Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing
In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants su...
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creator | Liu, Hongjun Qin, Cheng Chen, Zhe Zuo, Tao Yang, Xuerong Zhou, Huangkai Xu, Meng Cao, Shiliang Shen, Yaou Lin, Haijian He, Xiujing Zhang, Yinchao Li, Lujiang Ding, Haiping Lübberstedt, Thomas Zhang, Zhiming Pan, Guangtang |
description | In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana. In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages.
We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed.
This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development. |
doi_str_mv | 10.1186/1471-2164-15-25 |
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We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed.
This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/1471-2164-15-25</identifier><identifier>PMID: 24422852</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Analysis ; Arabidopsis - genetics ; Arabidopsis - metabolism ; Arabidopsis thaliana ; Computational Biology ; Databases, Genetic ; Droughts ; Epigenetic inheritance ; Gene Expression Regulation, Plant - drug effects ; Genes ; Genes, Plant ; Genetic aspects ; Genomes ; Genomics ; High-Throughput Nucleotide Sequencing ; MicroRNAs - genetics ; MicroRNAs - metabolism ; Nitrates - chemistry ; Nitrates - pharmacology ; Oryza - genetics ; Oryza - metabolism ; Oryza sativa ; Physiological aspects ; Plant biology ; RNA Cleavage ; RNA, Plant - genetics ; RNA, Plant - metabolism ; RNA, Small Interfering - genetics ; RNA, Small Interfering - metabolism ; Salts - chemistry ; Salts - pharmacology ; Software ; Studies ; Transcriptome ; Transposons ; Zea mays ; Zea mays - genetics ; Zea mays - growth & development ; Zea mays - metabolism</subject><ispartof>BMC genomics, 2014-01, Vol.15 (1), p.25-25, Article 25</ispartof><rights>COPYRIGHT 2014 BioMed Central Ltd.</rights><rights>2014 liu et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</rights><rights>Copyright © 2014 liu et al.; licensee BioMed Central Ltd. 2014 liu et al.; licensee BioMed Central Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b5295-201f417f7d2d6dc79562a8b084535c935a43dea3ce4cde204b2fc40ddbc4e26b3</citedby><cites>FETCH-LOGICAL-b5295-201f417f7d2d6dc79562a8b084535c935a43dea3ce4cde204b2fc40ddbc4e26b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901417/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901417/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24422852$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Liu, Hongjun</creatorcontrib><creatorcontrib>Qin, Cheng</creatorcontrib><creatorcontrib>Chen, Zhe</creatorcontrib><creatorcontrib>Zuo, Tao</creatorcontrib><creatorcontrib>Yang, Xuerong</creatorcontrib><creatorcontrib>Zhou, Huangkai</creatorcontrib><creatorcontrib>Xu, Meng</creatorcontrib><creatorcontrib>Cao, Shiliang</creatorcontrib><creatorcontrib>Shen, Yaou</creatorcontrib><creatorcontrib>Lin, Haijian</creatorcontrib><creatorcontrib>He, Xiujing</creatorcontrib><creatorcontrib>Zhang, Yinchao</creatorcontrib><creatorcontrib>Li, Lujiang</creatorcontrib><creatorcontrib>Ding, Haiping</creatorcontrib><creatorcontrib>Lübberstedt, Thomas</creatorcontrib><creatorcontrib>Zhang, Zhiming</creatorcontrib><creatorcontrib>Pan, Guangtang</creatorcontrib><title>Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana. In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages.
We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed.
This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development.</description><subject>Analysis</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis - metabolism</subject><subject>Arabidopsis thaliana</subject><subject>Computational Biology</subject><subject>Databases, Genetic</subject><subject>Droughts</subject><subject>Epigenetic inheritance</subject><subject>Gene Expression Regulation, Plant - drug effects</subject><subject>Genes</subject><subject>Genes, Plant</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - metabolism</subject><subject>Nitrates - chemistry</subject><subject>Nitrates - pharmacology</subject><subject>Oryza - genetics</subject><subject>Oryza - metabolism</subject><subject>Oryza sativa</subject><subject>Physiological aspects</subject><subject>Plant biology</subject><subject>RNA Cleavage</subject><subject>RNA, Plant - genetics</subject><subject>RNA, Plant - metabolism</subject><subject>RNA, Small Interfering - genetics</subject><subject>RNA, Small Interfering - metabolism</subject><subject>Salts - chemistry</subject><subject>Salts - pharmacology</subject><subject>Software</subject><subject>Studies</subject><subject>Transcriptome</subject><subject>Transposons</subject><subject>Zea mays</subject><subject>Zea mays - genetics</subject><subject>Zea mays - growth & development</subject><subject>Zea mays - metabolism</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp1ks1vFCEYhydGY2v17M2QeNHDtMDAfFxM1kbbTRpNqp4JA-9MaQZYYaZa_3qZbrvZMTUcIPC8D_CDLHtN8DEhdXlCWEVySkqWE55T_iQ73M083RsfZC9ivMaYVDXlz7MDyhilNaeH2a-1Bjeazig5Gu-Q75A1l19WEUmn0XgFJqBRhh5G1IODiIxDGm5g8BvjemSl-QMIZIiovUXK29Y40ChaOQwoae4sGvogtbeAIvycwKlU-TJ71skhwqv7_ij78fnT99Pz_OLr2fp0dZG3nDbpSph0jFRdpakutaoaXlJZt7hmvOCqKbhkhQZZKGBKA8WspZ1iWOtWMaBlWxxlH7bezdRa0CpdNshBbIKxMtwKL41YrjhzJXp_I4oGk7RzEnzcClrj_yNYrqQQxBy8mIMXhAvKk-Td_SmCTwnEUVgTFQyDdOCnmCiMq5qRmiX07T_otZ-CSxkla0M4wRXbo3o5gDCu82lvNUvFihdNhUlTzWc_foRKTYM1yjvoTJpfFLxfFCRmhN9jL6cYxfrb5ZI92bIq-BgDdLtMCBbz53wkhTf7b7HjH35j8RfGp96H</recordid><startdate>20140114</startdate><enddate>20140114</enddate><creator>Liu, 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of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing</title><author>Liu, Hongjun ; Qin, Cheng ; Chen, Zhe ; Zuo, Tao ; Yang, Xuerong ; Zhou, Huangkai ; Xu, Meng ; Cao, Shiliang ; Shen, Yaou ; Lin, Haijian ; He, Xiujing ; Zhang, Yinchao ; Li, Lujiang ; Ding, Haiping ; Lübberstedt, Thomas ; Zhang, Zhiming ; Pan, Guangtang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b5295-201f417f7d2d6dc79562a8b084535c935a43dea3ce4cde204b2fc40ddbc4e26b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Analysis</topic><topic>Arabidopsis - genetics</topic><topic>Arabidopsis - metabolism</topic><topic>Arabidopsis thaliana</topic><topic>Computational Biology</topic><topic>Databases, Genetic</topic><topic>Droughts</topic><topic>Epigenetic inheritance</topic><topic>Gene Expression Regulation, Plant - drug effects</topic><topic>Genes</topic><topic>Genes, Plant</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Genomics</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>MicroRNAs - genetics</topic><topic>MicroRNAs - metabolism</topic><topic>Nitrates - chemistry</topic><topic>Nitrates - pharmacology</topic><topic>Oryza - genetics</topic><topic>Oryza - metabolism</topic><topic>Oryza sativa</topic><topic>Physiological aspects</topic><topic>Plant biology</topic><topic>RNA Cleavage</topic><topic>RNA, Plant - genetics</topic><topic>RNA, Plant - metabolism</topic><topic>RNA, Small Interfering - genetics</topic><topic>RNA, Small Interfering - metabolism</topic><topic>Salts - chemistry</topic><topic>Salts - pharmacology</topic><topic>Software</topic><topic>Studies</topic><topic>Transcriptome</topic><topic>Transposons</topic><topic>Zea mays</topic><topic>Zea mays - genetics</topic><topic>Zea mays - growth & development</topic><topic>Zea mays - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liu, Hongjun</creatorcontrib><creatorcontrib>Qin, Cheng</creatorcontrib><creatorcontrib>Chen, Zhe</creatorcontrib><creatorcontrib>Zuo, Tao</creatorcontrib><creatorcontrib>Yang, Xuerong</creatorcontrib><creatorcontrib>Zhou, Huangkai</creatorcontrib><creatorcontrib>Xu, Meng</creatorcontrib><creatorcontrib>Cao, Shiliang</creatorcontrib><creatorcontrib>Shen, Yaou</creatorcontrib><creatorcontrib>Lin, Haijian</creatorcontrib><creatorcontrib>He, Xiujing</creatorcontrib><creatorcontrib>Zhang, Yinchao</creatorcontrib><creatorcontrib>Li, Lujiang</creatorcontrib><creatorcontrib>Ding, Haiping</creatorcontrib><creatorcontrib>Lübberstedt, Thomas</creatorcontrib><creatorcontrib>Zhang, Zhiming</creatorcontrib><creatorcontrib>Pan, Guangtang</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE 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Xuerong</au><au>Zhou, Huangkai</au><au>Xu, Meng</au><au>Cao, Shiliang</au><au>Shen, Yaou</au><au>Lin, Haijian</au><au>He, Xiujing</au><au>Zhang, Yinchao</au><au>Li, Lujiang</au><au>Ding, Haiping</au><au>Lübberstedt, Thomas</au><au>Zhang, Zhiming</au><au>Pan, Guangtang</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2014-01-14</date><risdate>2014</risdate><volume>15</volume><issue>1</issue><spage>25</spage><epage>25</epage><pages>25-25</pages><artnum>25</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana. In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages.
We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed.
This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>24422852</pmid><doi>10.1186/1471-2164-15-25</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Analysis Arabidopsis - genetics Arabidopsis - metabolism Arabidopsis thaliana Computational Biology Databases, Genetic Droughts Epigenetic inheritance Gene Expression Regulation, Plant - drug effects Genes Genes, Plant Genetic aspects Genomes Genomics High-Throughput Nucleotide Sequencing MicroRNAs - genetics MicroRNAs - metabolism Nitrates - chemistry Nitrates - pharmacology Oryza - genetics Oryza - metabolism Oryza sativa Physiological aspects Plant biology RNA Cleavage RNA, Plant - genetics RNA, Plant - metabolism RNA, Small Interfering - genetics RNA, Small Interfering - metabolism Salts - chemistry Salts - pharmacology Software Studies Transcriptome Transposons Zea mays Zea mays - genetics Zea mays - growth & development Zea mays - metabolism |
title | Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing |
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