With the availability of new technologies, it is now feasible to complete regulatory networks controlling complex developmental programs and understand their logic, which can improve considerably the success of diagnosis and therapies for diseases related to development or cancer. However, in order to fully understand how gene expression is regulated, epigenetic aspects need to be identified and integrated with genetic levels of regulatory networks. While the number of protein-coding genes has little variation between species, the extent of non-coding sequences is highly correlated with organismal complexity, suggesting that the expansion of non-coding RNAs (ncRNA) help to provide the regulatory potential to generate organismal diversity and complexity. Circumstantial evidence implicates long ncRNAs as important players in development, yet there is currently no thorough study of their role within a developing embryo. Our main objective is to conduct a detailed analysis of ncRNA expression and assess their role in vivo, taking advantage of Drosophila mesoderm development as a very well established model system. We will perform the first comprehensive analysis of ncRNA expression in a specific tissue during its development taking a genomic and bioinformatics approach. In addition, since long non-coding RNAs often recruit chromatin-remodeling complexes, we will assess the molecular complexes of selected long ncRNA using biochemical mass-spec based approach. Finally, for a number of selected ncRNA, we will assess their function and requirement for mesoderm development, taking advantage of Drosophila genetics. This project will consolidate the current prestige of the host institution on the intersection between genomics and developmental biology by incorporating ncRNAs to developmental gene regulatory networks. At the same time, it will contribute to create long term collaborative projects with RNA-centered research groups, incorporating RNA functional genomics.