We are witnessing a tremendous increase in methodology and resources that allow detailed studies of gene regulation. Especially research on the model organism Drosophila melanogster has greatly benefited over the past years, for example from the sequencing of entire genomes for 11 additional Drosophila species and from systematic genome-wide studies, e.g. of transcription factor binding.

In this talk, I will review insights into pre- and post-transcriptional gene regulation enabled by comparative genomics and systematic genome-wide studies and discuss recent approaches and unsolved challenges.