Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces

Vladimir Reinharz (1, 2) , Yann Ponty (3) , Jérôme Waldispühl (2)

1 MCB - McGill Centre for Bioinformatics
2 McGill University = Université McGill [Montréal, Canada]
3 AMIB - Algorithms and Models for Integrative Biology

Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map 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 mutate-and-map 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.

Domaines: Bio-informatique [q-bio.QM]

Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl. Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces. Nucleic Acids Research, 2016, 44 (11), pp.e104 - e104. ⟨10.1093/nar/gkw217⟩. ⟨hal-01291754⟩