| HAL-Inria | Publications, software ... of Inria's scientists |
Journal articles
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 Connect in order to contact the contributor
Submitted on : Tuesday, March 22, 2016 - 9:24:21 AM
Last modification on : Thursday, July 8, 2021 - 3:49:26 AM
Long-term archiving on: : Sunday, November 13, 2016 - 10:07:42 PM
Contributor : Yann Ponty Connect in order to contact the contributor
Submitted on : Tuesday, March 22, 2016 - 9:24:21 AM
Last modification on : Thursday, July 8, 2021 - 3:49:26 AM
Long-term archiving on: : Sunday, November 13, 2016 - 10:07:42 PM
Files
main_NAR.pdf
Files produced by the author(s)
Licence
Distributed under a Creative Commons Attribution 4.0 International License