Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces.
Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map (MaM) protocol give us a direct access into the genetic robustness of ncRNA structures. Comparative studies of homologous sequences provide a distinct, yet complementary, approach to analyze structural and functional properties of non-coding RNAs. In this paper, we introduce a formal framework to combine the biochemical signal collected from MaM experiments, with the evolutionary information available in multiple sequence alignments. We apply neutral theory principles to detect complex long-range dependencies between nucleotides of a single stranded RNA, and implement these ideas into a software called aRNhAck We illustrate the biological significance of this signal and show that the nucleotides networks calculated with aRNhAck are correlated with nucleotides located in RNA-RNA, RNA-protein, RNA-DNA and RNA-ligand interfaces. aRNhAck is freely available at http://csb.cs.mcgill.ca/arnhack.
School of Computer Science, McGill University, Montreal, Québec H3A 0E9, Canada.
Vladimir
V
Reinharz
Laboratoire d'informatique, École Polytechnique, 91128 Palaiseau, France yann.ponty@lix.polytechnique.fr.
Yann
Y
Ponty
School of Computer Science, McGill University, Montreal, Québec H3A 0E9, Canada jeromew@cs.mcgill.ca.
Jérôme
J
Waldispühl
D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry; D019143:Evolution, Molecular; D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000737:chemistry / Q000235:genetics*; D012984:Software; D064878:Web Browser
D011506:Proteins; D012313:RNA; D004247:DNA