A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs.
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.
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.
Elena
E
Rivas
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.
Jody
J
Clements
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.|Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA.|FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA.|John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.
Sean R
0000-0001-6676-4706
SR
Eddy
D020029:Base Pairing; D001483:Base Sequence; D019143:Evolution, Molecular; D006801:Humans; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D062085:RNA, Long Noncoding / Q000737:chemistry* / Q000235:genetics*
D062085:RNA, Long Noncoding