microRNAs (miRNAs) bind to specific messenger RNA targets to posttranscriptionally modulate their expression. Understanding the regulatory relationships between miRNAs and targets remains a major challenge. Many miRNAs reduce expression of their targets to inconsequential levels. It has also been proposed that miRNAs might adjust target expression to an optimal level. Here we analyze the consequences of mutating the conserved miRNA miR-8 in Drosophila. We identify atrophin as a direct target of miR-8. miR-8 mutant phenotypes are attributable to elevated atrophin activity, resulting in elevated apoptosis in the brain and in behavioral defects. Reduction of atrophin levels in miR-8-expressing cells to below the level generated by miR-8 regulation is detrimental, providing evidence for a "tuning target" relationship between them. Drosophila atrophin is related to the atrophin family of mammalian transcriptional regulators, implicated in the neurodegenerative disorder DRPLA. The regulatory relationship between miR-8 and atrophin orthologs is conserved in mammals.

The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs with premature translation termination codons (PTCs). The mechanisms by which PTCs and natural stop codons are discriminated remain unclear. We show that the position of stops relative to the poly(A) tail (and thus of PABPC1) is a critical determinant for PTC definition in Drosophila melanogaster. Indeed, tethering of PABPC1 downstream of a PTC abolishes NMD. Conversely, natural stops trigger NMD when the length of the 3 0 UTR is increased. However, many endogenous transcripts with exceptionally long 3 0 UTRs escape NMD, suggesting that the increase in 3 0 UTR length has co-evolved with the acquisition of features that suppress NMD. We provide evidence for the existence of 3 0 UTRs conferring immunity to NMD. We also show that PABPC1 binding is sufficient for PTC recognition, regardless of cleavage or polyadenylation. The role of PABPC1 in NMD must go beyond that of providing positional information for PTC definition, because its depletion suppresses NMD under conditions in which translation efficiency is not affected. These findings reveal a conserved role for PABPC1 in mRNA surveillance.

Highlights d Drosophila ELAV regulates all sites of neuronal alternative polyadenylation in vivo d ELAV directly binds to sites of neuron-specific splicing and 3 0 end processing d ELAV represses inclusion of an fne mini-exon that mediates FNE nuclear localization d In ELAV's absence, FNE rescues neuronal alternative polyadenylation and splicing

Post-transcriptional gene regulation is prevalent in the nervous system, where multiple tiers of regulatory complexity contribute to the development and function of highly specialized cell types. Whole-genome studies in Drosophila have identified several hundred genes containing long 39 extensions in neural tissues. We show that ELAV (embryonic-lethal abnormal visual system) is a key mediator of these neural-specific extensions. Misexpression of ELAV results in the ectopic synthesis of long messenger RNAs (mRNAs) in transgenic embryos. RNA immunoprecipitation assays suggest that ELAV directly binds the proximal polyadenylation signals of many target mRNAs. Finally, ELAV is sufficient to suppress 39 end formation at a strong polyadenylation signal when tethered to a synthetic RNA. We propose that this mechanism for coordinating 39 UTR extension may be generally used in a variety of cellular processes.

SUMMARY Alternative polyadenylation (APA) has been implicated in a variety of developmental and disease processes. A particularly dramatic form of APA occurs in the developing nervous system of flies and mammals, whereby various developmental genes undergo coordinate 3′ UTR extension. In Drosophila, the RNA-binding protein ELAV inhibits RNA processing at proximal polyadenylation sites, thereby fostering the formation of exceptionally long 3′ UTRs. Here, we present evidence that paused Pol II promotes recruitment of ELAV to extended genes. Replacing promoters of extended genes with heterologous promoters blocks normal 3′ extension in the nervous system, while extension-associated promoters can induce 3′ extension in ectopic tissues expressing ELAV. Computational analyses suggest that promoter regions of extended genes tend to contain paused Pol II and associated cis-regulatory elements such as GAGA. ChIP-Seq assays identify ELAV in the promoter regions of extended genes. Our study provides evidence for a regulatory link between promoter-proximal pausing and APA.