Date Available
8-26-2014
Year of Publication
2014
Degree Name
Master of Science (MS)
Document Type
Master's Thesis
College
Arts and Sciences
Department/School/Program
Biology
First Advisor
Dr. Randal Voss
Second Advisor
Dr. Jeramiah Smith
Abstract
The sea lamprey (Petromyzon marinus) undergoes programmed genome rearrangements (PGRs) during embryogenesis that results in the deletion of ~0.5 Gb of germline DNA from the somatic lineage. The underlying mechanism of these rearrangements remains largely unknown. miRNAs (microRNAs) and piRNAs (PIWI interacting RNAs) are two classes of small noncoding RNAs that play important roles in early vertebrate development, including differentiation of cell lineages, modulation of signaling pathways, and clearing of maternal transcripts. Here, I utilized next generation sequencing to determine the temporal expression of miRNAs, piRNAs, and other small noncoding RNAs during the first five days of lamprey embryogenesis, a time series that spans the 24-32 cell stage to the formation of the neural crest. I obtained expression patterns for thousands of miRNA and piRNA species. These studies identified several thousand small RNAs that are expressed immediately before, during, and immediately after PGR. Significant sequence variation was observed at the 3’ end of miRNAs, representing template-independent covalent modifications. Patterns observed in lamprey are consistent with expectations that the addition of adenosine and uracil residues plays a role in regulation of miRNA stability during the maternal-zygotic transition. We also identified a conserved motif present in sequences without any known annotation that is expressed exclusively during PGR. This motif is similar to binding motifs of known DNA binding and nuclear export factors, and our data could represent a novel class of small noncoding RNAs operating in lamprey.
Recommended Citation
Herdy, Joseph R. III, "SMALL RNA EXPRESSION DURING PROGRAMMED REARRAGEMENT OF A VERTEBRATE GENOME" (2014). Theses and Dissertations--Biology. 25.
https://uknowledge.uky.edu/biology_etds/25
Included in
Bioinformatics Commons, Biology Commons, Computational Biology Commons, Developmental Biology Commons, Genetics Commons, Genomics Commons, Molecular Genetics Commons