In the past years, uncovering the molecular mechanisms underlying RNA production and processing have become one of the main interests in our group.
We have made some important contributions to the field: the discovery of a role for chromatin structure in the regulation of splicing, that splicing occurs mostly co-transcriptionally, and that genes regulated during development are transcribed in the absence of canonically activating chromatin marks.
Under ERC funding, we have traced the transcriptomic and epigenetic profiles along dynamic processes, in particular, across human pre-B cells transdifferentiation into macrophages and along fruit fly tissue development. With this goal, we have generated extensive data on transcriptomics from different cellular fractions, whole cell proteomics and nine histone modifications in twelve time points along the transdifferentiation from pre-B cells into macrophages, and whole tissue transcriptomics and nine histone modification profiles in four Drosophila tissues (wing, eye, leg and antenna) along three developmental stages (third instar larvae, white pupa and late pupa).
We have further implemented RNA-MAPS, a web portal to retrieve and consult all data generated. We have implemented both experimental and computational tools to generate and analyze the data, such as the FLEA-ChIP-Seq, a Fast, Low-input, Easy and Affordable protocol to perform chromatin immunoprecipitation assays from as few as 500 human cells or one fruit fly imaginal disc GRAPE-nf, a computational pipeline to reproducibly analyze transcriptomics data developed under NextFlow environment, and ChIP-nf, a NextFlow tool to map and call peaks from ChIP-Seq data, both of them following gold standards from ENCODE and IHEC projects.