Literature DB >> 27819659

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs.

Elena Rivas1, Jody Clements2, Sean R Eddy1,3,4,5.   

Abstract

Many functional RNAs have an evolutionarily conserved secondary structure. Conservation of RNA base pairing induces pairwise covariations in sequence alignments. We developed a computational method, R-scape (RNA Structural Covariation Above Phylogenetic Expectation), that quantitatively tests whether covariation analysis supports the presence of a conserved RNA secondary structure. R-scape analysis finds no statistically significant support for proposed secondary structures of the long noncoding RNAs HOTAIR, SRA, and Xist.

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Year:  2016        PMID： 27819659      PMCID： PMC5554622          DOI： 10.1038/nmeth.4066

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  40 in total

1.  Secondary structure prediction for aligned RNA sequences.

Authors:  Ivo L Hofacker; Martin Fekete; Peter F Stadler
Journal:  J Mol Biol       Date:  2002-06-21       Impact factor: 5.469

2.  Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods.

Authors:  R R Gutell; A Power; G Z Hertz; E J Putz; G D Stormo
Journal:  Nucleic Acids Res       Date:  1992-11-11       Impact factor: 16.971

3.  A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

Authors:  Elena Rivas; Raymond Lang; Sean R Eddy
Journal:  RNA       Date:  2011-12-22       Impact factor: 4.942

4.  FastTree 2--approximately maximum-likelihood trees for large alignments.

Authors:  Morgan N Price; Paramvir S Dehal; Adam P Arkin
Journal:  PLoS One       Date:  2010-03-10       Impact factor: 3.240

5.  Volume changes in protein evolution.

Authors:  M Gerstein; E L Sonnhammer; C Chothia
Journal:  J Mol Biol       Date:  1994-03-04       Impact factor: 5.469

6.  Structural architecture of the human long non-coding RNA, steroid receptor RNA activator.

Authors:  Irina V Novikova; Scott P Hennelly; Karissa Y Sanbonmatsu
Journal:  Nucleic Acids Res       Date:  2012-02-22       Impact factor: 16.971

7.  A survey of sRNA families in α-proteobacteria.

Authors:  Coral del Val; Rocío Romero-Zaliz; Omar Torres-Quesada; Alexandra Peregrina; Nicolás Toro; Jose I Jiménez-Zurdo
Journal:  RNA Biol       Date:  2012-02-01       Impact factor: 4.652

8.  Rfam 12.0: updates to the RNA families database.

Authors:  Eric P Nawrocki; Sarah W Burge; Alex Bateman; Jennifer Daub; Ruth Y Eberhardt; Sean R Eddy; Evan W Floden; Paul P Gardner; Thomas A Jones; John Tate; Robert D Finn
Journal:  Nucleic Acids Res       Date:  2014-11-11       Impact factor: 19.160

9.  Parameterizing sequence alignment with an explicit evolutionary model.

Authors:  Elena Rivas; Sean R Eddy
Journal:  BMC Bioinformatics       Date:  2015-12-10       Impact factor: 3.169

10.  2-D structure of the A region of Xist RNA and its implication for PRC2 association.

Authors:  Sylvain Maenner; Magali Blaud; Laetitia Fouillen; Anne Savoye; Virginie Marchand; Agnès Dubois; Sarah Sanglier-Cianférani; Alain Van Dorsselaer; Philippe Clerc; Philip Avner; Athanase Visvikis; Christiane Branlant
Journal:  PLoS Biol       Date:  2010-01-05       Impact factor: 8.029
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  138 in total

Review 1.  The RNA Base-Pairing Problem and Base-Pairing Solutions.

Authors:  Zhipeng Lu; Howard Y Chang
Journal:  Cold Spring Harb Perspect Biol       Date:  2018-12-03       Impact factor: 10.005

2.  Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity.

Authors:  Zasha Weinberg; James W Nelson; Christina E Lünse; Madeline E Sherlock; Ronald R Breaker
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-06       Impact factor: 11.205

3.  Determining parameters for non-linear models of multi-loop free energy change.

Authors:  Max Ward; Hongying Sun; Amitava Datta; Michael Wise; David H Mathews
Journal:  Bioinformatics       Date:  2019-11-01       Impact factor: 6.937

4.  Opportunities and Challenges in RNA Structural Modeling and Design.

Authors:  Tamar Schlick; Anna Marie Pyle
Journal:  Biophys J       Date:  2017-02-02       Impact factor: 4.033

5.  Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures.

Authors:  Rafael C A Tavares; Anna Marie Pyle; Srinivas Somarowthu
Journal:  J Mol Biol       Date:  2019-03-16       Impact factor: 5.469

6.  Targeting RNA with Small Molecules To Capture Opportunities at the Intersection of Chemistry, Biology, and Medicine.

Authors:  Matthew D Disney
Journal:  J Am Chem Soc       Date:  2019-04-19       Impact factor: 15.419

Review 7.  Non-coding RNAs: the riddle of the transcriptome and their perspectives in cancer.

Authors:  Marios A Diamantopoulos; Panagiotis Tsiakanikas; Andreas Scorilas
Journal:  Ann Transl Med       Date:  2018-06

Review 8.  Long Noncoding RNA in Cancer: Wiring Signaling Circuitry.

Authors:  Chunru Lin; Liuqing Yang
Journal:  Trends Cell Biol       Date:  2017-12-20       Impact factor: 20.808

9.  Structural divergence creates new functional features in alphavirus genomes.

Authors:  Katrina M Kutchko; Emily A Madden; Clayton Morrison; Kenneth S Plante; Wes Sanders; Heather A Vincent; Marta C Cruz Cisneros; Kristin M Long; Nathaniel J Moorman; Mark T Heise; Alain Laederach
Journal:  Nucleic Acids Res       Date:  2018-04-20       Impact factor: 16.971

10.  In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs.

Authors:  Lisa Marie Simon; Edoardo Morandi; Anna Luganini; Giorgio Gribaudo; Luis Martinez-Sobrido; Douglas H Turner; Salvatore Oliviero; Danny Incarnato
Journal:  Nucleic Acids Res       Date:  2019-07-26       Impact factor: 16.971
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