Karenia brevis 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 K. brevis. 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 K. brevis 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 cis-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.
","abstract_html":"<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>","abstract_has_math":false,"creators":["Anglin, Scott Boyd"],"institution":null,"degree_name":"Master of Science (MS)","degree_level":"Masters Thesis","degree_discipline":"Biological Sciences","degree_department":null,"school":null,"contributors":["Timothy McLean","Glenmore Shearer","Chaoyang Zhang"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2014,"date_issued":"2014-08-01T07:00:00Z","date_published":"2014-08-01T07:00:00Z","updated_at":"2026-07-24T05:44:27Z","subjects":["Karemia brevis","Dinoflagellates","harmful algal blooms","molecular","miRNAs","NATs","Biology","Computational Biology","Life Sciences","Molecular Biology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://aquila.usm.edu/masters_theses/55","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Timothy McLean","Glenmore Shearer","Chaoyang Zhang"]},{"key":"dc:creator","label":"Author","values":["Anglin, Scott Boyd"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2016-08-05T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biological Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Masters Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science (MS)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Karemia brevis","Dinoflagellates","harmful algal blooms","molecular","miRNAs","NATs","Biology","Computational Biology","Life Sciences","Molecular Biology"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://aquila.usm.edu/masters_theses/55"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Karenia brevis 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 K. brevis. 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 K. brevis 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 cis-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.
"]},{"key":"dc:title","label":"Title","values":["Characterizing Populations of Non-Coding RNAs in Karenia brevis at Different Times of the Diel Cycle"]}]}],"canonical_facts":{"dc:contributor":["Timothy McLean","Glenmore Shearer","Chaoyang Zhang"],"dc:creator":["Anglin, Scott Boyd"],"dc:date.available":["2016-08-05T07:00:00Z"],"dc:description.abstract":["Karenia brevis 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 K. brevis. 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 K. brevis 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 cis-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.
"],"dc:identifier":["https://aquila.usm.edu/masters_theses/55"],"dc:subject":["Karemia brevis","Dinoflagellates","harmful algal blooms","molecular","miRNAs","NATs","Biology","Computational Biology","Life Sciences","Molecular Biology"],"dc:title":["Characterizing Populations of Non-Coding RNAs in Karenia brevis at Different Times of the Diel Cycle"],"thesis:degree_discipline":["Biological Sciences"],"thesis:degree_level":["Masters Thesis"],"thesis:degree_name":["Master of Science (MS)"]},"updated_at":"2026-07-24T05:44:27Z"}