Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching.
Identifieur interne : 001069 ( Main/Exploration ); précédent : 001068; suivant : 001070Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching.
Auteurs : Sergei A. Filichkin [États-Unis] ; Michael Hamilton [États-Unis] ; Palitha D. Dharmawardhana [États-Unis] ; Sunil K. Singh [États-Unis] ; Christopher Sullivan [États-Unis] ; Asa Ben-Hur [États-Unis] ; Anireddy S N. Reddy [États-Unis] ; Pankaj Jaiswal [États-Unis]Source :
- Frontiers in plant science [ 1664-462X ] ; 2018.
Abstract
Abiotic stresses affect plant physiology, development, growth, and alter pre-mRNA splicing. Western poplar is a model woody tree and a potential bioenergy feedstock. To investigate the extent of stress-regulated alternative splicing (AS), we conducted an in-depth survey of leaf, root, and stem xylem transcriptomes under drought, salt, or temperature stress. Analysis of approximately one billion of genome-aligned RNA-Seq reads from tissue- or stress-specific libraries revealed over fifteen millions of novel splice junctions. Transcript models supported by both RNA-Seq and single molecule isoform sequencing (Iso-Seq) data revealed a broad array of novel stress- and/or tissue-specific isoforms. Analysis of Iso-Seq data also resulted in the discovery of 15,087 novel transcribed regions of which 164 show AS. Our findings demonstrate that abiotic stresses profoundly perturb transcript isoform profiles and trigger widespread intron retention (IR) events. Stress treatments often increased or decreased retention of specific introns - a phenomenon described here as differential intron retention (DIR). Many differentially retained introns were regulated in a stress- and/or tissue-specific manner. A subset of transcripts harboring super stress-responsive DIR events showed persisting fluctuations in the degree of IR across all treatments and tissue types. To investigate coordinated dynamics of intron-containing transcripts in the study we quantified absolute copy number of isoforms of two conserved transcription factors (TFs) using Droplet Digital PCR. This case study suggests that stress treatments can be associated with coordinated switches in relative ratios between fully spliced and intron-retaining isoforms and may play a role in adjusting transcriptome to abiotic stresses.
DOI: 10.3389/fpls.2018.00005
PubMed: 29483921
PubMed Central: PMC5816337
Affiliations:
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Filichkin</name><affiliation wicri:level="2"><nlm:affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author><author><name sortKey="Hamilton, Michael" sort="Hamilton, Michael" uniqKey="Hamilton M" first="Michael" last="Hamilton">Michael Hamilton</name><affiliation wicri:level="2"><nlm:affiliation>Department of Computer Science, Colorado State University, Fort Collins, CO, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Colorado State University, Fort Collins, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Dharmawardhana, Palitha D" sort="Dharmawardhana, Palitha D" uniqKey="Dharmawardhana P" first="Palitha D" last="Dharmawardhana">Palitha D. 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Singh</name><affiliation wicri:level="2"><nlm:affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author><author><name sortKey="Sullivan, Christopher" sort="Sullivan, Christopher" uniqKey="Sullivan C" first="Christopher" last="Sullivan">Christopher Sullivan</name><affiliation wicri:level="2"><nlm:affiliation>Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author><author><name sortKey="Ben Hur, Asa" sort="Ben Hur, Asa" uniqKey="Ben Hur A" first="Asa" last="Ben-Hur">Asa Ben-Hur</name><affiliation wicri:level="2"><nlm:affiliation>Department of Computer Science, Colorado State University, Fort Collins, CO, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Colorado State University, Fort Collins, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Reddy, Anireddy S N" sort="Reddy, Anireddy S N" uniqKey="Reddy A" first="Anireddy S N" last="Reddy">Anireddy S N. Reddy</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Jaiswal, Pankaj" sort="Jaiswal, Pankaj" uniqKey="Jaiswal P" first="Pankaj" last="Jaiswal">Pankaj Jaiswal</name><affiliation wicri:level="2"><nlm:affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abiotic stresses affect plant physiology, development, growth, and alter pre-mRNA splicing. Western poplar is a model woody tree and a potential bioenergy feedstock. To investigate the extent of stress-regulated alternative splicing (AS), we conducted an in-depth survey of leaf, root, and stem xylem transcriptomes under drought, salt, or temperature stress. Analysis of approximately one billion of genome-aligned RNA-Seq reads from tissue- or stress-specific libraries revealed over fifteen millions of novel splice junctions. Transcript models supported by both RNA-Seq and single molecule isoform sequencing (Iso-Seq) data revealed a broad array of novel stress- and/or tissue-specific isoforms. Analysis of Iso-Seq data also resulted in the discovery of 15,087 novel transcribed regions of which 164 show AS. Our findings demonstrate that abiotic stresses profoundly perturb transcript isoform profiles and trigger widespread intron retention (IR) events. Stress treatments often increased or decreased retention of specific introns - a phenomenon described here as differential intron retention (DIR). Many differentially retained introns were regulated in a stress- and/or tissue-specific manner. A subset of transcripts harboring super stress-responsive DIR events showed persisting fluctuations in the degree of IR across all treatments and tissue types. To investigate coordinated dynamics of intron-containing transcripts in the study we quantified absolute copy number of isoforms of two conserved transcription factors (TFs) using Droplet Digital PCR. This case study suggests that stress treatments can be associated with coordinated switches in relative ratios between fully spliced and intron-retaining isoforms and may play a role in adjusting transcriptome to abiotic stresses.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">29483921</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>9</Volume><PubDate><Year>2018</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching.</ArticleTitle><Pagination><MedlinePgn>5</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2018.00005</ELocationID><Abstract><AbstractText>Abiotic stresses affect plant physiology, development, growth, and alter pre-mRNA splicing. Western poplar is a model woody tree and a potential bioenergy feedstock. To investigate the extent of stress-regulated alternative splicing (AS), we conducted an in-depth survey of leaf, root, and stem xylem transcriptomes under drought, salt, or temperature stress. Analysis of approximately one billion of genome-aligned RNA-Seq reads from tissue- or stress-specific libraries revealed over fifteen millions of novel splice junctions. Transcript models supported by both RNA-Seq and single molecule isoform sequencing (Iso-Seq) data revealed a broad array of novel stress- and/or tissue-specific isoforms. Analysis of Iso-Seq data also resulted in the discovery of 15,087 novel transcribed regions of which 164 show AS. Our findings demonstrate that abiotic stresses profoundly perturb transcript isoform profiles and trigger widespread intron retention (IR) events. Stress treatments often increased or decreased retention of specific introns - a phenomenon described here as differential intron retention (DIR). Many differentially retained introns were regulated in a stress- and/or tissue-specific manner. A subset of transcripts harboring super stress-responsive DIR events showed persisting fluctuations in the degree of IR across all treatments and tissue types. To investigate coordinated dynamics of intron-containing transcripts in the study we quantified absolute copy number of isoforms of two conserved transcription factors (TFs) using Droplet Digital PCR. This case study suggests that stress treatments can be associated with coordinated switches in relative ratios between fully spliced and intron-retaining isoforms and may play a role in adjusting transcriptome to abiotic stresses.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Filichkin</LastName><ForeName>Sergei A</ForeName><Initials>SA</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hamilton</LastName><ForeName>Michael</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Computer Science, Colorado State University, Fort Collins, CO, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dharmawardhana</LastName><ForeName>Palitha D</ForeName><Initials>PD</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Singh</LastName><ForeName>Sunil K</ForeName><Initials>SK</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sullivan</LastName><ForeName>Christopher</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ben-Hur</LastName><ForeName>Asa</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Computer Science, Colorado State University, Fort Collins, CO, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Reddy</LastName><ForeName>Anireddy S N</ForeName><Initials>ASN</Initials><AffiliationInfo><Affiliation>Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jaiswal</LastName><ForeName>Pankaj</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>02</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">abiotic stress</Keyword><Keyword MajorTopicYN="N">alternative splicing</Keyword><Keyword MajorTopicYN="N">differential intron retention</Keyword><Keyword MajorTopicYN="N">isoform switching</Keyword><Keyword MajorTopicYN="N">stress adaptation</Keyword><Keyword MajorTopicYN="N">transcriptome</Keyword><Keyword MajorTopicYN="N">western poplar</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>10</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>01</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>2</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>2</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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Filichkin</name></region><name sortKey="Ben Hur, Asa" sort="Ben Hur, Asa" uniqKey="Ben Hur A" first="Asa" last="Ben-Hur">Asa Ben-Hur</name><name sortKey="Dharmawardhana, Palitha D" sort="Dharmawardhana, Palitha D" uniqKey="Dharmawardhana P" first="Palitha D" last="Dharmawardhana">Palitha D. Dharmawardhana</name><name sortKey="Hamilton, Michael" sort="Hamilton, Michael" uniqKey="Hamilton M" first="Michael" last="Hamilton">Michael Hamilton</name><name sortKey="Jaiswal, Pankaj" sort="Jaiswal, Pankaj" uniqKey="Jaiswal P" first="Pankaj" last="Jaiswal">Pankaj Jaiswal</name><name sortKey="Reddy, Anireddy S N" sort="Reddy, Anireddy S N" uniqKey="Reddy A" first="Anireddy S N" last="Reddy">Anireddy S N. Reddy</name><name sortKey="Singh, Sunil K" sort="Singh, Sunil K" uniqKey="Singh S" first="Sunil K" last="Singh">Sunil K. Singh</name><name sortKey="Sullivan, Christopher" sort="Sullivan, Christopher" uniqKey="Sullivan C" first="Christopher" last="Sullivan">Christopher Sullivan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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