Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs

MicroRNA (miRNA) genes give rise to small regulatory RNAs in a wide variety of organisms. We used computational methods to predict miRNAs conserved among Drosophila species and large-scale sequencing of small RNAs from Drosophila melanogaster to experimentally confirm and complement these prediction...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Genome Research 2007-12, Vol.17 (12), p.1850-1864
Hauptverfasser: Ruby, J Graham, Stark, Alexander, Johnston, Wendy K, Kellis, Manolis, Bartel, David P, Lai, Eric C
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 1864
container_issue 12
container_start_page 1850
container_title Genome Research
container_volume 17
creator Ruby, J Graham
Stark, Alexander
Johnston, Wendy K
Kellis, Manolis
Bartel, David P
Lai, Eric C
description MicroRNA (miRNA) genes give rise to small regulatory RNAs in a wide variety of organisms. We used computational methods to predict miRNAs conserved among Drosophila species and large-scale sequencing of small RNAs from Drosophila melanogaster to experimentally confirm and complement these predictions. In addition to validating 20 of our top 45 predictions for novel miRNA loci, the large-scale sequencing identified many miRNAs that had not been predicted. In total, 59 novel genes were identified, increasing our tally of confirmed fly miRNAs to 148. The large-scale sequencing also refined the identities of previously known miRNAs and provided insights into their biogenesis and expression. Many miRNAs were expressed in particular developmental contexts, with a large cohort of miRNAs expressed primarily in imaginal discs. Conserved miRNAs typically were expressed more broadly and robustly than were nonconserved miRNAs, and those conserved miRNAs with more restricted expression tended to have fewer predicted targets than those expressed more broadly. Predicted targets for the expanded set of microRNAs substantially increased and revised the miRNA-target relationships that appear conserved among the fly species. Insights were also provided into miRNA gene evolution, including evidence for emergent regulatory function deriving from the opposite arm of the miRNA hairpin, exemplified by mir-10, and even the opposite strand of the DNA, exemplified by mir-iab-4.
doi_str_mv 10.1101/gr.6597907
format Article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2099593</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>69046507</sourcerecordid><originalsourceid>FETCH-LOGICAL-c473t-7498a832297fa677a060b6b1025e21be9ac1faf9e1f3c14ec6755d8488509a6a3</originalsourceid><addsrcrecordid>eNqFkc9v1TAMxyMEYuPBhT8A5cQBrSNpm6S-IE1jG0gTSAjOkdu6XVBf8xa3E_vvyWNP_DhxsmV__JXtrxAvtTrVWum3Yzq1Bhwo90gca1NDYWoLj3OumqYAZfSReMb8XSlV1U3zVBxpBw2Upj4Wtxd3cVqXEOcT2YY40kwc-ETSj10i5l91nHu5YBppkbnYh26Ps4yDRMlrywvOS8Bput9PZZh6yZnN_fcpctzdhAnlNnQpfvl0xs_FkwEnpheHuBHfLi--nn8orj9ffTw_uy662lVL4WposKnKEtyA1jlUVrW21ao0VOqWADs94ACkh6rTNXXWGdM3-T6jAC1WG_HuQXe3tlvqO5qXhJPfpbDFdO8jBv9vZw43fox3vlQABqos8PogkOLtSrz4beCOpglniit7C6q2Rrn_gqUyoE2W3Ig3D2B-BXOi4fc2Wvm9lX5M_mBlhl_9vf8f9OBd9RM4O5w6</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>20591559</pqid></control><display><type>article</type><title>Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs</title><source>MEDLINE</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Alma/SFX Local Collection</source><creator>Ruby, J Graham ; Stark, Alexander ; Johnston, Wendy K ; Kellis, Manolis ; Bartel, David P ; Lai, Eric C</creator><creatorcontrib>Ruby, J Graham ; Stark, Alexander ; Johnston, Wendy K ; Kellis, Manolis ; Bartel, David P ; Lai, Eric C</creatorcontrib><description>MicroRNA (miRNA) genes give rise to small regulatory RNAs in a wide variety of organisms. We used computational methods to predict miRNAs conserved among Drosophila species and large-scale sequencing of small RNAs from Drosophila melanogaster to experimentally confirm and complement these predictions. In addition to validating 20 of our top 45 predictions for novel miRNA loci, the large-scale sequencing identified many miRNAs that had not been predicted. In total, 59 novel genes were identified, increasing our tally of confirmed fly miRNAs to 148. The large-scale sequencing also refined the identities of previously known miRNAs and provided insights into their biogenesis and expression. Many miRNAs were expressed in particular developmental contexts, with a large cohort of miRNAs expressed primarily in imaginal discs. Conserved miRNAs typically were expressed more broadly and robustly than were nonconserved miRNAs, and those conserved miRNAs with more restricted expression tended to have fewer predicted targets than those expressed more broadly. Predicted targets for the expanded set of microRNAs substantially increased and revised the miRNA-target relationships that appear conserved among the fly species. Insights were also provided into miRNA gene evolution, including evidence for emergent regulatory function deriving from the opposite arm of the miRNA hairpin, exemplified by mir-10, and even the opposite strand of the DNA, exemplified by mir-iab-4.</description><identifier>ISSN: 1088-9051</identifier><identifier>EISSN: 1549-5469</identifier><identifier>EISSN: 1549-5477</identifier><identifier>DOI: 10.1101/gr.6597907</identifier><identifier>PMID: 17989254</identifier><language>eng</language><publisher>United States: Cold Spring Harbor Laboratory Press</publisher><subject>Animals ; Base Sequence ; Computational Biology - methods ; Conserved Sequence ; Drosophila melanogaster ; Drosophila melanogaster - embryology ; Drosophila melanogaster - genetics ; Evolution, Molecular ; Gene Expression Regulation, Developmental - physiology ; Genomes/Letter ; MicroRNAs - biosynthesis ; MicroRNAs - genetics ; MicroRNAs - metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Messenger - metabolism</subject><ispartof>Genome Research, 2007-12, Vol.17 (12), p.1850-1864</ispartof><rights>Copyright © 2007, Cold Spring Harbor Laboratory Press 2007</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c473t-7498a832297fa677a060b6b1025e21be9ac1faf9e1f3c14ec6755d8488509a6a3</citedby><cites>FETCH-LOGICAL-c473t-7498a832297fa677a060b6b1025e21be9ac1faf9e1f3c14ec6755d8488509a6a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099593/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099593/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17989254$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ruby, J Graham</creatorcontrib><creatorcontrib>Stark, Alexander</creatorcontrib><creatorcontrib>Johnston, Wendy K</creatorcontrib><creatorcontrib>Kellis, Manolis</creatorcontrib><creatorcontrib>Bartel, David P</creatorcontrib><creatorcontrib>Lai, Eric C</creatorcontrib><title>Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs</title><title>Genome Research</title><addtitle>Genome Res</addtitle><description>MicroRNA (miRNA) genes give rise to small regulatory RNAs in a wide variety of organisms. We used computational methods to predict miRNAs conserved among Drosophila species and large-scale sequencing of small RNAs from Drosophila melanogaster to experimentally confirm and complement these predictions. In addition to validating 20 of our top 45 predictions for novel miRNA loci, the large-scale sequencing identified many miRNAs that had not been predicted. In total, 59 novel genes were identified, increasing our tally of confirmed fly miRNAs to 148. The large-scale sequencing also refined the identities of previously known miRNAs and provided insights into their biogenesis and expression. Many miRNAs were expressed in particular developmental contexts, with a large cohort of miRNAs expressed primarily in imaginal discs. Conserved miRNAs typically were expressed more broadly and robustly than were nonconserved miRNAs, and those conserved miRNAs with more restricted expression tended to have fewer predicted targets than those expressed more broadly. Predicted targets for the expanded set of microRNAs substantially increased and revised the miRNA-target relationships that appear conserved among the fly species. Insights were also provided into miRNA gene evolution, including evidence for emergent regulatory function deriving from the opposite arm of the miRNA hairpin, exemplified by mir-10, and even the opposite strand of the DNA, exemplified by mir-iab-4.</description><subject>Animals</subject><subject>Base Sequence</subject><subject>Computational Biology - methods</subject><subject>Conserved Sequence</subject><subject>Drosophila melanogaster</subject><subject>Drosophila melanogaster - embryology</subject><subject>Drosophila melanogaster - genetics</subject><subject>Evolution, Molecular</subject><subject>Gene Expression Regulation, Developmental - physiology</subject><subject>Genomes/Letter</subject><subject>MicroRNAs - biosynthesis</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - metabolism</subject><subject>Molecular Sequence Data</subject><subject>Nucleic Acid Conformation</subject><subject>RNA, Messenger - metabolism</subject><issn>1088-9051</issn><issn>1549-5469</issn><issn>1549-5477</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc9v1TAMxyMEYuPBhT8A5cQBrSNpm6S-IE1jG0gTSAjOkdu6XVBf8xa3E_vvyWNP_DhxsmV__JXtrxAvtTrVWum3Yzq1Bhwo90gca1NDYWoLj3OumqYAZfSReMb8XSlV1U3zVBxpBw2Upj4Wtxd3cVqXEOcT2YY40kwc-ETSj10i5l91nHu5YBppkbnYh26Ps4yDRMlrywvOS8Bput9PZZh6yZnN_fcpctzdhAnlNnQpfvl0xs_FkwEnpheHuBHfLi--nn8orj9ffTw_uy662lVL4WposKnKEtyA1jlUVrW21ao0VOqWADs94ACkh6rTNXXWGdM3-T6jAC1WG_HuQXe3tlvqO5qXhJPfpbDFdO8jBv9vZw43fox3vlQABqos8PogkOLtSrz4beCOpglniit7C6q2Rrn_gqUyoE2W3Ig3D2B-BXOi4fc2Wvm9lX5M_mBlhl_9vf8f9OBd9RM4O5w6</recordid><startdate>20071201</startdate><enddate>20071201</enddate><creator>Ruby, J Graham</creator><creator>Stark, Alexander</creator><creator>Johnston, Wendy K</creator><creator>Kellis, Manolis</creator><creator>Bartel, David P</creator><creator>Lai, Eric C</creator><general>Cold Spring Harbor Laboratory Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20071201</creationdate><title>Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs</title><author>Ruby, J Graham ; Stark, Alexander ; Johnston, Wendy K ; Kellis, Manolis ; Bartel, David P ; Lai, Eric C</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c473t-7498a832297fa677a060b6b1025e21be9ac1faf9e1f3c14ec6755d8488509a6a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Animals</topic><topic>Base Sequence</topic><topic>Computational Biology - methods</topic><topic>Conserved Sequence</topic><topic>Drosophila melanogaster</topic><topic>Drosophila melanogaster - embryology</topic><topic>Drosophila melanogaster - genetics</topic><topic>Evolution, Molecular</topic><topic>Gene Expression Regulation, Developmental - physiology</topic><topic>Genomes/Letter</topic><topic>MicroRNAs - biosynthesis</topic><topic>MicroRNAs - genetics</topic><topic>MicroRNAs - metabolism</topic><topic>Molecular Sequence Data</topic><topic>Nucleic Acid Conformation</topic><topic>RNA, Messenger - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ruby, J Graham</creatorcontrib><creatorcontrib>Stark, Alexander</creatorcontrib><creatorcontrib>Johnston, Wendy K</creatorcontrib><creatorcontrib>Kellis, Manolis</creatorcontrib><creatorcontrib>Bartel, David P</creatorcontrib><creatorcontrib>Lai, Eric C</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genome Research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ruby, J Graham</au><au>Stark, Alexander</au><au>Johnston, Wendy K</au><au>Kellis, Manolis</au><au>Bartel, David P</au><au>Lai, Eric C</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs</atitle><jtitle>Genome Research</jtitle><addtitle>Genome Res</addtitle><date>2007-12-01</date><risdate>2007</risdate><volume>17</volume><issue>12</issue><spage>1850</spage><epage>1864</epage><pages>1850-1864</pages><issn>1088-9051</issn><eissn>1549-5469</eissn><eissn>1549-5477</eissn><abstract>MicroRNA (miRNA) genes give rise to small regulatory RNAs in a wide variety of organisms. We used computational methods to predict miRNAs conserved among Drosophila species and large-scale sequencing of small RNAs from Drosophila melanogaster to experimentally confirm and complement these predictions. In addition to validating 20 of our top 45 predictions for novel miRNA loci, the large-scale sequencing identified many miRNAs that had not been predicted. In total, 59 novel genes were identified, increasing our tally of confirmed fly miRNAs to 148. The large-scale sequencing also refined the identities of previously known miRNAs and provided insights into their biogenesis and expression. Many miRNAs were expressed in particular developmental contexts, with a large cohort of miRNAs expressed primarily in imaginal discs. Conserved miRNAs typically were expressed more broadly and robustly than were nonconserved miRNAs, and those conserved miRNAs with more restricted expression tended to have fewer predicted targets than those expressed more broadly. Predicted targets for the expanded set of microRNAs substantially increased and revised the miRNA-target relationships that appear conserved among the fly species. Insights were also provided into miRNA gene evolution, including evidence for emergent regulatory function deriving from the opposite arm of the miRNA hairpin, exemplified by mir-10, and even the opposite strand of the DNA, exemplified by mir-iab-4.</abstract><cop>United States</cop><pub>Cold Spring Harbor Laboratory Press</pub><pmid>17989254</pmid><doi>10.1101/gr.6597907</doi><tpages>15</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1088-9051
ispartof Genome Research, 2007-12, Vol.17 (12), p.1850-1864
issn 1088-9051
1549-5469
1549-5477
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2099593
source MEDLINE; EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection
subjects Animals
Base Sequence
Computational Biology - methods
Conserved Sequence
Drosophila melanogaster
Drosophila melanogaster - embryology
Drosophila melanogaster - genetics
Evolution, Molecular
Gene Expression Regulation, Developmental - physiology
Genomes/Letter
MicroRNAs - biosynthesis
MicroRNAs - genetics
MicroRNAs - metabolism
Molecular Sequence Data
Nucleic Acid Conformation
RNA, Messenger - metabolism
title Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-26T02%3A55%3A36IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Evolution,%20biogenesis,%20expression,%20and%20target%20predictions%20of%20a%20substantially%20expanded%20set%20of%20Drosophila%20microRNAs&rft.jtitle=Genome%20Research&rft.au=Ruby,%20J%20Graham&rft.date=2007-12-01&rft.volume=17&rft.issue=12&rft.spage=1850&rft.epage=1864&rft.pages=1850-1864&rft.issn=1088-9051&rft.eissn=1549-5469&rft_id=info:doi/10.1101/gr.6597907&rft_dat=%3Cproquest_pubme%3E69046507%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=20591559&rft_id=info:pmid/17989254&rfr_iscdi=true