{"id":{"repo_id":"wustl","oai_identifier":"oai:openscholarship.wustl.edu:etd-1595"},"canonical_url":"https://search.dev.ndltd.org/etd/wustl/oai:openscholarship.wustl.edu:etd-1595","repository":{"repo_id":"wustl","name":"Washington University in St. Louis","base_url":"https://openscholarship.wustl.edu/do/oai/"},"display":{"title":"Systematic Identification of Independent Functional Non-coding RNA Genes in Oxytricha trifallax","abstract":"Functional noncoding RNAs participate in a variety of biological processes: for example, modulating translation, catalyzing biochemical reactions, sensing environments etc. Independent of conventional approaches such as transcriptomics and computational comparative analysis, we took advantage of the unusual genomic organization of the ciliated unicellular protozoan <italic>Oxytricha trifallax</italic> to screen for eukaryotic independent functional noncoding RNA genes. The <italic>Oxytricha</italic> macronuclear genome consists of thousands of gene-sized \"nanochromosomes\", each of which usually contains only a single gene. Using a draft <italic>Oxytricha trifallax</italic> genome assembly and a custom-written noncoding nanochromosome classifier, we identified a subset of nanochromosomes that lack any detectable protein coding gene, thereby strongly enriching for nanochromosomes that carry noncoding RNA genes. Surprisingly, we found only a small proportion of noncoding nanochromosomes, suggesting that <italic>Oxytricha</italic> has few independent functional noncoding RNA genes besides homologs of already known noncoding RNAs. Other than new members of known noncoding RNA classes including C/D and H/ACA snoRNAs, our screen identified a single novel family of small RNA genes, named the Arisong RNAs, which share some of the features of small nuclear RNAs. The small number of novel independent functional noncoding RNA genes identified in this screen contrasts to numerous recent reports of a large number of noncoding RNAs in a variety of eukaryotes. We think the difficulty of distinguishing functional noncoding RNA genes from other sources of putative noncoding RNAs has been underestimated.","abstract_html":"Functional noncoding RNAs participate in a variety of biological processes: for example, modulating translation, catalyzing biochemical reactions, sensing environments etc. Independent of conventional approaches such as transcriptomics and computational comparative analysis, we took advantage of the unusual genomic organization of the ciliated unicellular protozoan &lt;italic&gt;Oxytricha trifallax&lt;/italic&gt; to screen for eukaryotic independent functional noncoding RNA genes. The &lt;italic&gt;Oxytricha&lt;/italic&gt; macronuclear genome consists of thousands of gene-sized &quot;nanochromosomes&quot;, each of which usually contains only a single gene. Using a draft &lt;italic&gt;Oxytricha trifallax&lt;/italic&gt; genome assembly and a custom-written noncoding nanochromosome classifier, we identified a subset of nanochromosomes that lack any detectable protein coding gene, thereby strongly enriching for nanochromosomes that carry noncoding RNA genes. Surprisingly, we found only a small proportion of noncoding nanochromosomes, suggesting that &lt;italic&gt;Oxytricha&lt;/italic&gt; has few independent functional noncoding RNA genes besides homologs of already known noncoding RNAs. Other than new members of known noncoding RNA classes including C/D and H/ACA snoRNAs, our screen identified a single novel family of small RNA genes, named the Arisong RNAs, which share some of the features of small nuclear RNAs. The small number of novel independent functional noncoding RNA genes identified in this screen contrasts to numerous recent reports of a large number of noncoding RNAs in a variety of eukaryotes. We think the difficulty of distinguishing functional noncoding RNA genes from other sources of putative noncoding RNAs has been underestimated.","abstract_has_math":false,"creators":["Jung, Seolkyoung"],"institution":null,"degree_name":"Doctor of Philosophy (PhD)","degree_level":"Dissertation","degree_discipline":"Biology and Biomedical Sciences: Computational and Systems Biology","degree_department":null,"school":null,"contributors":["Sean Eddy"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2011,"date_issued":"2011-01-01T08:00:00Z","date_published":"2011-01-01T08:00:00Z","updated_at":"2026-07-24T06:13:23Z","subjects":["Bioinformatics","Molecular biology","Arisong RNA","noncoding RNA genes","Oxytricha trifallax"],"languages":["English (en)"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.7936/K7GH9FZ3"],"render_values":[{"text":"https://doi.org/10.7936/K7GH9FZ3","href":"https://doi.org/10.7936/K7GH9FZ3","code":true}]}]},"links":{"outbound_url":"https://openscholarship.wustl.edu/etd/596","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Sean Eddy"]},{"key":"dc:creator","label":"Author","values":["Jung, Seolkyoung"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2012-05-17T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biology and Biomedical Sciences: Computational and Systems Biology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Bioinformatics","Molecular biology","Arisong RNA","noncoding RNA genes","Oxytricha trifallax"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["English (en)"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://openscholarship.wustl.edu/etd/596"]},{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.7936/K7GH9FZ3"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Functional noncoding RNAs participate in a variety of biological processes: for example, modulating translation, catalyzing biochemical reactions, sensing environments etc. Independent of conventional approaches such as transcriptomics and computational comparative analysis, we took advantage of the unusual genomic organization of the ciliated unicellular protozoan <italic>Oxytricha trifallax</italic> to screen for eukaryotic independent functional noncoding RNA genes. The <italic>Oxytricha</italic> macronuclear genome consists of thousands of gene-sized \"nanochromosomes\", each of which usually contains only a single gene. Using a draft <italic>Oxytricha trifallax</italic> genome assembly and a custom-written noncoding nanochromosome classifier, we identified a subset of nanochromosomes that lack any detectable protein coding gene, thereby strongly enriching for nanochromosomes that carry noncoding RNA genes. Surprisingly, we found only a small proportion of noncoding nanochromosomes, suggesting that <italic>Oxytricha</italic> has few independent functional noncoding RNA genes besides homologs of already known noncoding RNAs. Other than new members of known noncoding RNA classes including C/D and H/ACA snoRNAs, our screen identified a single novel family of small RNA genes, named the Arisong RNAs, which share some of the features of small nuclear RNAs. The small number of novel independent functional noncoding RNA genes identified in this screen contrasts to numerous recent reports of a large number of noncoding RNAs in a variety of eukaryotes. We think the difficulty of distinguishing functional noncoding RNA genes from other sources of putative noncoding RNAs has been underestimated."]},{"key":"dc:title","label":"Title","values":["Systematic Identification of Independent Functional Non-coding RNA Genes in Oxytricha trifallax"]}]}],"canonical_facts":{"dc:contributor":["Sean Eddy"],"dc:creator":["Jung, Seolkyoung"],"dc:date.available":["2012-05-17T07:00:00Z"],"dc:description.abstract":["Functional noncoding RNAs participate in a variety of biological processes: for example, modulating translation, catalyzing biochemical reactions, sensing environments etc. Independent of conventional approaches such as transcriptomics and computational comparative analysis, we took advantage of the unusual genomic organization of the ciliated unicellular protozoan <italic>Oxytricha trifallax</italic> to screen for eukaryotic independent functional noncoding RNA genes. The <italic>Oxytricha</italic> macronuclear genome consists of thousands of gene-sized \"nanochromosomes\", each of which usually contains only a single gene. Using a draft <italic>Oxytricha trifallax</italic> genome assembly and a custom-written noncoding nanochromosome classifier, we identified a subset of nanochromosomes that lack any detectable protein coding gene, thereby strongly enriching for nanochromosomes that carry noncoding RNA genes. Surprisingly, we found only a small proportion of noncoding nanochromosomes, suggesting that <italic>Oxytricha</italic> has few independent functional noncoding RNA genes besides homologs of already known noncoding RNAs. Other than new members of known noncoding RNA classes including C/D and H/ACA snoRNAs, our screen identified a single novel family of small RNA genes, named the Arisong RNAs, which share some of the features of small nuclear RNAs. The small number of novel independent functional noncoding RNA genes identified in this screen contrasts to numerous recent reports of a large number of noncoding RNAs in a variety of eukaryotes. We think the difficulty of distinguishing functional noncoding RNA genes from other sources of putative noncoding RNAs has been underestimated."],"dc:identifier":["https://openscholarship.wustl.edu/etd/596"],"dc:identifier.doi":["https://doi.org/10.7936/K7GH9FZ3"],"dc:language":["English (en)"],"dc:subject":["Bioinformatics","Molecular biology","Arisong RNA","noncoding RNA genes","Oxytricha trifallax"],"dc:title":["Systematic Identification of Independent Functional Non-coding RNA Genes in Oxytricha trifallax"],"thesis:degree_discipline":["Biology and Biomedical Sciences: Computational and Systems Biology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-24T06:13:23Z"}