Annotation of Novel Dynamic UTRs as Functional Targets of miRNAs During Cardiac Development

Abstract

Small noncoding microRNAs (miRNAs) play essential roles in post-transcriptional gene regulation in development and disease, predominantly through interactions with mRNA untranslated regions (UTRs). However, the dynamic and tissue specific expression of miRNAs and target UTRs throughout development is poorly characterized. In order to understand the RNA regulatory events that drive cardiac morphogenesis, we captured a simultaneous small RNA and total RNA-seq time course in zebrafish hearts. We extracted de novo transcriptome annotation of dynamically changing UTRs, revealing over ten thousand significantly altered transcripts, with novel 5’ and 3’UTRs for approximately half of all protein coding genes, and predicted regulatory miRNA/UTR interactions during development. In addition to miRNA and mRNA transcriptome resources for studies of RNA regulatory events in cardiac development and disease, this study provides a robust bioinformatic pipeline that should facilitate discovery of posttranscriptional regulatory networks in other developmental systems.