Biology subjects

Delli Ponti, R.

Publications and source records attributed to Delli Ponti, R..

2 recordsLinked to original sources

bioRxiv2018

A method for RNA structure prediction shows evidence for structure in lncRNAs

To compare the secondary structures of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure at single-nucleotide resolution using sequence information, and the Dynamic Time Warping (DTW) method to align profiles of different lengths. We applied CROSSalign to investigate the structural conservation of long non-coding RNAs such as XIST and HOTAIR as well as ssRNA viruses including HIV. In a pool of sequences with the same secondary structure CROSSalign accurately recognizes repeat A of XIST and domain D2 of HOTAIR and outperforms other methods based on covariance modelling. CROSSalign can be applied to perform pair-wise comparisons and is able to find homologues between thousands of matches identifying the exact regions of similarity between profiles of different lengths. The algorithm is freely available at the webpage http://service.tartaglialab.com//new_submission/CROSSalign.

bioinformatics↗

bioRxiv2018

Phase Separations Driven by RNA Scaffolds and Protein Sequestration in FXTAS

Recent evidence indicates that specific RNAs promote formation of ribonucleoprotein condensates by acting as scaffolds for RNA-binding proteins (RBPs).\n\nWe systematically investigated RNA-RBP interaction networks to understand ribonucleoprotein assembly. We found that highly-contacted RNAs are highly structured, have long untranslated regions (UTRs) and contain nucleotide repeat expansions. Among the RNAs with such properties, we identified the FMR1 3 UTR that harbors CGG expansions implicated in Fragile X-associated Tremor/Ataxia Syndrome (FXTAS).\n\nWe studied FMR1 binding partners in silico and in vitro and prioritized the splicing regulator TRA2A for further characterization. In a FXTAS cellular model we validated TRA2A-FRM1 interaction and investigated implications of its sequestration at both transcriptomic and post-transcriptomic levels. We found that TRA2A co-aggregates with FMR1 in a FXTAS mouse model and in post mortem human samples.\n\nOur integrative study identifies key components of ribonucleoprotein aggregates, providing links to neurodegenerative disease and allowing the discovery of new therapeutic targets.

molecular biology↗