalo,Ileana Tossolini,Tomasz Gulanicz,Tomasz Gulanicz,Damián Alejandro Cambiagno,Damián Alejandro Cambiagno,Anna Kasprowicz-Maluski,Jan Dariusz Smolinski,Sebastian Marquardt,Zofia Szweykowska-Kulinska,Artur Jarmolowski,Pablo Andrés Manavella +11 more
TL;DR: In this article, the authors show that plant miRNA biogenesis is coupled to transcription in a process that relies on the formation of DNA:RNA hybrids (R-loops) between the nascent transcript and the encoding loci.
References
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ViennaRNA Package 2.0
Ronny Lorenz,Stephan H. Bernhart,Christian Höner zu Siederdissen,Hakim Tafer,Christoph Flamm,Peter F. Stadler,Ivo L. Hofacker,Ivo L. Hofacker +7 more
TL;DR: In this article, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties of nucleic acids based on carefully measured thermodynamic parameters.
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A practical guide to single-molecule FRET
TL;DR: A practical guide to using smFRET, focusing on the study of immobilized molecules that allow measurements of single-molecule reaction trajectories from 1 ms to many minutes, is provided.
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How RNA folds.
Ignacio Tinoco,Carlos Bustamante +1 more
TL;DR: A folding algorithm to predict the structure of an RNA from its sequence is suggested, but to solve the RNA folding problem one needs thermodynamic data on tertiary structure interactions, and identification and characterization of metal-ion binding sites.
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Deciphering the splicing code
Yoseph Barash,John A. Calarco,Weijun Gao,Qun Pan,Xinchen Wang,Ofer Shai,Benjamin J. Blencowe,Brendan J. Frey,Brendan J. Frey +8 more
TL;DR: The assembly of a ‘splicing code’ is described, which uses combinations of hundreds of RNA features to predict tissue-dependent changes in alternative splicing for thousands of exons and facilitates the discovery and detailed characterization of regulatedAlternative splicing events on a genome-wide scale.
Journal ArticleDOI
Context-dependent control of alternative splicing by RNA-binding proteins
Xiang-Dong Fu,Manuel Ares +1 more
TL;DR: Some of the emerging rules that govern the highly context-dependent and combinatorial nature of alternative splicing regulation are described.
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