Genome-wide profiling of populus small RNAs.
Identifieur interne : 003608 ( Main/Exploration ); précédent : 003607; suivant : 003609Genome-wide profiling of populus small RNAs.
Auteurs : Daniel Klevebring [Suède] ; Nathaniel R. Street ; Noah Fahlgren ; Kristin D. Kasschau ; James C. Carrington ; Joakim Lundeberg ; Stefan JanssonSource :
- BMC genomics [ 1471-2164 ] ; 2009.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : MicroRNAs, RNA, Plant, RNA, Small Interfering.
- genetics : Chromosomes, Plant, Genome, Plant, Plant Leaves, Populus.
- Genome-Wide Association Study.
Abstract
BACKGROUND
Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing.
RESULTS
The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs).
CONCLUSIONS
The short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis thaliana. We provide a first genome-wide view of short RNA production for P. trichocarpa and identify new, non-conserved miRNAs.
DOI: 10.1186/1471-2164-10-620
PubMed: 20021695
PubMed Central: PMC2811130
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Street</name></author><author><name sortKey="Fahlgren, Noah" sort="Fahlgren, Noah" uniqKey="Fahlgren N" first="Noah" last="Fahlgren">Noah Fahlgren</name></author><author><name sortKey="Kasschau, Kristin D" sort="Kasschau, Kristin D" uniqKey="Kasschau K" first="Kristin D" last="Kasschau">Kristin D. Kasschau</name></author><author><name sortKey="Carrington, James C" sort="Carrington, James C" uniqKey="Carrington J" first="James C" last="Carrington">James C. 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Street</name></author><author><name sortKey="Fahlgren, Noah" sort="Fahlgren, Noah" uniqKey="Fahlgren N" first="Noah" last="Fahlgren">Noah Fahlgren</name></author><author><name sortKey="Kasschau, Kristin D" sort="Kasschau, Kristin D" uniqKey="Kasschau K" first="Kristin D" last="Kasschau">Kristin D. Kasschau</name></author><author><name sortKey="Carrington, James C" sort="Carrington, James C" uniqKey="Carrington J" first="James C" last="Carrington">James C. Carrington</name></author><author><name sortKey="Lundeberg, Joakim" sort="Lundeberg, Joakim" uniqKey="Lundeberg J" first="Joakim" last="Lundeberg">Joakim Lundeberg</name></author><author><name sortKey="Jansson, Stefan" sort="Jansson, Stefan" uniqKey="Jansson S" first="Stefan" last="Jansson">Stefan Jansson</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosomes, Plant (genetics)</term><term>Genome, Plant (genetics)</term><term>Genome-Wide Association Study (MeSH)</term><term>MicroRNAs (genetics)</term><term>Plant Leaves (genetics)</term><term>Populus (genetics)</term><term>RNA, Plant (genetics)</term><term>RNA, Small Interfering (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes (génétique)</term><term>Chromosomes de plante (génétique)</term><term>Feuilles de plante (génétique)</term><term>Génome végétal (génétique)</term><term>Petit ARN interférent (génétique)</term><term>Populus (génétique)</term><term>microARN (génétique)</term><term>Étude d'association pangénomique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term><term>RNA, Plant</term><term>RNA, Small Interfering</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes, Plant</term><term>Genome, Plant</term><term>Plant Leaves</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN des plantes</term><term>Chromosomes de plante</term><term>Feuilles de plante</term><term>Génome végétal</term><term>Petit ARN interférent</term><term>Populus</term><term>microARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome-Wide Association Study</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Étude d'association pangénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs).</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>The short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis thaliana. We provide a first genome-wide view of short RNA production for P. trichocarpa and identify new, non-conserved miRNAs.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20021695</PMID><DateCompleted><Year>2010</Year><Month>03</Month><Day>11</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><PubDate><Year>2009</Year><Month>Dec</Month><Day>20</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Genome-wide profiling of populus small RNAs.</ArticleTitle><Pagination><MedlinePgn>620</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-10-620</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs).</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis thaliana. 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ValidYN="Y"><LastName>Lundeberg</LastName><ForeName>Joakim</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Jansson</LastName><ForeName>Stefan</ForeName><Initials>S</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2009</Year><Month>12</Month><Day>20</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018749">RNA, 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Carrington</name><name sortKey="Fahlgren, Noah" sort="Fahlgren, Noah" uniqKey="Fahlgren N" first="Noah" last="Fahlgren">Noah Fahlgren</name><name sortKey="Jansson, Stefan" sort="Jansson, Stefan" uniqKey="Jansson S" first="Stefan" last="Jansson">Stefan Jansson</name><name sortKey="Kasschau, Kristin D" sort="Kasschau, Kristin D" uniqKey="Kasschau K" first="Kristin D" last="Kasschau">Kristin D. Kasschau</name><name sortKey="Lundeberg, Joakim" sort="Lundeberg, Joakim" uniqKey="Lundeberg J" first="Joakim" last="Lundeberg">Joakim Lundeberg</name><name sortKey="Street, Nathaniel R" sort="Street, Nathaniel R" uniqKey="Street N" first="Nathaniel R" last="Street">Nathaniel R. Street</name></noCountry><country name="Suède"><noRegion><name sortKey="Klevebring, Daniel" sort="Klevebring, Daniel" uniqKey="Klevebring D" first="Daniel" last="Klevebring">Daniel Klevebring</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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