The polyadenosine RNA binding protein Nab2 regulates alternative splicing and intron retention during Drosophila melanogaster brain development

Abstract

The regulation of cell-specific gene expression patterns requires the coordinated actions of hundreds of proteins, including transcription factors, processing enzymes, and many RNA binding proteins (RBPs). RBPs often become associated with an mRNA immediately after its production and can coordinate processing and quality control steps. Since RBPs can regulate multiple post-transcriptional processing steps, mutations within RBP-encoding genes often lead to pleiotropic effects that alter the physiology of multiple cell types. Thus, identifying how an RBP functions during RNA processing can provide a better understanding of both tissue physiology and mechanisms of disease. In the current study, we investigated how the Drosophila RNA binding protein Nab2, an evolutionary conserved ortholog of human ZC3H14, coordinates mRNA splicing and polyadenylation. ZC3H14 loss in human patients has previously been linked to alterations in nervous system function and disease. Both fly Nab2 and vertebrate ZC3H14 bind to polyadenosine RNA and have been implicated in the control of poly(A) tail length. Here we show that Nab2 loss from developing fly brain tissue also causes widespread changes in alternative splicing and intron retention. Retained introns in Nab2 null larval brains are most often first introns, are surrounded by adenosine-rich sequences, and are often associated with extended poly(A) tails, suggesting that Nab2 coordinates the splicing and polyadenylation of target transcripts. Alterations in splicing patterns ultimately lead to changes in protein abundance in Nab2 null developing brains. Overall, these studies highlight the importance of Nab2 and ZC3H14 in the post-transcriptional regulation of gene expression and provide critical insight into how this family of RBPs coordinates RNA processing during brain development.