REVERSE ENGINEERING THE EYE DEVELOPMENTAL GENE REGULATORY NETWORK BY LARGE-SCALE TRANSCRIPTOME PERTURBATIONS

Gene regulation is fundamental to the execution of developmental programs, the generation of cellular and evolutionary diversity. Recent advances in regulatory genomics have provided insight into some aspects of transcriptional regulation, but the overall knowledge of the genomic cis-regulatory code and the emerging transcriptional networks, remains sparse. Here we aim to unravel transcriptional networks and to elucidate novel aspects of the syntax and semantics of cis-regulatory logic through an integrated computational and experimental approach. Using Drosophila eye development as a model system, and taking advantage of recent progress both in next-generation sequencing and in Drosophila genetics, we have performed 72 RNA-seq experiments for transcriptome perturbations including various wild type strains, transcription factor (TF) mutants, over-expression of TFs, knockdown of TFs, and specific cell types obtained by FACS cell sorting throughout the developing compound eye. Then we dissected the resulting data in silico to infer direct regulatory interactions between transcription factors and target enhancers and constructed a large network. We finally validate this network by checking some of the predictions in vivo through enhancer-reporter assays, by using RNAi and by comparing the predicted interactions with known regulatory interactions. In conclusion, we were able to reverse engineer a gene regulatory network by combining gene expression data and motif discovery across multiple perturbation experiments.status: publishe