In the Functional Genomics laboratory, we analyse effects of non-coding RNAs in several pathologies and in particular in skeletal muscle plasticity and in melanoma progression.

In our laboratory genome wide studies (microarray and DNA/RNA sequencing) are usually used as screening approaches. We have Agilent microarray and Ion PGM sequencing platforms. This approach allows us to have a broad view of the biological problem. For this reason, we analyse data in our own laboratory performing the identification of differentially expressed genes and/or pathways affected. Moreover, we use bioinformatics to predict microRNA (miRNA) and long noncoding RNA (lncRNA) functions. In the case of miRNA analyses, predicted targets are experimentally validated (a) by luciferase assay, (b) by modulating their expression in vitro or in vivo to evaluate if the target is modulated or (c) by high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). The function of lncRNAs is predicted by their expression correlation with coding genes and than validated by altering lncRNA expression to evaluate if also coding genes are influenced. Alternatively, we perform Chromatin isolation by RNA purification (ChIRP) to identify proteins and DNA fragments associated with lncRNAs. We perform gene expression of specific miRNAs, lncRNAs and coding RNAs using qRT-PCR or digital PCR. Our laboratory is equipped with the BioRad CFX96, CFX384, digital droplet PCR and 7500 Applied Biosystems qRT-PCR systems and with Agilent Bioanalyzer for RNA/DNA quality control.

Functional analyses are performed both in vitro using our cell culture facility and in vivo using our mice host facility associated with imaging analyses. We can access to optical and electron microscopy facility of the Department of Biology to produce images we use to analyse skeletal muscle and mitochondrial structure.