Document Type

Honors Thesis

Publication Date

Spring 5-2016


Over the years microRNA have been shown to play a role in the regulation of genes involved in regeneration of zebrafish (Danio rerio) tissues. However, recent research suggest that there may be other types of small RNA that play a regulatory role in these regenerative processes. For the most part these other small RNA (sRNA), such as transfer RNA (tRNA) derived fragments, ribosomal RNA (rRNA) derived fragments, and small nucleolar RNA, are disregarded. Here I analyzed the expression pattern of these sRNA during the regeneration of the zebrafish caudal fin. High-throughput sequencing was used to characterize the expression of small RNAs during zebrafish caudal fin regeneration at zero and four days post amputation using biological triplicate samples. Sequence data for each sample were processed to generate a set of 100,170 unique sequence tags that were present in all samples. The abundance of each tag in each sample was recorded as the number of reads that exactly matched the tag. Tags were annotated to various sRNA classes through sequence alignment to small RNA and genome databases in a hierarchical fashion. The observed abundance and the differential expression of the various types of sRNA were analyzed. This analyses showed that microRNA and tRNA derived fragments were the most abundant sRNA types. These included miR-21, tRNA412-LysCTT, and a novel small RNA, Tag_41941 5’- GGGATGAGTCCCTATCACGGCACAGGAGTGTGACTTT-3’. The differential expression of these tRNA derived fragments and previous research into gene silencing by sRNA suggest that these other sRNA have the potential to play a regulatory role in zebrafish caudal fin regeneration.

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