As soon as DNA is transcribed into RNA, various RNA-binding proteins (RBPs) interact with the RNA, and thereby regulate the expression of proteins. This is particularly important in highly polarised cells, such as neurons and glia in the brain. RBPs control production of alternative mRNA isoforms and localisation of these mRNAs to specific cellular compartments, where mRNA translation can then be regulated in response to local stimuli. We have uncovered new regulatory features in transcripts that are produced in the brain, including transposable elements and zero-length exons. I will discuss how these features contribute to the regulation, diversity and evolution of gene expression. I will also present interactions of RBPs with the secondary structure of mRNAs. We recently developed a high-throughput method that can identify RNA duplexes that interact with RBPs in vivo. This revealed the existence of long-range RNA loops, which regulate mRNA stability and translation. Together, I will discuss how protein-RNA interactions enable the diverse and unique mechanisms for regulating gene expression in the brain.