The RNA interactomes of Imp and Syp reveal temporal RNA regulatory network in Drosophila brain development

The temporal patterning of neural stem cells is a powerful mechanism to generate neural diversity. In Drosophila, the progression of post-embryonic neurogenesis is driven by RNA-binding proteins Imp (IGF2BP) and Syp (SYNCRIP), however how they achieve their function is not well understood, since little is known about their RNA targets in the brain. Here, we present comprehensive RNA interactomes of Imp and Syp at different time points during larval brain development. Imp and Syp target highly overlapping sets of mRNAs whose encoded proteins impact fate specification, stem cell maintenance and tumourigenesis. Within these transcripts, Imp and Syp footprints exhibit limited overlap, instead we show their binding sites have co-evolved, suggesting a combinatorial or cooperative mode of regulation rather than competitive binding. Further, we identify RNAs dynamically interacting with Imp/Syp across development, consisting of existing and potentially new candidates of the neurogenesis program, and loss of Imp or Syp disrupts expression of key transcripts denotative of early or late-born neurons. Together, our findings highlight a post-transcriptional regulatory network that influences temporal order, and our study is a valuable resource for future studies finely-dissecting molecular mechanisms of neuronal fate specifications. iCLIP of Imp and Syp in developing Drosophila nervous system at 24, 48 and 96 hours after larval hatching. 2-3 replicates each for immunoprecipitate and size-mated input samples.