Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts.
Identifieur interne : 001706 ( Main/Exploration ); précédent : 001705; suivant : 001707Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts.
Auteurs : Laurence Josset [États-Unis] ; Nicolas Tchitchek [États-Unis] ; Lisa E. Gralinski [États-Unis] ; Martin T. Ferris [États-Unis] ; Amie J. Eisfeld [États-Unis] ; Richard R. Green [États-Unis] ; Matthew J. Thomas [États-Unis] ; Jennifer Tisoncik-Go [États-Unis] ; Gary P. Schroth [États-Unis] ; Yoshihiro Kawaoka [États-Unis] ; Fernando Pardo Manuel De Villena [États-Unis] ; Ralph S. Baric [États-Unis] ; Mark T. Heise [États-Unis] ; Xinxia Peng [États-Unis] ; Michael G. Katze [États-Unis]Source :
- RNA biology [ 1555-8584 ] ; 2014.
Descripteurs français
- KwdFr :
- ARN long non codant (génétique), Analyse de profil d'expression de gènes, Analyse de séquence d'ARN, Animaux, Annotation de séquence moléculaire, Antiviraux (administration et posologie), Antiviraux (pharmacologie), Femelle, Infections à virus à ARN (génétique), Infections à virus à ARN (traitement médicamenteux), Infections à virus à ARN (virologie), Interféron alpha (administration et posologie), Interféron alpha (pharmacologie), Lignée cellulaire, Poumon (métabolisme), Poumon (virologie), Régulation de l'expression des gènes (), Souris, Souris de lignée C57BL, Virus de la grippe A (), Virus de la grippe A (physiologie), Virus du SRAS (), Virus du SRAS (physiologie).
- MESH :
- administration et posologie : Antiviraux, Interféron alpha.
- génétique : ARN long non codant, Infections à virus à ARN.
- métabolisme : Poumon.
- pharmacologie : Antiviraux, Interféron alpha.
- physiologie : Virus de la grippe A, Virus du SRAS.
- traitement médicamenteux : Infections à virus à ARN.
- virologie : Infections à virus à ARN, Poumon.
- Analyse de profil d'expression de gènes, Analyse de séquence d'ARN, Animaux, Annotation de séquence moléculaire, Femelle, Lignée cellulaire, Régulation de l'expression des gènes, Souris, Souris de lignée C57BL, Virus de la grippe A, Virus du SRAS.
English descriptors
- KwdEn :
- Animals, Antiviral Agents (administration & dosage), Antiviral Agents (pharmacology), Cell Line, Female, Gene Expression Profiling, Gene Expression Regulation (drug effects), Influenza A virus (drug effects), Influenza A virus (physiology), Interferon-alpha (administration & dosage), Interferon-alpha (pharmacology), Lung (metabolism), Lung (virology), Mice, Mice, Inbred C57BL, Molecular Sequence Annotation, RNA Virus Infections (drug therapy), RNA Virus Infections (genetics), RNA Virus Infections (virology), RNA, Long Noncoding (genetics), SARS Virus (drug effects), SARS Virus (physiology), Sequence Analysis, RNA.
- MESH :
- chemical , administration & dosage : Antiviral Agents, Interferon-alpha.
- chemical , genetics : RNA, Long Noncoding.
- chemical , pharmacology : Antiviral Agents, Interferon-alpha.
- drug effects : Gene Expression Regulation, Influenza A virus, SARS Virus.
- drug therapy : RNA Virus Infections.
- genetics : RNA Virus Infections.
- metabolism : Lung.
- physiology : Influenza A virus, SARS Virus.
- virology : Lung, RNA Virus Infections.
- Animals, Cell Line, Female, Gene Expression Profiling, Mice, Mice, Inbred C57BL, Molecular Sequence Annotation, Sequence Analysis, RNA.
Abstract
The outcome of respiratory virus infection is determined by a complex interplay of viral and host factors. Some potentially important host factors for the antiviral response, whose functions remain largely unexplored, are long non-coding RNAs (lncRNAs). Here we systematically inferred the regulatory functions of host lncRNAs in response to influenza A virus and severe acute respiratory syndrome coronavirus (SARS-CoV) based on their similarity in expression with genes of known function. We performed total RNA-Seq on viral-infected lungs from eight mouse strains, yielding a large data set of transcriptional responses. Overall 5,329 lncRNAs were differentially expressed after infection. Most of the lncRNAs were co-expressed with coding genes in modules enriched in genes associated with lung homeostasis pathways or immune response processes. Each lncRNA was further individually annotated using a rank-based method, enabling us to associate 5,295 lncRNAs to at least one gene set and to predict their potential cis effects. We validated the lncRNAs predicted to be interferon-stimulated by profiling mouse responses after interferon-α treatment. Altogether, these results provide a broad categorization of potential lncRNA functions and identify subsets of lncRNAs with likely key roles in respiratory virus pathogenesis. These data are fully accessible through the MOuse NOn-Code Lung interactive database (MONOCLdb).
DOI: 10.4161/rna.29442
PubMed: 24922324
Affiliations:
- États-Unis
- Californie, Caroline du Nord, Oregon, Wisconsin
- Madison (Wisconsin)
- Université du Wisconsin à Madison
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Le document en format XML
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Schroth</name><affiliation wicri:level="2"><nlm:affiliation>Illumina, Inc.; San Diego, CA USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Illumina, Inc.; San Diego</wicri:cityArea></affiliation></author><author><name sortKey="Kawaoka, Yoshihiro" sort="Kawaoka, Yoshihiro" uniqKey="Kawaoka Y" first="Yoshihiro" last="Kawaoka">Yoshihiro Kawaoka</name><affiliation wicri:level="2"><nlm:affiliation>Department of Pathobiological Sciences; Influenza Research Institute; University of Wisconsin-Madison; Madison, WI USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Wisconsin</region></placeName><wicri:cityArea>Department of Pathobiological Sciences; Influenza Research Institute; University of Wisconsin-Madison; Madison</wicri:cityArea><placeName><settlement type="city">Madison (Wisconsin)</settlement><region type="state">Wisconsin</region></placeName><orgName type="university" n="3">Université du Wisconsin à Madison</orgName></affiliation></author><author><name sortKey="Manuel De Villena, Fernando Pardo" sort="Manuel De Villena, Fernando Pardo" uniqKey="Manuel De Villena F" first="Fernando Pardo" last="Manuel De Villena">Fernando Pardo Manuel De Villena</name><affiliation wicri:level="2"><nlm:affiliation>Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill, NC USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Caroline du Nord</region></placeName><wicri:cityArea>Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill</wicri:cityArea></affiliation></author><author><name sortKey="Baric, Ralph S" sort="Baric, Ralph S" uniqKey="Baric R" first="Ralph S" last="Baric">Ralph S. Baric</name><affiliation wicri:level="2"><nlm:affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA; Department of Epidemiology; University of North Carolina-Chapel Hill; Chapel Hill, NC USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Caroline du Nord</region></placeName><wicri:cityArea>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA; Department of Epidemiology; University of North Carolina-Chapel Hill; Chapel Hill</wicri:cityArea></affiliation></author><author><name sortKey="Heise, Mark T" sort="Heise, Mark T" uniqKey="Heise M" first="Mark T" last="Heise">Mark T. Heise</name><affiliation wicri:level="2"><nlm:affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA; Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill, NC USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Caroline du Nord</region></placeName><wicri:cityArea>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA; Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill</wicri:cityArea></affiliation></author><author><name sortKey="Peng, Xinxia" sort="Peng, Xinxia" uniqKey="Peng X" first="Xinxia" last="Peng">Xinxia Peng</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Oregon</region></placeName><wicri:cityArea>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland</wicri:cityArea></affiliation></author><author><name sortKey="Katze, Michael G" sort="Katze, Michael G" uniqKey="Katze M" first="Michael G" last="Katze">Michael G. Katze</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Oregon</region></placeName><wicri:cityArea>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24922324</idno><idno type="pmid">24922324</idno><idno type="doi">10.4161/rna.29442</idno><idno type="wicri:Area/PubMed/Corpus">000F82</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000F82</idno><idno type="wicri:Area/PubMed/Curation">000F82</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000F82</idno><idno type="wicri:Area/PubMed/Checkpoint">001047</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001047</idno><idno type="wicri:Area/Ncbi/Merge">002902</idno><idno type="wicri:Area/Ncbi/Curation">002902</idno><idno type="wicri:Area/Ncbi/Checkpoint">002902</idno><idno type="wicri:Area/Main/Merge">001712</idno><idno type="wicri:Area/Main/Curation">001706</idno><idno type="wicri:Area/Main/Exploration">001706</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts.</title><author><name sortKey="Josset, Laurence" sort="Josset, Laurence" uniqKey="Josset L" first="Laurence" last="Josset">Laurence Josset</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Oregon</region></placeName><wicri:cityArea>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland</wicri:cityArea></affiliation></author><author><name sortKey="Tchitchek, Nicolas" sort="Tchitchek, Nicolas" uniqKey="Tchitchek N" first="Nicolas" last="Tchitchek">Nicolas Tchitchek</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Oregon</region></placeName><wicri:cityArea>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland</wicri:cityArea></affiliation></author><author><name sortKey="Gralinski, Lisa E" sort="Gralinski, Lisa E" uniqKey="Gralinski L" first="Lisa E" last="Gralinski">Lisa E. Gralinski</name><affiliation wicri:level="2"><nlm:affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA; Department of Epidemiology; University of North Carolina-Chapel Hill; Chapel Hill, NC USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Caroline du Nord</region></placeName><wicri:cityArea>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA; Department of Epidemiology; University of North Carolina-Chapel Hill; Chapel Hill</wicri:cityArea></affiliation></author><author><name sortKey="Ferris, Martin T" sort="Ferris, Martin T" uniqKey="Ferris M" first="Martin T" last="Ferris">Martin T. Ferris</name><affiliation wicri:level="2"><nlm:affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA; Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill, NC USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Caroline du Nord</region></placeName><wicri:cityArea>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA; Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill</wicri:cityArea></affiliation></author><author><name sortKey="Eisfeld, Amie J" sort="Eisfeld, Amie J" uniqKey="Eisfeld A" first="Amie J" last="Eisfeld">Amie J. Eisfeld</name><affiliation wicri:level="2"><nlm:affiliation>Department of Pathobiological Sciences; Influenza Research Institute; University of Wisconsin-Madison; Madison, WI USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Wisconsin</region></placeName><wicri:cityArea>Department of Pathobiological Sciences; Influenza Research Institute; University of Wisconsin-Madison; Madison</wicri:cityArea></affiliation></author><author><name sortKey="Green, Richard R" sort="Green, Richard R" uniqKey="Green R" first="Richard R" last="Green">Richard R. Green</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Oregon</region></placeName><wicri:cityArea>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland</wicri:cityArea></affiliation></author><author><name sortKey="Thomas, Matthew J" sort="Thomas, Matthew J" uniqKey="Thomas M" first="Matthew J" last="Thomas">Matthew J. Thomas</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Oregon</region></placeName><wicri:cityArea>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland</wicri:cityArea></affiliation></author><author><name sortKey="Tisoncik Go, Jennifer" sort="Tisoncik Go, Jennifer" uniqKey="Tisoncik Go J" first="Jennifer" last="Tisoncik-Go">Jennifer Tisoncik-Go</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Oregon</region></placeName><wicri:cityArea>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland</wicri:cityArea></affiliation></author><author><name sortKey="Schroth, Gary P" sort="Schroth, Gary P" uniqKey="Schroth G" first="Gary P" last="Schroth">Gary P. Schroth</name><affiliation wicri:level="2"><nlm:affiliation>Illumina, Inc.; San Diego, CA USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Illumina, Inc.; San Diego</wicri:cityArea></affiliation></author><author><name sortKey="Kawaoka, Yoshihiro" sort="Kawaoka, Yoshihiro" uniqKey="Kawaoka Y" first="Yoshihiro" last="Kawaoka">Yoshihiro Kawaoka</name><affiliation wicri:level="2"><nlm:affiliation>Department of Pathobiological Sciences; Influenza Research Institute; University of Wisconsin-Madison; Madison, WI USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Wisconsin</region></placeName><wicri:cityArea>Department of Pathobiological Sciences; Influenza Research Institute; University of Wisconsin-Madison; Madison</wicri:cityArea><placeName><settlement type="city">Madison (Wisconsin)</settlement><region type="state">Wisconsin</region></placeName><orgName type="university" n="3">Université du Wisconsin à Madison</orgName></affiliation></author><author><name sortKey="Manuel De Villena, Fernando Pardo" sort="Manuel De Villena, Fernando Pardo" uniqKey="Manuel De Villena F" first="Fernando Pardo" last="Manuel De Villena">Fernando Pardo Manuel De Villena</name><affiliation wicri:level="2"><nlm:affiliation>Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill, NC USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Caroline du Nord</region></placeName><wicri:cityArea>Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill</wicri:cityArea></affiliation></author><author><name sortKey="Baric, Ralph S" sort="Baric, Ralph S" uniqKey="Baric R" first="Ralph S" last="Baric">Ralph S. Baric</name><affiliation wicri:level="2"><nlm:affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA; Department of Epidemiology; University of North Carolina-Chapel Hill; Chapel Hill, NC USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Caroline du Nord</region></placeName><wicri:cityArea>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA; Department of Epidemiology; University of North Carolina-Chapel Hill; Chapel Hill</wicri:cityArea></affiliation></author><author><name sortKey="Heise, Mark T" sort="Heise, Mark T" uniqKey="Heise M" first="Mark T" last="Heise">Mark T. Heise</name><affiliation wicri:level="2"><nlm:affiliation>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA; Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill, NC USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Caroline du Nord</region></placeName><wicri:cityArea>Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA; Department of Genetics; University of North Carolina-Chapel Hill; Chapel Hill</wicri:cityArea></affiliation></author><author><name sortKey="Peng, Xinxia" sort="Peng, Xinxia" uniqKey="Peng X" first="Xinxia" last="Peng">Xinxia Peng</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Oregon</region></placeName><wicri:cityArea>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland</wicri:cityArea></affiliation></author><author><name sortKey="Katze, Michael G" sort="Katze, Michael G" uniqKey="Katze M" first="Michael G" last="Katze">Michael G. Katze</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland, OR USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Oregon</region></placeName><wicri:cityArea>Department of Microbiology; School of Medicine; University of Washington; Seattle, WA USA; Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research; Portland</wicri:cityArea></affiliation></author></analytic><series><title level="j">RNA biology</title><idno type="eISSN">1555-8584</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Antiviral Agents (administration & dosage)</term><term>Antiviral Agents (pharmacology)</term><term>Cell Line</term><term>Female</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation (drug effects)</term><term>Influenza A virus (drug effects)</term><term>Influenza A virus (physiology)</term><term>Interferon-alpha (administration & dosage)</term><term>Interferon-alpha (pharmacology)</term><term>Lung (metabolism)</term><term>Lung (virology)</term><term>Mice</term><term>Mice, Inbred C57BL</term><term>Molecular Sequence Annotation</term><term>RNA Virus Infections (drug therapy)</term><term>RNA Virus Infections (genetics)</term><term>RNA Virus Infections (virology)</term><term>RNA, Long Noncoding (genetics)</term><term>SARS Virus (drug effects)</term><term>SARS Virus (physiology)</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN long non codant (génétique)</term><term>Analyse de profil d'expression de gènes</term><term>Analyse de séquence d'ARN</term><term>Animaux</term><term>Annotation de séquence moléculaire</term><term>Antiviraux (administration et posologie)</term><term>Antiviraux (pharmacologie)</term><term>Femelle</term><term>Infections à virus à ARN (génétique)</term><term>Infections à virus à ARN (traitement médicamenteux)</term><term>Infections à virus à ARN (virologie)</term><term>Interféron alpha (administration et posologie)</term><term>Interféron alpha (pharmacologie)</term><term>Lignée cellulaire</term><term>Poumon (métabolisme)</term><term>Poumon (virologie)</term><term>Régulation de l'expression des gènes ()</term><term>Souris</term><term>Souris de lignée C57BL</term><term>Virus de la grippe A ()</term><term>Virus de la grippe A (physiologie)</term><term>Virus du SRAS ()</term><term>Virus du SRAS (physiologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="administration & dosage" xml:lang="en"><term>Antiviral Agents</term><term>Interferon-alpha</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Long Noncoding</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Antiviral Agents</term><term>Interferon-alpha</term></keywords><keywords scheme="MESH" qualifier="administration et posologie" xml:lang="fr"><term>Antiviraux</term><term>Interféron alpha</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Gene Expression Regulation</term><term>Influenza A virus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="drug therapy" xml:lang="en"><term>RNA Virus Infections</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>RNA Virus Infections</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN long non codant</term><term>Infections à virus à ARN</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Lung</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Poumon</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Antiviraux</term><term>Interféron alpha</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Virus de la grippe A</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Influenza A virus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="traitement médicamenteux" xml:lang="fr"><term>Infections à virus à ARN</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à virus à ARN</term><term>Poumon</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Lung</term><term>RNA Virus Infections</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Cell Line</term><term>Female</term><term>Gene Expression Profiling</term><term>Mice</term><term>Mice, Inbred C57BL</term><term>Molecular Sequence Annotation</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de séquence d'ARN</term><term>Animaux</term><term>Annotation de séquence moléculaire</term><term>Femelle</term><term>Lignée cellulaire</term><term>Régulation de l'expression des gènes</term><term>Souris</term><term>Souris de lignée C57BL</term><term>Virus de la grippe A</term><term>Virus du SRAS</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The outcome of respiratory virus infection is determined by a complex interplay of viral and host factors. Some potentially important host factors for the antiviral response, whose functions remain largely unexplored, are long non-coding RNAs (lncRNAs). Here we systematically inferred the regulatory functions of host lncRNAs in response to influenza A virus and severe acute respiratory syndrome coronavirus (SARS-CoV) based on their similarity in expression with genes of known function. We performed total RNA-Seq on viral-infected lungs from eight mouse strains, yielding a large data set of transcriptional responses. Overall 5,329 lncRNAs were differentially expressed after infection. Most of the lncRNAs were co-expressed with coding genes in modules enriched in genes associated with lung homeostasis pathways or immune response processes. Each lncRNA was further individually annotated using a rank-based method, enabling us to associate 5,295 lncRNAs to at least one gene set and to predict their potential cis effects. We validated the lncRNAs predicted to be interferon-stimulated by profiling mouse responses after interferon-α treatment. Altogether, these results provide a broad categorization of potential lncRNA functions and identify subsets of lncRNAs with likely key roles in respiratory virus pathogenesis. These data are fully accessible through the MOuse NOn-Code Lung interactive database (MONOCLdb). </div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li><li>Caroline du Nord</li><li>Oregon</li><li>Wisconsin</li></region><settlement><li>Madison (Wisconsin)</li></settlement><orgName><li>Université du Wisconsin à Madison</li></orgName></list><tree><country name="États-Unis"><region name="Oregon"><name sortKey="Josset, Laurence" sort="Josset, Laurence" uniqKey="Josset L" first="Laurence" last="Josset">Laurence Josset</name></region><name sortKey="Baric, Ralph S" sort="Baric, Ralph S" uniqKey="Baric R" first="Ralph S" last="Baric">Ralph S. Baric</name><name sortKey="Eisfeld, Amie J" sort="Eisfeld, Amie J" uniqKey="Eisfeld A" first="Amie J" last="Eisfeld">Amie J. Eisfeld</name><name sortKey="Ferris, Martin T" sort="Ferris, Martin T" uniqKey="Ferris M" first="Martin T" last="Ferris">Martin T. Ferris</name><name sortKey="Gralinski, Lisa E" sort="Gralinski, Lisa E" uniqKey="Gralinski L" first="Lisa E" last="Gralinski">Lisa E. Gralinski</name><name sortKey="Green, Richard R" sort="Green, Richard R" uniqKey="Green R" first="Richard R" last="Green">Richard R. Green</name><name sortKey="Heise, Mark T" sort="Heise, Mark T" uniqKey="Heise M" first="Mark T" last="Heise">Mark T. Heise</name><name sortKey="Katze, Michael G" sort="Katze, Michael G" uniqKey="Katze M" first="Michael G" last="Katze">Michael G. Katze</name><name sortKey="Kawaoka, Yoshihiro" sort="Kawaoka, Yoshihiro" uniqKey="Kawaoka Y" first="Yoshihiro" last="Kawaoka">Yoshihiro Kawaoka</name><name sortKey="Manuel De Villena, Fernando Pardo" sort="Manuel De Villena, Fernando Pardo" uniqKey="Manuel De Villena F" first="Fernando Pardo" last="Manuel De Villena">Fernando Pardo Manuel De Villena</name><name sortKey="Peng, Xinxia" sort="Peng, Xinxia" uniqKey="Peng X" first="Xinxia" last="Peng">Xinxia Peng</name><name sortKey="Schroth, Gary P" sort="Schroth, Gary P" uniqKey="Schroth G" first="Gary P" last="Schroth">Gary P. Schroth</name><name sortKey="Tchitchek, Nicolas" sort="Tchitchek, Nicolas" uniqKey="Tchitchek N" first="Nicolas" last="Tchitchek">Nicolas Tchitchek</name><name sortKey="Thomas, Matthew J" sort="Thomas, Matthew J" uniqKey="Thomas M" first="Matthew J" last="Thomas">Matthew J. Thomas</name><name sortKey="Tisoncik Go, Jennifer" sort="Tisoncik Go, Jennifer" uniqKey="Tisoncik Go J" first="Jennifer" last="Tisoncik-Go">Jennifer Tisoncik-Go</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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