Increasingly detailed analysis of vertebrate genomes has shown that the majority of the genome is transcribed into RNA but only a small fraction of the total RNA codes for protein. A much larger fraction consists of noncoding RNAs, both large and small. Broadly, we seek to understand the role that small noncoding RNAs play during vertebrate development focusing mostly on microRNAs (miRNAs).

These small RNAs primarily regulate gene expression at the post-transcriptional level via base pairing with specific mRNA targets. Because the pairing is imperfect, the challenge is to identify bona fide mRNA targets and understand the role that such regulation plays in early development. We have also shown that miRNAs play a key role during caudal fin regeneration and now seek to understand this process during retinal regeneration in zebra fish. To accomplish this, we are using next generation sequencing technologies to identify global changes in gene expression patterns for both mRNAs and miRNAs during retinal regeneration.