Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures. Issue 8 (5th April 2019)

• Record Type: Journal Article
• Authors: Tavares, Rafael C.A.; Pyle, Anna Marie; Somarowthu, Srinivas
• Is Part Of: Journal of molecular biology. Volume 431:Issue 8(2019)
• Page Start: 1592
• Page End: 1603
• Publication Date: 2019-04-05
• Subjects: R-scape RNA Structural Covariation Above Phylogenetic Expectation -- HOTAIR HOX transcript antisense RNA -- lncRNA long non-coding RNA -- MALAT1 metastasis-associated lung adenocarcinoma transcript 1 -- APC average product correction -- RAFS RNAalifold with stacking; long non-coding RNAs -- covariation analysis -- conserved structure -- lncRNA structure -- RNAalifold; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2019.03.012
• Languages: English
• ISSNs: 0022-2836

Abstract

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. Graphical Abstract: Unlabelled Image Highlights: Identifying conserved RNA structures in alignments with less diverse sequences is a challenging task. The detection of conserved structures in well-studied mammalian lncRNAs has been challenging with existing statistical tools. Here, we report strategies and improved parameters that allow for identification of conserved structures in lncRNAs.