Small RNA and mRNA Profiling of Arabidopsis in Response to Phytophthora Infection and PAMP Treatment.
Identifieur interne : 000921 ( Main/Exploration ); précédent : 000920; suivant : 000922Small RNA and mRNA Profiling of Arabidopsis in Response to Phytophthora Infection and PAMP Treatment.
Auteurs : Yingnan Hou [États-Unis] ; Wenbo Ma [États-Unis]Source :
- Methods in molecular biology (Clifton, N.J.) [ 1940-6029 ] ; 2017.
Descripteurs français
- KwdFr :
- ARN des plantes (génétique), ARN messager (génétique), Analyse de profil d'expression de gènes (méthodes), Analyse de séquence d'ARN (méthodes), Arabidopsis (génétique), Arabidopsis (immunologie), Arabidopsis (parasitologie), Immunité des plantes (MeSH), Maladies des plantes (génétique), Maladies des plantes (parasitologie), Molécules contenant des motifs associés aux pathogènes (immunologie), Petit ARN non traduit (génétique), Phytophthora (pathogénicité), Régulation de l'expression des gènes végétaux (MeSH), Réseaux de régulation génique (MeSH).
- MESH :
- génétique : ARN des plantes, ARN messager, Arabidopsis, Maladies des plantes, Petit ARN non traduit.
- immunologie : Arabidopsis, Molécules contenant des motifs associés aux pathogènes.
- méthodes : Analyse de profil d'expression de gènes, Analyse de séquence d'ARN.
- parasitologie : Arabidopsis, Maladies des plantes.
- pathogénicité : Phytophthora.
- Immunité des plantes, Régulation de l'expression des gènes végétaux, Réseaux de régulation génique.
English descriptors
- KwdEn :
- Arabidopsis (genetics), Arabidopsis (immunology), Arabidopsis (parasitology), Gene Expression Profiling (methods), Gene Expression Regulation, Plant (MeSH), Gene Regulatory Networks (MeSH), Pathogen-Associated Molecular Pattern Molecules (immunology), Phytophthora (pathogenicity), Plant Diseases (genetics), Plant Diseases (parasitology), Plant Immunity (MeSH), RNA, Messenger (genetics), RNA, Plant (genetics), RNA, Small Untranslated (genetics), Sequence Analysis, RNA (methods).
- MESH :
- chemical , genetics : RNA, Messenger, RNA, Plant, RNA, Small Untranslated.
- chemical , immunology : Pathogen-Associated Molecular Pattern Molecules.
- genetics : Arabidopsis, Plant Diseases.
- immunology : Arabidopsis.
- methods : Gene Expression Profiling, Sequence Analysis, RNA.
- parasitology : Arabidopsis, Plant Diseases.
- pathogenicity : Phytophthora.
- Gene Expression Regulation, Plant, Gene Regulatory Networks, Plant Immunity.
Abstract
Small non-coding RNAs (smRNAs) regulate gene expression at both transcriptional and post-transcriptional levels. Well known for their roles in development, smRNAs have emerged as important regulators of plant immunity. Upon pathogen perception, accumulation of specific smRNAs are found to be altered, presumably as a host defense response. Therefore, identification of differentially accumulated smRNAs and their target genes would provide important insight into the regulation mechanism of immune responses. Here, we describe the detailed experimental procedure using Illumina sequencing to analyze the expression profiles of smRNAs and mRNAs in Arabidopsis. We focus on a newly developed pathosystem using Phytophthora capsici as the pathogen and include the treatment of Arabidopsis leaves with pathogen-associated molecular patterns (PAMPs) of Phytophthora.
DOI: 10.1007/978-1-4939-6859-6_23
PubMed: 28220433
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Small RNA and mRNA Profiling of Arabidopsis in Response to Phytophthora Infection and PAMP Treatment.</title><author><name sortKey="Hou, Yingnan" sort="Hou, Yingnan" uniqKey="Hou Y" first="Yingnan" last="Hou">Yingnan Hou</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521</wicri:regionArea><wicri:noRegion>92521</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Plant Cell Biology, University of California, Riverside, CA, 92521</wicri:regionArea><wicri:noRegion>92521</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Wenbo" sort="Ma, Wenbo" uniqKey="Ma W" first="Wenbo" last="Ma">Wenbo Ma</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA. wenbo.ma@ucr.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521</wicri:regionArea><wicri:noRegion>92521</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA. wenbo.ma@ucr.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Plant Cell Biology, University of California, Riverside, CA, 92521</wicri:regionArea><wicri:noRegion>92521</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:28220433</idno><idno type="pmid">28220433</idno><idno type="doi">10.1007/978-1-4939-6859-6_23</idno><idno type="wicri:Area/Main/Corpus">000A33</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000A33</idno><idno type="wicri:Area/Main/Curation">000A33</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000A33</idno><idno type="wicri:Area/Main/Exploration">000A33</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Small RNA and mRNA Profiling of Arabidopsis in Response to Phytophthora Infection and PAMP Treatment.</title><author><name sortKey="Hou, Yingnan" sort="Hou, Yingnan" uniqKey="Hou Y" first="Yingnan" last="Hou">Yingnan Hou</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521</wicri:regionArea><wicri:noRegion>92521</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Plant Cell Biology, University of California, Riverside, CA, 92521</wicri:regionArea><wicri:noRegion>92521</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Wenbo" sort="Ma, Wenbo" uniqKey="Ma W" first="Wenbo" last="Ma">Wenbo Ma</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA. wenbo.ma@ucr.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521</wicri:regionArea><wicri:noRegion>92521</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA. wenbo.ma@ucr.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Plant Cell Biology, University of California, Riverside, CA, 92521</wicri:regionArea><wicri:noRegion>92521</wicri:noRegion></affiliation></author></analytic><series><title level="j">Methods in molecular biology (Clifton, N.J.)</title><idno type="eISSN">1940-6029</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Arabidopsis (immunology)</term><term>Arabidopsis (parasitology)</term><term>Gene Expression Profiling (methods)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>Pathogen-Associated Molecular Pattern Molecules (immunology)</term><term>Phytophthora (pathogenicity)</term><term>Plant Diseases (genetics)</term><term>Plant Diseases (parasitology)</term><term>Plant Immunity (MeSH)</term><term>RNA, Messenger (genetics)</term><term>RNA, Plant (genetics)</term><term>RNA, Small Untranslated (genetics)</term><term>Sequence Analysis, RNA (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes (génétique)</term><term>ARN messager (génétique)</term><term>Analyse de profil d'expression de gènes (méthodes)</term><term>Analyse de séquence d'ARN (méthodes)</term><term>Arabidopsis (génétique)</term><term>Arabidopsis (immunologie)</term><term>Arabidopsis (parasitologie)</term><term>Immunité des plantes (MeSH)</term><term>Maladies des plantes (génétique)</term><term>Maladies des plantes (parasitologie)</term><term>Molécules contenant des motifs associés aux pathogènes (immunologie)</term><term>Petit ARN non traduit (génétique)</term><term>Phytophthora (pathogénicité)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Réseaux de régulation génique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Messenger</term><term>RNA, Plant</term><term>RNA, Small Untranslated</term></keywords><keywords scheme="MESH" type="chemical" qualifier="immunology" xml:lang="en"><term>Pathogen-Associated Molecular Pattern Molecules</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN des plantes</term><term>ARN messager</term><term>Arabidopsis</term><term>Maladies des plantes</term><term>Petit ARN non traduit</term></keywords><keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>Arabidopsis</term><term>Molécules contenant des motifs associés aux pathogènes</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>Arabidopsis</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Gene Expression Profiling</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de séquence d'ARN</term></keywords><keywords scheme="MESH" qualifier="parasitologie" xml:lang="fr"><term>Arabidopsis</term><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Arabidopsis</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Phytophthora</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation, Plant</term><term>Gene Regulatory Networks</term><term>Plant Immunity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Immunité des plantes</term><term>Régulation de l'expression des gènes végétaux</term><term>Réseaux de régulation génique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Small non-coding RNAs (smRNAs) regulate gene expression at both transcriptional and post-transcriptional levels. Well known for their roles in development, smRNAs have emerged as important regulators of plant immunity. Upon pathogen perception, accumulation of specific smRNAs are found to be altered, presumably as a host defense response. Therefore, identification of differentially accumulated smRNAs and their target genes would provide important insight into the regulation mechanism of immune responses. Here, we describe the detailed experimental procedure using Illumina sequencing to analyze the expression profiles of smRNAs and mRNAs in Arabidopsis. We focus on a newly developed pathosystem using Phytophthora capsici as the pathogen and include the treatment of Arabidopsis leaves with pathogen-associated molecular patterns (PAMPs) of Phytophthora.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28220433</PMID><DateCompleted><Year>2018</Year><Month>02</Month><Day>05</Day></DateCompleted><DateRevised><Year>2018</Year><Month>05</Month><Day>03</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1940-6029</ISSN><JournalIssue CitedMedium="Internet"><Volume>1578</Volume><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>Methods in molecular biology (Clifton, N.J.)</Title><ISOAbbreviation>Methods Mol Biol</ISOAbbreviation></Journal><ArticleTitle>Small RNA and mRNA Profiling of Arabidopsis in Response to Phytophthora Infection and PAMP Treatment.</ArticleTitle><Pagination><MedlinePgn>273-283</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/978-1-4939-6859-6_23</ELocationID><Abstract><AbstractText>Small non-coding RNAs (smRNAs) regulate gene expression at both transcriptional and post-transcriptional levels. Well known for their roles in development, smRNAs have emerged as important regulators of plant immunity. Upon pathogen perception, accumulation of specific smRNAs are found to be altered, presumably as a host defense response. Therefore, identification of differentially accumulated smRNAs and their target genes would provide important insight into the regulation mechanism of immune responses. Here, we describe the detailed experimental procedure using Illumina sequencing to analyze the expression profiles of smRNAs and mRNAs in Arabidopsis. We focus on a newly developed pathosystem using Phytophthora capsici as the pathogen and include the treatment of Arabidopsis leaves with pathogen-associated molecular patterns (PAMPs) of Phytophthora.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hou</LastName><ForeName>Yingnan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Wenbo</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA. wenbo.ma@ucr.edu.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA. wenbo.ma@ucr.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></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Methods Mol Biol</MedlineTA><NlmUniqueID>9214969</NlmUniqueID><ISSNLinking>1064-3745</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000069452">Pathogen-Associated Molecular Pattern Molecules</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018749">RNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D058727">RNA, Small Untranslated</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000276" MajorTopicYN="N">immunology</QualifierName><QualifierName UI="Q000469" MajorTopicYN="Y">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="N">Gene Regulatory Networks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000069452" MajorTopicYN="N">Pathogen-Associated Molecular Pattern Molecules</DescriptorName><QualifierName UI="Q000276" MajorTopicYN="N">immunology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName><QualifierName UI="Q000472" MajorTopicYN="Y">pathogenicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000469" MajorTopicYN="N">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D057865" MajorTopicYN="N">Plant Immunity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018749" MajorTopicYN="N">RNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058727" MajorTopicYN="N">RNA, Small Untranslated</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Next-generation sequencing</Keyword><Keyword MajorTopicYN="Y">Pattern-triggered immune response</Keyword><Keyword MajorTopicYN="Y">Phytophthora infection</Keyword><Keyword MajorTopicYN="Y">RNA-Seq</Keyword><Keyword MajorTopicYN="Y">Small RNA-Seq</Keyword><Keyword MajorTopicYN="Y">Small RNA-regulated defense response</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>2</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>2</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>2</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28220433</ArticleId><ArticleId IdType="doi">10.1007/978-1-4939-6859-6_23</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Hou, Yingnan" sort="Hou, Yingnan" uniqKey="Hou Y" first="Yingnan" last="Hou">Yingnan Hou</name></noRegion><name sortKey="Hou, Yingnan" sort="Hou, Yingnan" uniqKey="Hou Y" first="Yingnan" last="Hou">Yingnan Hou</name><name sortKey="Ma, Wenbo" sort="Ma, Wenbo" uniqKey="Ma W" first="Wenbo" last="Ma">Wenbo Ma</name><name sortKey="Ma, Wenbo" sort="Ma, Wenbo" uniqKey="Ma W" first="Wenbo" last="Ma">Wenbo Ma</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PhytophthoraV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000921 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000921 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PhytophthoraV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:28220433
|texte= Small RNA and mRNA Profiling of Arabidopsis in Response to Phytophthora Infection and PAMP Treatment.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:28220433" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PhytophthoraV1
| This area was generated with Dilib version V0.6.38. |  |