PoplarV1, Main, Exploration, bibRecord, 001A85

Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing.

Identifieur interne : 001A85 ( Main/Exploration ); précédent : 001A84; suivant : 001A86

Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing.

Auteurs : Min Chen [République populaire de Chine] ; Hai Bao [République populaire de Chine] ; Qiuming Wu [République populaire de Chine] ; Yanwei Wang [République populaire de Chine]

Source :

International journal of molecular sciences [ 1422-0067 ] ; 2015.

RBID : pubmed:26096002

Descripteurs français

English descriptors

KwdEn :
- Base Sequence (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), High-Throughput Nucleotide Sequencing (methods), MicroRNAs (genetics), Molecular Sequence Annotation (MeSH), Molecular Sequence Data (MeSH), Nitrogen (deficiency), Populus (genetics), Populus (growth & development), RNA, Messenger (genetics), RNA, Plant (genetics), Real-Time Polymerase Chain Reaction (MeSH), Sequence Homology, Nucleic Acid (MeSH), Stress, Physiological (genetics), Transcriptome (MeSH).
MESH :
- chemical , deficiency : Nitrogen.
- chemical , genetics : MicroRNAs, RNA, Messenger, RNA, Plant.
- genetics : Populus, Stress, Physiological.
- growth & development : Populus.
- methods : High-Throughput Nucleotide Sequencing.
- Base Sequence, Gene Expression Regulation, Plant, Genes, Plant, Molecular Sequence Annotation, Molecular Sequence Data, Real-Time Polymerase Chain Reaction, Sequence Homology, Nucleic Acid, Transcriptome.

Abstract

miRNAs are endogenous non-coding small RNAs with important regulatory roles in stress responses. Nitrogen (N) is an indispensable macronutrient required for plant growth and development. Previous studies have identified a variety of known and novel miRNAs responsive to low N stress in plants, including Populus. However, miRNAs involved in the cleavage of target genes and the corresponding regulatory networks in response to N stress in Populus remain largely unknown. Consequently, degradome sequencing was employed for global detection and validation of N-responsive miRNAs and their targets. A total of 60 unique miRNAs (39 conserved, 13 non-conserved, and eight novel) were experimentally identified to target 64 mRNA transcripts and 21 precursors. Among them, we further verified the cleavage of 11 N-responsive miRNAs identified previously and provided empirical evidence for the cleavage mode of these miRNAs on their target mRNAs. Furthermore, five miRNA stars (miRNA*s) were shown to have cleavage function. The specificity and diversity of cleavage sites on the targets and miRNA precursors in P. tomentosa were further detected. Identification and annotation of miRNA-mediated cleavage of target genes in Populus can increase our understanding of miRNA-mediated molecular mechanisms of woody plants adapted to low N environments.

DOI: 10.3390/ijms160613937
PubMed: 26096002
PubMed Central: PMC4490532

Affiliations:

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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Genes, Plant (MeSH)</term>
<term>High-Throughput Nucleotide Sequencing (methods)</term>
<term>MicroRNAs (genetics)</term>
<term>Molecular Sequence Annotation (MeSH)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Nitrogen (deficiency)</term>
<term>Populus (genetics)</term>
<term>Populus (growth & development)</term>
<term>RNA, Messenger (genetics)</term>
<term>RNA, Plant (genetics)</term>
<term>Real-Time Polymerase Chain Reaction (MeSH)</term>
<term>Sequence Homology, Nucleic Acid (MeSH)</term>
<term>Stress, Physiological (genetics)</term>
<term>Transcriptome (MeSH)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes (génétique)</term>
<term>ARN messager (génétique)</term>
<term>Annotation de séquence moléculaire (MeSH)</term>
<term>Azote (déficit)</term>
<term>Données de séquences moléculaires (MeSH)</term>
<term>Gènes de plante (MeSH)</term>
<term>Populus (croissance et développement)</term>
<term>Populus (génétique)</term>
<term>Réaction de polymérisation en chaine en temps réel (MeSH)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Similitude de séquences d'acides nucléiques (MeSH)</term>
<term>Stress physiologique (génétique)</term>
<term>Séquence nucléotidique (MeSH)</term>
<term>Séquençage nucléotidique à haut débit (méthodes)</term>
<term>Transcriptome (MeSH)</term>
<term>microARN (génétique)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="deficiency" xml:lang="en"><term>Nitrogen</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term>
<term>RNA, Messenger</term>
<term>RNA, Plant</term>
</keywords>
<keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="déficit" xml:lang="fr"><term>Azote</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term>
<term>Stress, Physiological</term>
</keywords>
<keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN des plantes</term>
<term>ARN messager</term>
<term>Populus</term>
<term>Stress physiologique</term>
<term>microARN</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term>
</keywords>
<keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Séquençage nucléotidique à haut débit</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term>
<term>Gene Expression Regulation, Plant</term>
<term>Genes, Plant</term>
<term>Molecular Sequence Annotation</term>
<term>Molecular Sequence Data</term>
<term>Real-Time Polymerase Chain Reaction</term>
<term>Sequence Homology, Nucleic Acid</term>
<term>Transcriptome</term>
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<keywords scheme="MESH" xml:lang="fr"><term>Annotation de séquence moléculaire</term>
<term>Données de séquences moléculaires</term>
<term>Gènes de plante</term>
<term>Réaction de polymérisation en chaine en temps réel</term>
<term>Régulation de l'expression des gènes végétaux</term>
<term>Similitude de séquences d'acides nucléiques</term>
<term>Séquence nucléotidique</term>
<term>Transcriptome</term>
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<front><div type="abstract" xml:lang="en">miRNAs are endogenous non-coding small RNAs with important regulatory roles in stress responses. Nitrogen (N) is an indispensable macronutrient required for plant growth and development. Previous studies have identified a variety of known and novel miRNAs responsive to low N stress in plants, including Populus. However, miRNAs involved in the cleavage of target genes and the corresponding regulatory networks in response to N stress in Populus remain largely unknown. Consequently, degradome sequencing was employed for global detection and validation of N-responsive miRNAs and their targets. A total of 60 unique miRNAs (39 conserved, 13 non-conserved, and eight novel) were experimentally identified to target 64 mRNA transcripts and 21 precursors. Among them, we further verified the cleavage of 11 N-responsive miRNAs identified previously and provided empirical evidence for the cleavage mode of these miRNAs on their target mRNAs. Furthermore, five miRNA stars (miRNA*s) were shown to have cleavage function. The specificity and diversity of cleavage sites on the targets and miRNA precursors in P. tomentosa were further detected. Identification and annotation of miRNA-mediated cleavage of target genes in Populus can increase our understanding of miRNA-mediated molecular mechanisms of woody plants adapted to low N environments. </div>
</front>
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<DateCompleted><Year>2016</Year>
<Month>04</Month>
<Day>05</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
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<Issue>6</Issue>
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<Month>Jun</Month>
<Day>18</Day>
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<Title>International journal of molecular sciences</Title>
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<ArticleTitle>Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing.</ArticleTitle>
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<Abstract><AbstractText>miRNAs are endogenous non-coding small RNAs with important regulatory roles in stress responses. Nitrogen (N) is an indispensable macronutrient required for plant growth and development. Previous studies have identified a variety of known and novel miRNAs responsive to low N stress in plants, including Populus. However, miRNAs involved in the cleavage of target genes and the corresponding regulatory networks in response to N stress in Populus remain largely unknown. Consequently, degradome sequencing was employed for global detection and validation of N-responsive miRNAs and their targets. A total of 60 unique miRNAs (39 conserved, 13 non-conserved, and eight novel) were experimentally identified to target 64 mRNA transcripts and 21 precursors. Among them, we further verified the cleavage of 11 N-responsive miRNAs identified previously and provided empirical evidence for the cleavage mode of these miRNAs on their target mRNAs. Furthermore, five miRNA stars (miRNA*s) were shown to have cleavage function. The specificity and diversity of cleavage sites on the targets and miRNA precursors in P. tomentosa were further detected. Identification and annotation of miRNA-mediated cleavage of target genes in Populus can increase our understanding of miRNA-mediated molecular mechanisms of woody plants adapted to low N environments. </AbstractText>
</Abstract>
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<ForeName>Min</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China. chenmin19920219@126.com.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 100083, China. chenmin19920219@126.com.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China. chenmin19920219@126.com.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Bao</LastName>
<ForeName>Hai</ForeName>
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<AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China. holymagicmother@163.com.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 100083, China. holymagicmother@163.com.</Affiliation>
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<AffiliationInfo><Affiliation>College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China. holymagicmother@163.com.</Affiliation>
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</AffiliationInfo>
<AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 100083, China. qiumingwu930@126.com.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China. qiumingwu930@126.com.</Affiliation>
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<AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China. ywwang@bjfu.edu.cn.</Affiliation>
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Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing.

Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing.

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