Analyses comparing transcriptomes to genomes of mammalian species have established that approximately two-thirds of genomic DNA is pervasively transcribed, in sharp contrast to the less than 2% that is ultimately translated into proteins. In particular, multicellular organisms are characterized by the pervasive expression of different types of non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). They play crucial roles in gene expression control during development and differentiation and their deregulation is linked to many types of diseases. The relevance of RNA-based layers of control in the evolution of multicellular organisms is proved by their increase in complex organisms and especially in the brain where they are possibly involved in neuronal plasticity and in complex processes such as learning and memory. Current interest of the RNA group is the study of miRNAs, lncRNAs and circRNAs in the control of muscle, neural and hematopoietic differentiation and in the onset of different pathological conditions such as neuromuscular (Duchenne Muscular Dystrophy) and neurodegenerative (Amyotrophic Lateral Sclerosis) disorders as well as in cancers (leukemia). Besides discovering new circuitries of gene expression control these studies will also provide new tools for advanced diagnostic and therapeutic strategies.