{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/42462"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/42462","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"MicroRNA gene expression in the zebra finch brain","abstract":"Songbirds such as zebra finches communicate via learned vocalizations (songs) and studies have shown that experiencing song playback triggers complex genomic responses in the zebra finch auditory forebrain. MicroRNAs (miRNAs or miRs) are important regulators of gene expression which may coordinate complex biological processes through post-transcriptional mechanisms. This dissertation aims to explore the potential roles of miRs in the genomic response to song. This study began with a bioinformatic analysis of published microarray data and qPCR analysis of a specific conserved miR (miR-124) in zebra finch auditory forebrain, elements of which contributed to the primary paper describing the zebra finch genome (Warren et al. 2010). These preliminary studies are described in the Introduction to this thesis. Chapter 2 then presents a full de novo characterization of miRs in the songbird brain and demonstrates that song exposure has effects on several. This has now been published as Gunaratne, Lin et al. 2011 (co-first authors). A significant outcome of Chapter 2 was the identification of a novel sex-linked miR, miR-2954. Chapter 3 describes the tissue, cellular and subcellular distribution of miR-2954 and localizes it to subsets of cells in the brain. An antisense inhibitor of miR-2954 was then applied to a zebra finch cell line followed by RNA-seq analysis to test the hypothesis that changes in miR-2954 levels lead to changes in the network of genes expressed. The results confirm this hypothesis and suggest that the initial song-induced decline in miR-2954 expression described in Chapter 2 may help reprogram gene expression networks to support the metabolic changes associated with song habituation (Dong et al., 2009). This thesis research helps better understand the transcriptome of songbird brain and establishes novel roles for microRNAs in song perception, discrimination and memory.","abstract_html":"Songbirds such as zebra finches communicate via learned vocalizations (songs) and studies have shown that experiencing song playback triggers complex genomic responses in the zebra finch auditory forebrain. MicroRNAs (miRNAs or miRs) are important regulators of gene expression which may coordinate complex biological processes through post-transcriptional mechanisms. This dissertation aims to explore the potential roles of miRs in the genomic response to song. This study began with a bioinformatic analysis of published microarray data and qPCR analysis of a specific conserved miR (miR-124) in zebra finch auditory forebrain, elements of which contributed to the primary paper describing the zebra finch genome (Warren et al. 2010). These preliminary studies are described in the Introduction to this thesis. Chapter 2 then presents a full de novo characterization of miRs in the songbird brain and demonstrates that song exposure has effects on several. This has now been published as Gunaratne, Lin et al. 2011 (co-first authors). A significant outcome of Chapter 2 was the identification of a novel sex-linked miR, miR-2954. Chapter 3 describes the tissue, cellular and subcellular distribution of miR-2954 and localizes it to subsets of cells in the brain. An antisense inhibitor of miR-2954 was then applied to a zebra finch cell line followed by RNA-seq analysis to test the hypothesis that changes in miR-2954 levels lead to changes in the network of genes expressed. The results confirm this hypothesis and suggest that the initial song-induced decline in miR-2954 expression described in Chapter 2 may help reprogram gene expression networks to support the metabolic changes associated with song habituation (Dong et al., 2009). This thesis research helps better understand the transcriptome of songbird brain and establishes novel roles for microRNAs in song perception, discrimination and memory.","abstract_has_math":false,"creators":["Lin, Ya-Chi"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Cell and Developmental Biology","degree_department":null,"school":null,"contributors":["Clayton, David F.","Schuler, Mary A.","Robinson, Gene E.","Ceman, Stephanie S.","Prasanth, Kannanganattu V."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2013,"date_issued":"2013-02-03T19:46:25Z","date_published":"2013-02-03T19:46:25Z","updated_at":"2026-07-22T22:25:33Z","subjects":["MicroRNA","Zebra Finch","Brain","Cell Line","RNA-seq","Genomics"],"languages":["en"],"rights":["Copyright 2012 Ya-Chi Lin"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/42462","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Clayton, David F.","Schuler, Mary A.","Robinson, Gene E.","Ceman, Stephanie S.","Prasanth, Kannanganattu V."]},{"key":"dc:creator","label":"Author","values":["Lin, Ya-Chi"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2013-02-03T19:46:25Z","2015-02-03T11:01:00Z","2012-12"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Cell and Developmental Biology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["MicroRNA","Zebra Finch","Brain","Cell Line","RNA-seq","Genomics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2012 Ya-Chi Lin"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/42462"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Songbirds such as zebra finches communicate via learned vocalizations (songs) and studies have shown that experiencing song playback triggers complex genomic responses in the zebra finch auditory forebrain. MicroRNAs (miRNAs or miRs) are important regulators of gene expression which may coordinate complex biological processes through post-transcriptional mechanisms. This dissertation aims to explore the potential roles of miRs in the genomic response to song. This study began with a bioinformatic analysis of published microarray data and qPCR analysis of a specific conserved miR (miR-124) in zebra finch auditory forebrain, elements of which contributed to the primary paper describing the zebra finch genome (Warren et al. 2010). These preliminary studies are described in the Introduction to this thesis. Chapter 2 then presents a full de novo characterization of miRs in the songbird brain and demonstrates that song exposure has effects on several. This has now been published as Gunaratne, Lin et al. 2011 (co-first authors). A significant outcome of Chapter 2 was the identification of a novel sex-linked miR, miR-2954. Chapter 3 describes the tissue, cellular and subcellular distribution of miR-2954 and localizes it to subsets of cells in the brain. An antisense inhibitor of miR-2954 was then applied to a zebra finch cell line followed by RNA-seq analysis to test the hypothesis that changes in miR-2954 levels lead to changes in the network of genes expressed. The results confirm this hypothesis and suggest that the initial song-induced decline in miR-2954 expression described in Chapter 2 may help reprogram gene expression networks to support the metabolic changes associated with song habituation (Dong et al., 2009). This thesis research helps better understand the transcriptome of songbird brain and establishes novel roles for microRNAs in song perception, discrimination and memory.","Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2012-09-26T14:34:50Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 2 Lin_Ya-Chi.doc: 41779712 bytes, checksum: 3208d381db454640f0d94ab05df37383 (MD5) Lin_Ya-Chi.pdf: 3497874 bytes, checksum: 2df694b107df3637ebdf5705021eed92 (MD5)","Made available in DSpace on 2013-02-03T19:46:25Z (GMT). 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MicroRNAs (miRNAs or miRs) are important regulators of gene expression which may coordinate complex biological processes through post-transcriptional mechanisms. This dissertation aims to explore the potential roles of miRs in the genomic response to song. This study began with a bioinformatic analysis of published microarray data and qPCR analysis of a specific conserved miR (miR-124) in zebra finch auditory forebrain, elements of which contributed to the primary paper describing the zebra finch genome (Warren et al. 2010). These preliminary studies are described in the Introduction to this thesis. Chapter 2 then presents a full de novo characterization of miRs in the songbird brain and demonstrates that song exposure has effects on several. This has now been published as Gunaratne, Lin et al. 2011 (co-first authors). A significant outcome of Chapter 2 was the identification of a novel sex-linked miR, miR-2954. Chapter 3 describes the tissue, cellular and subcellular distribution of miR-2954 and localizes it to subsets of cells in the brain. An antisense inhibitor of miR-2954 was then applied to a zebra finch cell line followed by RNA-seq analysis to test the hypothesis that changes in miR-2954 levels lead to changes in the network of genes expressed. The results confirm this hypothesis and suggest that the initial song-induced decline in miR-2954 expression described in Chapter 2 may help reprogram gene expression networks to support the metabolic changes associated with song habituation (Dong et al., 2009). This thesis research helps better understand the transcriptome of songbird brain and establishes novel roles for microRNAs in song perception, discrimination and memory.","Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2012-09-26T14:34:50Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 2 Lin_Ya-Chi.doc: 41779712 bytes, checksum: 3208d381db454640f0d94ab05df37383 (MD5) Lin_Ya-Chi.pdf: 3497874 bytes, checksum: 2df694b107df3637ebdf5705021eed92 (MD5)","Made available in DSpace on 2013-02-03T19:46:25Z (GMT). No. of bitstreams: 3 Ya-Chi_Lin.pdf: 3497874 bytes, checksum: 2df694b107df3637ebdf5705021eed92 (MD5) Lin_Ya-Chi.doc: 41779712 bytes, checksum: 3208d381db454640f0d94ab05df37383 (MD5) license.txt: 4058 bytes, checksum: e022e1da30e60306239db1116cdb06a9 (MD5)","Item marked as restricted to the 'Administrator' Group (id=1) by Seth Robbins (srobbins@illinois.edu) on 2013-02-03T19:47:57Z Item is restricted until 2015-02-03T19:47:48Z","Restriction data tranferred 2014-07-01T11:12:07-05:00 Original Data Group with Access Administrator Release Date: 2015-02-03 13:47:48 UTC Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited Restriction Lifted for Item 42410 on 2015-02-03T11:01:00Z."],"dc:identifier":["http://hdl.handle.net/2142/42462"],"dc:language":["en"],"dc:rights":["Copyright 2012 Ya-Chi Lin"],"dc:subject":["MicroRNA","Zebra Finch","Brain","Cell Line","RNA-seq","Genomics"],"dc:title":["MicroRNA gene expression in the zebra finch brain"],"dc:type":["text"],"thesis:degree_discipline":["Cell and Developmental Biology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:33Z"}