Reference genes for accurate normalization of gene expression in wood-decomposing fungi.
Identifieur interne : 000220 ( Main/Exploration ); précédent : 000219; suivant : 000221Reference genes for accurate normalization of gene expression in wood-decomposing fungi.
Auteurs : Jiwei Zhang [États-Unis] ; Hugh D. Mitchell [États-Unis] ; Lye Meng Markillie [États-Unis] ; Matthew J. Gaffrey [États-Unis] ; Galya Orr [États-Unis] ; Jonathan Schilling [États-Unis]Source :
- Fungal genetics and biology : FG & B [ 1096-0937 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Bois, Champignons, Lignine, Régulation de l'expression des gènes fongiques.
- microbiologie : Bois.
- Analyse de profil d'expression de gènes.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Lignin.
- genetics : Fungi, Gene Expression Regulation, Fungal, Wood.
- microbiology : Wood.
- Gene Expression Profiling.
Abstract
Wood-decomposing fungi efficiently decompose plant lignocellulose, and there is increasing interest in characterizing and perhaps harnessing the fungal gene regulation strategies that enable wood decomposition. Proper interpretation of these fungal mechanisms relies on accurate quantification of gene expression, demanding reliable internal control genes (ICGs) as references. Commonly used ICGs such as actin, however, fluctuate among wood-decomposing fungi under defined conditions. In this study, by mining RNA-seq data in silico and validating ICGs in vitro using qRT-PCR, we targeted more reliable ICGs for studying transcriptional responses in wood-decomposing fungi, particularly responses to changing environments (e.g., carbon sources, decomposition stages) in various culture conditions. Using the model brown rot fungus Postia placenta in a first-pass study, our mining efforts yielded 15 constitutively-expressed genes robust in variable carbon sources (e.g., no carbon, glucose, cellobiose, aspen) and cultivation stages (e.g., 15 h, 72 h) in submerged cultures. Of these, we found 7 genes as most suitable ICGs. Expression stabilities of these newly selected ICGs were better than commonly used ICGs, analyzed by NormFinder algorithm and qRT-PCR. In a second-pass, multi-species study in solid wood, our RNA-seq mining efforts revealed hundreds of highly constitutively expressed genes among four wood-decomposing fungi with varying nutritional modes (brown rot, white rot), including a shared core set of ICGs numbering 11 genes. Together, the newly selected ICGs highlighted here will increase reliability when studying gene regulatory mechanisms of wood-decomposing fungi.
DOI: 10.1016/j.fgb.2018.11.005
PubMed: 30529285
Affiliations:
Links toward previous steps (curation, corpus...)
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Mitchell</name><affiliation wicri:level="2"><nlm:affiliation>Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Markillie, Lye Meng" sort="Markillie, Lye Meng" uniqKey="Markillie L" first="Lye Meng" last="Markillie">Lye Meng Markillie</name><affiliation wicri:level="2"><nlm:affiliation>Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Gaffrey, Matthew J" sort="Gaffrey, Matthew J" uniqKey="Gaffrey M" first="Matthew J" last="Gaffrey">Matthew J. Gaffrey</name><affiliation wicri:level="2"><nlm:affiliation>Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Orr, Galya" sort="Orr, Galya" uniqKey="Orr G" first="Galya" last="Orr">Galya Orr</name><affiliation wicri:level="2"><nlm:affiliation>Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Schilling, Jonathan" sort="Schilling, Jonathan" uniqKey="Schilling J" first="Jonathan" last="Schilling">Jonathan Schilling</name><affiliation wicri:level="2"><nlm:affiliation>Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States. Electronic address: schillin@umn.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></affiliation></author></analytic><series><title level="j">Fungal genetics and biology : FG & B</title><idno type="eISSN">1096-0937</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Fungi (genetics)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Fungal (genetics)</term><term>Lignin (genetics)</term><term>Wood (genetics)</term><term>Wood (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Bois (génétique)</term><term>Bois (microbiologie)</term><term>Champignons (génétique)</term><term>Lignine (génétique)</term><term>Régulation de l'expression des gènes fongiques (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Lignin</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fungi</term><term>Gene Expression Regulation, Fungal</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bois</term><term>Champignons</term><term>Lignine</term><term>Régulation de l'expression des gènes fongiques</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Bois</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Wood</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Wood-decomposing fungi efficiently decompose plant lignocellulose, and there is increasing interest in characterizing and perhaps harnessing the fungal gene regulation strategies that enable wood decomposition. Proper interpretation of these fungal mechanisms relies on accurate quantification of gene expression, demanding reliable internal control genes (ICGs) as references. Commonly used ICGs such as actin, however, fluctuate among wood-decomposing fungi under defined conditions. In this study, by mining RNA-seq data in silico and validating ICGs in vitro using qRT-PCR, we targeted more reliable ICGs for studying transcriptional responses in wood-decomposing fungi, particularly responses to changing environments (e.g., carbon sources, decomposition stages) in various culture conditions. Using the model brown rot fungus Postia placenta in a first-pass study, our mining efforts yielded 15 constitutively-expressed genes robust in variable carbon sources (e.g., no carbon, glucose, cellobiose, aspen) and cultivation stages (e.g., 15 h, 72 h) in submerged cultures. Of these, we found 7 genes as most suitable ICGs. Expression stabilities of these newly selected ICGs were better than commonly used ICGs, analyzed by NormFinder algorithm and qRT-PCR. In a second-pass, multi-species study in solid wood, our RNA-seq mining efforts revealed hundreds of highly constitutively expressed genes among four wood-decomposing fungi with varying nutritional modes (brown rot, white rot), including a shared core set of ICGs numbering 11 genes. Together, the newly selected ICGs highlighted here will increase reliability when studying gene regulatory mechanisms of wood-decomposing fungi.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30529285</PMID><DateCompleted><Year>2019</Year><Month>06</Month><Day>24</Day></DateCompleted><DateRevised><Year>2019</Year><Month>06</Month><Day>24</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1096-0937</ISSN><JournalIssue CitedMedium="Internet"><Volume>123</Volume><PubDate><Year>2019</Year><Month>02</Month></PubDate></JournalIssue><Title>Fungal genetics and biology : FG & B</Title><ISOAbbreviation>Fungal Genet Biol</ISOAbbreviation></Journal><ArticleTitle>Reference genes for accurate normalization of gene expression in wood-decomposing fungi.</ArticleTitle><Pagination><MedlinePgn>33-40</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S1087-1845(18)30212-3</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.fgb.2018.11.005</ELocationID><Abstract><AbstractText>Wood-decomposing fungi efficiently decompose plant lignocellulose, and there is increasing interest in characterizing and perhaps harnessing the fungal gene regulation strategies that enable wood decomposition. Proper interpretation of these fungal mechanisms relies on accurate quantification of gene expression, demanding reliable internal control genes (ICGs) as references. Commonly used ICGs such as actin, however, fluctuate among wood-decomposing fungi under defined conditions. In this study, by mining RNA-seq data in silico and validating ICGs in vitro using qRT-PCR, we targeted more reliable ICGs for studying transcriptional responses in wood-decomposing fungi, particularly responses to changing environments (e.g., carbon sources, decomposition stages) in various culture conditions. Using the model brown rot fungus Postia placenta in a first-pass study, our mining efforts yielded 15 constitutively-expressed genes robust in variable carbon sources (e.g., no carbon, glucose, cellobiose, aspen) and cultivation stages (e.g., 15 h, 72 h) in submerged cultures. Of these, we found 7 genes as most suitable ICGs. Expression stabilities of these newly selected ICGs were better than commonly used ICGs, analyzed by NormFinder algorithm and qRT-PCR. In a second-pass, multi-species study in solid wood, our RNA-seq mining efforts revealed hundreds of highly constitutively expressed genes among four wood-decomposing fungi with varying nutritional modes (brown rot, white rot), including a shared core set of ICGs numbering 11 genes. Together, the newly selected ICGs highlighted here will increase reliability when studying gene regulatory mechanisms of wood-decomposing fungi.</AbstractText><CopyrightInformation>Copyright © 2018 Elsevier Inc. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Jiwei</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mitchell</LastName><ForeName>Hugh D</ForeName><Initials>HD</Initials><AffiliationInfo><Affiliation>Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Markillie</LastName><ForeName>Lye Meng</ForeName><Initials>LM</Initials><AffiliationInfo><Affiliation>Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gaffrey</LastName><ForeName>Matthew J</ForeName><Initials>MJ</Initials><AffiliationInfo><Affiliation>Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Orr</LastName><ForeName>Galya</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schilling</LastName><ForeName>Jonathan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States. Electronic address: schillin@umn.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>12</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Fungal Genet Biol</MedlineTA><NlmUniqueID>9607601</NlmUniqueID><ISSNLinking>1087-1845</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>11132-73-3</RegistryNumber><NameOfSubstance UI="C036909">lignocellulose</NameOfSubstance></Chemical><Chemical><RegistryNumber>9005-53-2</RegistryNumber><NameOfSubstance UI="D008031">Lignin</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005658" MajorTopicYN="N">Fungi</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015966" MajorTopicYN="N">Gene Expression Regulation, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Basidiomycete</Keyword><Keyword MajorTopicYN="Y">Fungi</Keyword><Keyword MajorTopicYN="Y">Gene expression quantification</Keyword><Keyword MajorTopicYN="Y">Reference gene</Keyword><Keyword MajorTopicYN="Y">Wood decomposition</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>09</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2018</Year><Month>11</Month><Day>08</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>11</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>12</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>6</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>12</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30529285</ArticleId><ArticleId IdType="pii">S1087-1845(18)30212-3</ArticleId><ArticleId IdType="doi">10.1016/j.fgb.2018.11.005</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Minnesota</li><li>Washington (État)</li></region></list><tree><country name="États-Unis"><region name="Minnesota"><name sortKey="Zhang, Jiwei" sort="Zhang, Jiwei" uniqKey="Zhang J" first="Jiwei" last="Zhang">Jiwei Zhang</name></region><name sortKey="Gaffrey, Matthew J" sort="Gaffrey, Matthew J" uniqKey="Gaffrey M" first="Matthew J" last="Gaffrey">Matthew J. Gaffrey</name><name sortKey="Markillie, Lye Meng" sort="Markillie, Lye Meng" uniqKey="Markillie L" first="Lye Meng" last="Markillie">Lye Meng Markillie</name><name sortKey="Mitchell, Hugh D" sort="Mitchell, Hugh D" uniqKey="Mitchell H" first="Hugh D" last="Mitchell">Hugh D. Mitchell</name><name sortKey="Orr, Galya" sort="Orr, Galya" uniqKey="Orr G" first="Galya" last="Orr">Galya Orr</name><name sortKey="Schilling, Jonathan" sort="Schilling, Jonathan" uniqKey="Schilling J" first="Jonathan" last="Schilling">Jonathan Schilling</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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