Genome-wide mapping of cardiac regulatory elements

Developmental processes are complex and intricate by nature hence they cannot be deciphered solely by investigating single gene interactions. Cutting-edge genome-wide scale interrogation techniques allow addressing organogenesis at a whole-systems level, and these technologies continue to revolutionize biomedical science. By taking advantage of these novel technologies, the Ramialison laboratory is developing and applying bioinformatics tools to advance our understanding of heart development, disease and evolution. This involves the generation of a unique collection of genome-wide cardiac-specific datasets that will allow to decipher in a systematic manner, the genes and interactions that lead to proper heart formation.

Raw-data will be obtained using the ChIP-seq (mapping of cardiac regulatory elements), RNA-seq (mapping of cardiac-specific genes) and Cage technologies (mapping of both). The raw data will be aligned to the corresponding reference genomes (processed data) and subjected to downstream analysis. As the laboratory is composed of a multidisciplinary team of computational and molecular biologists, they will performing tailored analysis based on their specific research question (heart development, congenital heart disease and/or evolution) using different algorithms (for data analysis).

This dataset generated in the Ramialison laboratory will be the first genome-wide available resource for cardiac regulatory elements in zebrafish. It will be of great importance to the cardiac and developmental field community, as it can be reused to identify novel genes and regions implicated in cardiogenesis. Beyond the context of heart development or disease, further analysis of this dataset can contribute to uncovering the principles of organ development. It is essential that the data can be provided in its original format, so it could be easily reanalysed and integrated in the computational pipelines of other groups world-wide.