Characterizing Populations of Non-Coding RNAs in <i>Karenia brevis</i> at Different Times of the Diel Cycle

<p><em>Karenia brevis </em>is a mixotrophic, marine dinoflagellate found in the Gulf of Mexico that generates periodic, if not annual, harmful algal blooms (also known as “red tides”) in certain coastal areas. In an effort to better understand the biology of this organism, a functional genomics project has been initiated. As part of that project, it has been determined that a significant number of natural antisense transcripts (NATs) as well as double-stranded RNA (dsRNA) molecules exist within the transcriptome of <em>K. brevis</em>. I hypothesize that the non-coding NATs, similar to microRNAs (miRNAs) in other organisms play a role in regulating gene expression. To test this prediction, I extracted total RNA from cells grown under different culture conditions, isolated and cloned the dsRNAs and miRNAs separately, and sequenced all transcripts from each sample. Bioinformatic analyses were used to assess the relative expression of miRNAs, NATs, and mRNAs. My determination of any differential expression between day and night conditions should either support or falsify the hypothesis of NATs and/or miRNAs regulating the expression of genes via a post-transcriptional mechanism. The miRNA analysis revealed many mature miRNA candidates, but visualization software suggests that the miRNA pathway may not be present in the <em>K. brevis </em>genome. Also, length distribution of the miRNA samples suggests that the small RNAs are too long to be bound be the Argonaute protein, which is a key factor in miRNA synthesis. Cleavage patterns, transcript shape and read alignment patterns resemble a <em>cis</em>-Nat pathway, although it is undetermined whether this leads to siRNAs or an alternate small RNA. The RNA-seq analysis discovered that a large number of transcripts exhibited differential expression between the two time points of the diel cycle.</p>

Name thesis:degree_name

Master of Science (MS)

Level thesis:degree_level

Masters Thesis

Discipline thesis:degree_discipline

Biological Sciences

Year dc:date.available

2014

Author dc:creator

• Anglin, Scott Boyd

Contributors dc:contributor

• Timothy McLean
• Glenmore Shearer
• Chaoyang Zhang

• Karemia brevis
• Dinoflagellates
• harmful algal blooms
• molecular
• miRNAs
• NATs
• Biology
• Computational Biology
• Life Sciences
• Molecular Biology

Repository record dc:identifier

https://aquila.usm.edu/masters_theses/55

OAI identifier oai:identifier

oai:aquila.usm.edu:masters_theses-1034