Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures

Rafael C A Tavares; Anna Marie Pyle; Srinivas Somarowthu

doi:10.1016/j.jmb.2019.03.012

Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures

J Mol Biol. 2019 Apr 5;431(8):1592-1603. doi: 10.1016/j.jmb.2019.03.012. Epub 2019 Mar 16.

Authors

Rafael C A Tavares¹, Anna Marie Pyle², Srinivas Somarowthu³

Affiliations

¹ Department of Chemistry, Yale University, New Haven, CT 06511, USA.
² Department of Chemistry, Yale University, New Haven, CT 06511, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address: anna.pyle@yale.edu.
³ Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA. Electronic address: ss4473@drexel.edu.

Abstract

The existence of evolutionary conservation in base pairing is strong evidence for functional elements of RNA structure, although available tools for rigorous identification of structural conservation are limited. R-scape is a recently developed program for statistical prediction of pairwise covariation from sequence alignments, but it initially showed limited utility on long RNAs, especially those of eukaryotic origin. Here we show that R-scape can be adapted for a more powerful analysis of structure conservation in long RNA molecules, including mammalian lncRNAs.

Keywords: RNAalifold; conserved structure; covariation analysis; lncRNA structure; long non-coding RNAs.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Base Sequence
Conserved Sequence
Evolution, Molecular
Humans
Nucleic Acid Conformation
Phylogeny
RNA, Long Noncoding / chemistry
RNA, Long Noncoding / genetics*

Substances

RNA, Long Noncoding

Grants and funding

R01 GM050313/GM/NIGMS NIH HHS/United States