Intron retention enhances gene regulatory complexity in vertebrates.
Identifieur interne : 000929 ( PubMed/Checkpoint ); précédent : 000928; suivant : 000930Intron retention enhances gene regulatory complexity in vertebrates.
Auteurs : Ulf Schmitz [Australie] ; Natalia Pinello [Australie] ; Fangzhi Jia [Australie] ; Sultan Alasmari [Australie] ; William Ritchie [France] ; Maria-Cristina Keightley [Australie] ; Shaniko Shini [Australie] ; Graham J. Lieschke [Australie] ; Justin J-L Wong [Australie] ; John E J. Rasko [Australie]Source :
- Genome biology [ 1474-760X ] ; 2017.
Abstract
While intron retention (IR) is now widely accepted as an important mechanism of mammalian gene expression control, it remains the least studied form of alternative splicing. To delineate conserved features of IR, we performed an exhaustive phylogenetic analysis in a highly purified and functionally defined cell type comprising neutrophilic granulocytes from five vertebrate species spanning 430 million years of evolution.
DOI: 10.1186/s13059-017-1339-3
PubMed: 29141666
Affiliations:
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Rasko</name><affiliation wicri:level="4"><nlm:affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia. j.rasko@centenary.org.au.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW</wicri:regionArea><orgName type="university">Université de Sydney</orgName><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:29141666</idno><idno type="pmid">29141666</idno><idno type="doi">10.1186/s13059-017-1339-3</idno><idno type="wicri:Area/PubMed/Corpus">000007</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000007</idno><idno 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type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author><author><name sortKey="Pinello, Natalia" sort="Pinello, Natalia" uniqKey="Pinello N" first="Natalia" last="Pinello">Natalia Pinello</name><affiliation wicri:level="4"><nlm:affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW</wicri:regionArea><orgName type="university">Université de Sydney</orgName><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author><author><name sortKey="Jia, Fangzhi" sort="Jia, Fangzhi" uniqKey="Jia F" first="Fangzhi" last="Jia">Fangzhi Jia</name><affiliation wicri:level="4"><nlm:affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW</wicri:regionArea><orgName type="university">Université de Sydney</orgName><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author><author><name sortKey="Alasmari, Sultan" sort="Alasmari, Sultan" uniqKey="Alasmari S" first="Sultan" last="Alasmari">Sultan Alasmari</name><affiliation wicri:level="1"><nlm:affiliation>Australian Regenerative Medicine Institute, Monash University, Clayton, 3800, VIC, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Australian Regenerative Medicine Institute, Monash University, Clayton, 3800, VIC</wicri:regionArea><wicri:noRegion>VIC</wicri:noRegion></affiliation></author><author><name sortKey="Ritchie, William" sort="Ritchie, William" uniqKey="Ritchie W" first="William" last="Ritchie">William Ritchie</name><affiliation wicri:level="1"><nlm:affiliation>CNRS, UMR 5203, Montpellier, 34094, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CNRS, UMR 5203, Montpellier, 34094</wicri:regionArea><wicri:noRegion>34094</wicri:noRegion><wicri:noRegion>34094</wicri:noRegion></affiliation></author><author><name sortKey="Keightley, Maria Cristina" sort="Keightley, Maria Cristina" uniqKey="Keightley M" first="Maria-Cristina" last="Keightley">Maria-Cristina Keightley</name><affiliation wicri:level="1"><nlm:affiliation>Australian Regenerative Medicine Institute, Monash University, Clayton, 3800, VIC, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Australian Regenerative Medicine Institute, Monash University, Clayton, 3800, VIC</wicri:regionArea><wicri:noRegion>VIC</wicri:noRegion></affiliation></author><author><name sortKey="Shini, Shaniko" sort="Shini, Shaniko" uniqKey="Shini S" first="Shaniko" last="Shini">Shaniko Shini</name><affiliation wicri:level="1"><nlm:affiliation>School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072</wicri:regionArea><wicri:noRegion>4072</wicri:noRegion></affiliation></author><author><name sortKey="Lieschke, Graham J" sort="Lieschke, Graham J" uniqKey="Lieschke G" first="Graham J" last="Lieschke">Graham J. Lieschke</name><affiliation wicri:level="1"><nlm:affiliation>Australian Regenerative Medicine Institute, Monash University, Clayton, 3800, VIC, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Australian Regenerative Medicine Institute, Monash University, Clayton, 3800, VIC</wicri:regionArea><wicri:noRegion>VIC</wicri:noRegion></affiliation></author><author><name sortKey="Wong, Justin J L" sort="Wong, Justin J L" uniqKey="Wong J" first="Justin J-L" last="Wong">Justin J-L Wong</name><affiliation wicri:level="4"><nlm:affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW</wicri:regionArea><orgName type="university">Université de Sydney</orgName><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author><author><name sortKey="Rasko, John E J" sort="Rasko, John E J" uniqKey="Rasko J" first="John E J" last="Rasko">John E J. Rasko</name><affiliation wicri:level="4"><nlm:affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia. j.rasko@centenary.org.au.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW</wicri:regionArea><orgName type="university">Université de Sydney</orgName><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author></analytic><series><title level="j">Genome biology</title><idno type="eISSN">1474-760X</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">While intron retention (IR) is now widely accepted as an important mechanism of mammalian gene expression control, it remains the least studied form of alternative splicing. To delineate conserved features of IR, we performed an exhaustive phylogenetic analysis in a highly purified and functionally defined cell type comprising neutrophilic granulocytes from five vertebrate species spanning 430 million years of evolution.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">29141666</PMID><DateCreated><Year>2017</Year><Month>11</Month><Day>16</Day></DateCreated><DateRevised><Year>2017</Year><Month>11</Month><Day>16</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1474-760X</ISSN><JournalIssue CitedMedium="Internet"><Volume>18</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>Nov</Month><Day>16</Day></PubDate></JournalIssue><Title>Genome biology</Title><ISOAbbreviation>Genome Biol.</ISOAbbreviation></Journal><ArticleTitle>Intron retention enhances gene regulatory complexity in vertebrates.</ArticleTitle><Pagination><MedlinePgn>216</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s13059-017-1339-3</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">While intron retention (IR) is now widely accepted as an important mechanism of mammalian gene expression control, it remains the least studied form of alternative splicing. To delineate conserved features of IR, we performed an exhaustive phylogenetic analysis in a highly purified and functionally defined cell type comprising neutrophilic granulocytes from five vertebrate species spanning 430 million years of evolution.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Our RNA-sequencing-based analysis suggests that IR increases gene regulatory complexity, which is indicated by a strong anti-correlation between the number of genes affected by IR and the number of protein-coding genes in the genome of individual species. Our results confirm that IR affects many orthologous or functionally related genes in granulocytes. Further analysis uncovers new and unanticipated conserved characteristics of intron-retaining transcripts. We find that intron-retaining genes are transcriptionally co-regulated from bidirectional promoters. Intron-retaining genes have significantly longer 3' UTR sequences, with a corresponding increase in microRNA binding sites, some of which include highly conserved sequence motifs. This suggests that intron-retaining genes are highly regulated post-transcriptionally.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Our study provides unique insights concerning the role of IR as a robust and evolutionarily conserved mechanism of gene expression regulation. Our findings enhance our understanding of gene regulatory complexity by adding another contributor to evolutionary adaptation.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Schmitz</LastName><ForeName>Ulf</ForeName><Initials>U</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-5806-4662</Identifier><AffiliationInfo><Affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Sydney Medical School, University of Sydney, Camperdown, 2050, NSW, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pinello</LastName><ForeName>Natalia</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Sydney Medical School, University of Sydney, Camperdown, 2050, NSW, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jia</LastName><ForeName>Fangzhi</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Sydney Medical School, University of Sydney, Camperdown, 2050, NSW, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Alasmari</LastName><ForeName>Sultan</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Australian Regenerative Medicine Institute, Monash University, Clayton, 3800, VIC, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ritchie</LastName><ForeName>William</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>CNRS, UMR 5203, Montpellier, 34094, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Keightley</LastName><ForeName>Maria-Cristina</ForeName><Initials>MC</Initials><AffiliationInfo><Affiliation>Australian Regenerative Medicine Institute, Monash University, Clayton, 3800, VIC, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shini</LastName><ForeName>Shaniko</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lieschke</LastName><ForeName>Graham J</ForeName><Initials>GJ</Initials><AffiliationInfo><Affiliation>Australian Regenerative Medicine Institute, Monash University, Clayton, 3800, VIC, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wong</LastName><ForeName>Justin J-L</ForeName><Initials>JJ</Initials><AffiliationInfo><Affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Sydney Medical School, University of Sydney, Camperdown, 2050, NSW, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rasko</LastName><ForeName>John E J</ForeName><Initials>JEJ</Initials><AffiliationInfo><Affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, 2050, NSW, Australia. j.rasko@centenary.org.au.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Sydney Medical School, University of Sydney, Camperdown, 2050, NSW, Australia. j.rasko@centenary.org.au.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, NSW, Australia. j.rasko@centenary.org.au.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>, Locked Bag 6, Newtown, NSW, 2042, Australia. j.rasko@centenary.org.au.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>1061906</GrantID><Agency>National Health and Medical Research Council (AU)</Agency><Country>United States</Country></Grant><Grant><GrantID>1126306</GrantID><Agency>National Health and Medical Research Council</Agency><Country>United States</Country></Grant><Grant><GrantID>1126306</GrantID><Agency>National Health and Medical Research Council</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>11</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Genome Biol</MedlineTA><NlmUniqueID>100960660</NlmUniqueID><ISSNLinking>1474-7596</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Alternative splicing</Keyword><Keyword MajorTopicYN="N">Evolution</Keyword><Keyword MajorTopicYN="N">Gene regulation</Keyword><Keyword MajorTopicYN="N">Granulocytes</Keyword><Keyword MajorTopicYN="N">Intron retention</Keyword><Keyword MajorTopicYN="N">Transcriptomic complexity</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>10</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>10</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>11</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>11</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>11</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29141666</ArticleId><ArticleId IdType="doi">10.1186/s13059-017-1339-3</ArticleId><ArticleId IdType="pii">10.1186/s13059-017-1339-3</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Australie</li><li>France</li></country><region><li>Nouvelle-Galles du Sud</li></region><settlement><li>Sydney</li></settlement><orgName><li>Université de Sydney</li></orgName></list><tree><country name="Australie"><region name="Nouvelle-Galles du Sud"><name sortKey="Schmitz, Ulf" sort="Schmitz, Ulf" uniqKey="Schmitz U" first="Ulf" last="Schmitz">Ulf Schmitz</name></region><name sortKey="Alasmari, Sultan" sort="Alasmari, Sultan" uniqKey="Alasmari S" first="Sultan" last="Alasmari">Sultan Alasmari</name><name sortKey="Jia, Fangzhi" sort="Jia, Fangzhi" uniqKey="Jia F" first="Fangzhi" last="Jia">Fangzhi Jia</name><name sortKey="Keightley, Maria Cristina" sort="Keightley, Maria Cristina" uniqKey="Keightley M" first="Maria-Cristina" last="Keightley">Maria-Cristina Keightley</name><name sortKey="Lieschke, Graham J" sort="Lieschke, Graham J" uniqKey="Lieschke G" first="Graham J" last="Lieschke">Graham J. Lieschke</name><name sortKey="Pinello, Natalia" sort="Pinello, Natalia" uniqKey="Pinello N" first="Natalia" last="Pinello">Natalia Pinello</name><name sortKey="Rasko, John E J" sort="Rasko, John E J" uniqKey="Rasko J" first="John E J" last="Rasko">John E J. Rasko</name><name sortKey="Shini, Shaniko" sort="Shini, Shaniko" uniqKey="Shini S" first="Shaniko" last="Shini">Shaniko Shini</name><name sortKey="Wong, Justin J L" sort="Wong, Justin J L" uniqKey="Wong J" first="Justin J-L" last="Wong">Justin J-L Wong</name></country><country name="France"><noRegion><name sortKey="Ritchie, William" sort="Ritchie, William" uniqKey="Ritchie W" first="William" last="Ritchie">William Ritchie</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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