ABSTRACT
MicroRNAs (miRNAs) are known to modulate gene expression, but their activity at the tissue specific level remains largely uncharacterized. In order to study their contribution we developed novel tools to profile miRNA targets in the C. elegans intestine and body muscle tissues, and studied their composition and function. We validated many previously described interactions and identified hundreds of novel targets. Overall the miRNA targets obtained are known modulators of tissue function. The intestine tissue being more transcriptionally complex and larger, contains significantly more miRNA targets and includes key metabolic enzymes. Within our datasets we detect an unexpected enrichment of RNA binding proteins targeted by miRNA in both tissues, with a specific abundance of RNA splicing factors. We tested several miRNA-RNA splicing factor interactions in vivo, and found that miRNA-based regulation of specific RNA splicing factors influences alternative splicing in the intestine tissue. These results highlight an unexpected role for miRNAs in modulating tissue specific gene expression, where post-transcriptional regulation of RNA splicing factors influences tissue specific alternative splicing.