Literature DB >> 21850044

Understanding the transcriptome through RNA structure.

Yue Wan1, Michael Kertesz, Robert C Spitale, Eran Segal, Howard Y Chang.   

Abstract

RNA structure is crucial for gene regulation and function. In the past, transcriptomes have largely been parsed by primary sequences and expression levels, but it is now becoming feasible to annotate and compare transcriptomes based on RNA structure. In addition to computational prediction methods, the recent advent of experimental techniques to probe RNA structure by high-throughput sequencing has enabled genome-wide measurements of RNA structure and has provided the first picture of the structural organization of a eukaryotic transcriptome - the 'RNA structurome'. With additional advances in method refinement and interpretation, structural views of the transcriptome should help to identify and validate regulatory RNA motifs that are involved in diverse cellular processes and thereby increase understanding of RNA function.

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Year:  2011        PMID: 21850044      PMCID: PMC3858389          DOI: 10.1038/nrg3049

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  148 in total

1.  PseudoBase: structural information on RNA pseudoknots.

Authors:  F H van Batenburg; A P Gultyaev; C W Pleij
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  RNA pseudoknot prediction in energy-based models.

Authors:  R B Lyngsø; C N Pedersen
Journal:  J Comput Biol       Date:  2000       Impact factor: 1.479

3.  Use of dimethyl sulfate to probe RNA structure in vivo.

Authors:  S E Wells; J M Hughes; A H Igel; M Ares
Journal:  Methods Enzymol       Date:  2000       Impact factor: 1.600

4.  The structure of NoRC-associated RNA is crucial for targeting the chromatin remodelling complex NoRC to the nucleolus.

Authors:  Christine Mayer; Melanie Neubert; Ingrid Grummt
Journal:  EMBO Rep       Date:  2008-07-04       Impact factor: 8.807

5.  Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism.

Authors:  Changrui Lu; Angela M Smith; Ryan T Fuchs; Fang Ding; Kanagalaghatta Rajashankar; Tina M Henkin; Ailong Ke
Journal:  Nat Struct Mol Biol       Date:  2008-09-21       Impact factor: 15.369

6.  Regulation of ARE transcript 3' end processing by the yeast Cth2 mRNA decay factor.

Authors:  Manoël Prouteau; Marie-Claire Daugeron; Bertrand Séraphin
Journal:  EMBO J       Date:  2008-10-16       Impact factor: 11.598

7.  Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments.

Authors:  Stefan E Seemann; Jan Gorodkin; Rolf Backofen
Journal:  Nucleic Acids Res       Date:  2008-10-04       Impact factor: 16.971

8.  A small stem loop element directs internal initiation of the URE2 internal ribosome entry site in Saccharomyces cerevisiae.

Authors:  Lucas C Reineke; Anton A Komar; Mark G Caprara; William C Merrick
Journal:  J Biol Chem       Date:  2008-05-06       Impact factor: 5.157

9.  Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome.

Authors:  Jing Zhao; Bryan K Sun; Jennifer A Erwin; Ji-Joon Song; Jeannie T Lee
Journal:  Science       Date:  2008-10-31       Impact factor: 47.728

10.  The Vienna RNA websuite.

Authors:  Andreas R Gruber; Ronny Lorenz; Stephan H Bernhart; Richard Neuböck; Ivo L Hofacker
Journal:  Nucleic Acids Res       Date:  2008-04-19       Impact factor: 16.971

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  177 in total

Review 1.  Genome regulation by long noncoding RNAs.

Authors:  John L Rinn; Howard Y Chang
Journal:  Annu Rev Biochem       Date:  2012       Impact factor: 23.643

2.  Uncovering the role of genomic "dark matter" in human disease.

Authors:  Lance Martin; Howard Y Chang
Journal:  J Clin Invest       Date:  2012-05-01       Impact factor: 14.808

3.  Mutational interference mapping experiment (MIME) for studying RNA structure and function.

Authors:  Redmond P Smyth; Laurence Despons; Gong Huili; Serena Bernacchi; Marcel Hijnen; Johnson Mak; Fabrice Jossinet; Li Weixi; Jean-Christophe Paillart; Max von Kleist; Roland Marquet
Journal:  Nat Methods       Date:  2015-08-03       Impact factor: 28.547

4.  FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information.

Authors:  Tungadri Bose; Anirban Dutta; Mohammed Mh; Hemang Gandhi; Sharmila S Mande
Journal:  J Biosci       Date:  2015-09       Impact factor: 1.826

5.  Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing.

Authors:  Cuncong Zhong; Shaojie Zhang
Journal:  J Comput Biol       Date:  2014-04-01       Impact factor: 1.479

6.  The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites.

Authors:  Jason A West; Christopher P Davis; Hongjae Sunwoo; Matthew D Simon; Ruslan I Sadreyev; Peggy I Wang; Michael Y Tolstorukov; Robert E Kingston
Journal:  Mol Cell       Date:  2014-08-21       Impact factor: 17.970

7.  Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.

Authors:  Krishna Choudhary; Fei Deng; Sharon Aviran
Journal:  Quant Biol       Date:  2017-03-30

8.  Evolving insights into RNA modifications and their functional diversity in the brain.

Authors:  Sarah Nainar; Paul R Marshall; Christina R Tyler; Robert C Spitale; Timothy W Bredy
Journal:  Nat Neurosci       Date:  2016-09-27       Impact factor: 24.884

9.  Site-Selective RNA Functionalization via DNA-Induced Structure.

Authors:  Lu Xiao; Maryam Habibian; Eric T Kool
Journal:  J Am Chem Soc       Date:  2020-09-14       Impact factor: 15.419

10.  microRNA Regulation and Its Consequences in Cancer.

Authors:  Sonya Parpart; Xin Wei Wang
Journal:  Curr Pathobiol Rep       Date:  2012-12-18
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