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Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces
Abstract : 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.
Cited literature [36 references]
https://hal.inria.fr/hal-01291754
Contributor : Yann Ponty <>
Submitted on : Tuesday, March 22, 2016 - 9:24:21 AM
Last modification on : Thursday, June 18, 2020 - 12:32:05 PM
Document(s) archivé(s) le : Sunday, November 13, 2016 - 10:07:42 PM
Contributor : Yann Ponty <>
Submitted on : Tuesday, March 22, 2016 - 9:24:21 AM
Last modification on : Thursday, June 18, 2020 - 12:32:05 PM
Document(s) archivé(s) le : Sunday, November 13, 2016 - 10:07:42 PM
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