Publications

This page shows all publications that appeared in the IASI annual research reports. Authors currently affiliated with the Institute are always listed with the full name.

You can browse through them using either the links of the following line or those associated with author names.

Show all publications of the year  2013, with author ALL, in the category IASI Research Reports (or show them all):


IASI Research Report n. 13-21  (Previous )  

Giulia Fiscon, Paola Paci, Colombo T, Iannello G

Structural Analysis of Long Non-coding RNAs

ABSTRACT
The sequence-structural alignment of RNAs is a challenging and computational onerous issue in the field of structures prediction and study of functional RNAs. To date, the available tools for computing structural alignments are either based on heuristic approaches and thus produce suboptimal alignments or cannot handle instances of reasonable input size. The topic appears more challenging with the incoming of long non-coding RNAs (lncRNAs), a novel set of transcripts whose role in post-transcriptional regulation has been recently shown to be far more prominent than initially believed. Belonging to the huge family of RNAs that does not encode a protein, with a number of nucleotides longer than 200, lncRNAs fold in complex secondary structures and yet little is known about their biological function. We focus on their secondary structures thanks to which they can recruits different protein complexes. The latter particular functioning can constitute their revealing signatures of functional RNAs to search for. Thus, if two molecules are functionally related and have similar structures, it allows to draw conclusions about the structure of the unknown molecule or about function of molecule not yet functionally characterized. Our aim is to infer the mechanism of action of uncharacterized lncRNAs, looking for their shared secondary sub-structures with functionally characterized ones. To this end, the structure of a lncRNA with known function can be used as the reference to run pair-wise comparisons with all the others of unknown function. In such an approach, there are two main step involved: first, to assign a structure to the reference lncRNA and second, to look for structural motifs that match the ones characterizing the reference lncRNA. We developed two novel algorithms able to handle the two following tasks: structure prediction and matches evaluation, in order to improve or replace widespread tools, which are not suited to exhaustively deal with lncRNAs.
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