Section: Application Domains

Analysis of probing data

Participants : Yann Ponty, Mireille Régnier, Afaf Saaidi.

SHAPE probing  [47] is an experimental technique in which RNA is exposed to a reagent which, upon reverse-transcription, induces a modification (truncation, mutation) in the DNA. The prevalence of such modifications, which depends on the locally adopted structure(s) (or lack thereof), can be measured for each nucleotide using sequencing techniques, informing regarding the 2D structure. SHAPE probing data can thus be used by structure prediction methods, either to assess their consistency with a proposed structural model, or to restrict the conformation space.

As part of a colloboration with B. Sargueil's lab (Faculté de pharmacie, Paris V) funded by the Fondation pour la Recherche medical, we strive to propose a new paradigm for the analysis data produced using a new experimental technique, called Shape analysis (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension). This experimental setup produces an accessibility profile associated with the different positions of an RNA, the shadow of an RNA. We currently design new algorithmic strategies to infer the secondary structure of RNA from multiple Shape experiments performed by experimentalists at Paris V. Those are obtained on mutants, and will be coupled with a fragment-based 3D modeling strategy developed by our partners at McGill.