Romain Rivière AReNa –

 Characterise RNA families  Improve non-coding RNA identification in genomic data  Determine the RNA players in regulatory networks  Identify potential RNA drug targets

Yeast tRNA-Phe crystal structure (pdb 4TNA)

1. Enumerate all the motifs 2. Regroup by similarity 3. Find the building blocks

A motif is a set of connected nucleotides together with their interactions

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1. Enumerate all the motifs 2. Regroup by similarity 3. Find the building blocks

Matrix representation of the graph : 2 1 ≠ = = Scan through all permutations to decide if two graphs are isomorphic !

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Matrix representation of the graph : 2 1 ≠ = = Take the minimum through all permutations of the matrix representation

1. Enumerate all the motifs 2. Regroup by similarity 3. Find the building blocks

Type of motifsEdges … … Find a small set of types of motifs that covers the most edges

… General graphs are not compact enough Not usable for modelling

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 Motif discovery Biological relevance of block-function relationships?  RNA folding Practical usability?

François Major Sébastien Lemieux Véronique Lisi Karine St-Onge Philippe Thibault Patrick Gendron Martin Larose All other lab members

 We applied the method to the large ribosomal subunit  We restrict the graphs allowed for the base to cycles  We found 334 cycles that covers 90% of the structure.

 Canonical label of a graph : Take the minimum of the matrices over all the permutations  Property : 2 graphs have the same canonical label if and only if they are isomorphic

 Group together motifs which are identical  Done with canonical labelling Idea : associate a string to each graph such that two graphs are associated with the same string if and only if they are identical (isomorphic). Difficult problem well studied Potentially highly computation time.

 3^n. 10^n where n is the size of the structure  10^14 op/s world fastest computer

 RNA is a very important medium in the transfer of genetic information  Convey information through its structure in addition to its sequence  Example : miRNA

Similar secondary structure But, only one miRNA functional !

 3 main types of molecular interactions : Phosphodiester link Base pairing Base stacking