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

Nature Methods volume 14, pages 4548 (2017) | Download Citation

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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Acknowledgements

We thank S.E.R. Egnor for suggesting the name R-scape and the Centro de Ciencias de Benasque Pedro Pascual in Spain, where part of this manuscript was drafted.

Author information

Affiliations

  1. Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.

    • Elena Rivas
    •  & Sean R Eddy
  2. Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.

    • Jody Clements
  3. Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA.

    • Sean R Eddy
  4. FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA.

    • Sean R Eddy
  5. John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.

    • Sean R Eddy

Authors

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Contributions

E.R. and S.R.E. designed the method and wrote the manuscript. E.R. wrote the code, and designed and carried out the experiments. J.C. wrote the R-scape web application.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Elena Rivas.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–8.

Zip files

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    Supplementary Software

    Alignment data and R-scape source code.

  2. 2.

    Supplementary Dataset 1

    Alignment Data.

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DOI

https://doi.org/10.1038/nmeth.4066