植物microRNA靶基因的预测与验证技术研究进展
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摘要
MicroRNA(miRNA)是真核生物中具有重要调控功能的一类小分子RNA。植物miRNA通过碱基互补配对方式引导RNA沉默复合体识别靶基因并介导靶基因mRNA被剪切或蛋白质翻译被抑制,所以对植物miRNA靶基因的分析和验证是研究miRNA功能必不可少的一部分。植物miRNA靶基因可通过生物信息学方法预测,主要根据miRNA与mRNA的互补程度进行,然而理论上预测的靶基因尚有待于进一步的试验验证。简要介绍了植物miRNA产生过程的最新研究进展以及靶基因的预测方法,重点综述了植物miRNA靶基因的验证方法,包括RLM-5'RACE、降解组测序、瞬时共表达和转基因系统,为更深入地研究植物miRNA介导的调控机制提供参考。
MicroRNA( miRNA) is a class of small RNAs with important regulatory functions in eukaryotes. In plants,miRNA recognizes its target mRNA based on sequence complementarity,and regulates it by the mechanism of cleavage or translational repression,so analysis and validation of miRNA targets are essential for study of miRNA functions. miRNA targets can be predicted by bioinformatics based on sequence complementarity between miRNA and candidate target mRNA,while further experimental validation is required to confirm the authenticity of the predicted targets. The present review briefly summarized the recent progress on miRNA biogenesis in plant,and the pipelines used for miRNA targets prediction. The techniques used for miRNA target validation,such as RLM-5' RACE,degradome sequencing,transient co-expression and transgenic system,were systematically summarized in this review,which is useful for elucidating the regulation mechanism mediated by plant miRNA.
MicroRNA( miRNA) is a class of small RNAs with important regulatory functions in eukaryotes. In plants,miRNA recognizes its target mRNA based on sequence complementarity,and regulates it by the mechanism of cleavage or translational repression,so analysis and validation of miRNA targets are essential for study of miRNA functions. miRNA targets can be predicted by bioinformatics based on sequence complementarity between miRNA and candidate target mRNA,while further experimental validation is required to confirm the authenticity of the predicted targets. The present review briefly summarized the recent progress on miRNA biogenesis in plant,and the pipelines used for miRNA targets prediction. The techniques used for miRNA target validation,such as RLM-5' RACE,degradome sequencing,transient co-expression and transgenic system,were systematically summarized in this review,which is useful for elucidating the regulation mechanism mediated by plant miRNA.
引文
[1]柴连琴,王乐,苗迎春.miRNA对完全变态昆虫发育的调控作用研究进展[J].河南农业科学,2015,44(8):13-16,37.
[2]Sunkar R,Li Y F,Jagadeeswaran G.Functions of microRNAs in plant stress responses[J].Trends in Plant Science,2012,17(4):196-203.
[3]Law J A,Jacobsen S E.Establishing,maintaining and modifying DNA methylation patterns in plants and animals[J].Nature Reviews Genetics,2010,11(3):204-220.
[4]Yu B,Bi L,Zheng B,et al.The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis[J].Proceedings of the National Academy of Sciences USA,2008,105(29):10073-10078.
[5]Xie M,Zhang S,Yu B.MicroRNA biogenesis,degradation and activity in plants[J].Cellular and Molecular Life Science,2015,72(1):87-99.
[6]Reinhart B J,Weinstein E G,Rhoades M W,et al.MicroRNAs in plants[J].Genes&Development,2002,16(13):1616-1626.
[7]Kurihara Y,Watanabe Y.Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions[J].Proceedings of the National Academy of Sciences USA,2004,101(34):12753-12758.
[8]Fukudome A,Fukuhara T.Plant dicer-likeproteins:Double-stranded RNA cleaving enzymes for small RNA biogenesis[J].Journal of Plant Research,2017,130(1):33-44.
[9]Yu B,Yang Z,Li J,et al.Methylation as a crucial step in plant microRNA biogenesis[J].Science,2005,307(5711):932-935.
[10]Park M Y,Wu G,Gonzalez-Sulser A,et al.Nuclear processing and export of microRNAs in Arabidopsis[J].Proceedings of the National Academy of Sciences USA,2005,102(10):3691-3696.
[11]Chen X.A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development[J].Science,2004,303(5666):2022-2025.
[12]Schwab R,Palatnik J F,Riester M,et al.Specific effects of microRNAs on the plant transcriptome[J].Developmental Cell,2005,8(4):517-527.
[13]Bartel D P.MicroRNAs:Genomics,biogenesis,mechanism and function[J].Cell,2004,116(2):281-297.
[14]Gao F,Nan F,Feng J,et al.Identification and characterization of microRNAs in Eucheuma denticulatum by high-throughput sequencing and bioinformatics analysis[J].RNA Biology,2015,13(3):343-352.
[15]Okamura K,Phillips M D,Tyler D M,et al.The regulatory activity of microRNA*species has substantial influence on microRNA and 3'UTR evolution[J].Nature Structural&Molecular Biology,2008,15(4):354-363.
[16]Devers E,Branscheid A,May P,et al.Stars and symbiosis:MicroRNA and microRNA*-mediated transcript cleavage involved in arbuscular mycorrhizal symbiosis[J].Plant Physiol,2011,156(4):1990-2010.
[17]Zhang J,Huang M,Liang J,et al.Genome-wide mining for microRNAs and their targets in Betula luminifera using high-throughput sequencing and degradome analyses[J].Tree Genet Genomes,2016,12(5):99.
[18]Srivastava S,Zheng Y,Kudapa H,et al.High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea[J].Plant Science,2015,235:46-57.
[19]Kang M,Zhao Q,Zhu D,et al.Characterization of microRNAs expression during maize seed development[J].BMC Genomics,2012,13(1):360.
[20]Kim Y J,Zheng B,Yu Y,et al.The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana[J].The EMBO Journal,2011,30(5):814-822.
[21]Wang L,Song X,Gu L,et al.NOT2 proteins promote polymeraseⅡ-dependent transcription and interact with multiple microRNA biogenesis factors in Arabidopsis[J].The Plant Cell,2013,25(2):715-727.
[22]Fang X,Cui Y,Li Y,et al.Transcription and processing of primary microRNAs are coupled by Elongator complex in Arabidopsis[J].Nature Plants,2015,1(16):15075.
[23]Laubinger S,Sachsenberg T,Zeller G,et al.Dual roles of the nuclear cap-binding complex and SERRATE in premRNA splicing and microRNA processing in Arabidopsis thaliana[J].Proceedings of the National Academy of Sciences USA,2008,105(25):8795-8800.
[24]Hajheidari M,Farrona S,Huettel B,et al.CDKF;1 and CDKD protein kinases regulate phosphorylation of serine residues in the C-terminal domain of Arabidopsis RNA polymeraseⅡ[J].The Plant Cell,2012,24(4):1626-1642.
[25]Manavella P A,Hagmann J,Ott F,et al.Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1[J].Cell,2012,151(4):859-870.
[26]Su C,Li Z,Cheng J,et al.The protein phosphatase 4 and SMEK1 complex dephosphorylates HYL1 to promote miRNA biogenesis by antagonizing the MAPK cascade in Arabidopsis[J].Developmental Cell,2017,41(5):527-539.
[27]Karlsson P,Christie M D,Seymour D K,et al.KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1[J].Proceedings of the National Academy of Sciences USA,2015,112(45):14096-14101.
[28]Raghuram B,Sheikh A H,Rustagi Y,et al.MicroRNA biogenesis factor DRB1 is a phosphorylation target of mitogen activated protein kinase MPK3 in both rice and Arabidopsis[J].The FEBS Journal,2015,282(3):521-536.
[29]Yan J,Wang P,Wang B,et al.The SnRK2 kinases modulate miRNA accumulation in Arabidopsis[J].PLo S Genetics,2017,13(4):e1006753.
[30]Cho S K,Ben Chaabane S,Shah P,et al.COP1 E3 ligase protects HYL1 to retain microRNA biogenesis[J].Nature Communications,2014,5:5867.
[31]Yu Y,Jia T,Chen X.The‘how’and‘where’of plant microRNAs[J].New Phytologist,2017,216(4):1002-1017.
[32]Ben Chaabane S,Liu R,Chinnusamy V,et al.STA1,an Arabidopsis pre-mRNA processing factor 6 homolog,is a new player involved in miRNA biogenesis[J].Nucleic Acids Research,2013,4141(3):1984-1997.
[33]Zhan X,Wang B,Li H,et al.Arabidopsis proline-rich protein important for development and abiotic stress tolerance is involved in microRNA biogenesis[J].Proceedings of the National Academy of Sciences USA,2012,109(44):18198-18203.
[34]K9ster T,Meyer K,Weinholdt C,et al.Regulation of primiRNA processing by the hnRNP-like protein At GRP7in Arabidopsis[J].Nucleic Acids Research,2014,42(15):9925-9936.
[35]Ren G,Xie M,Dou Y,et al.Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis[J].Proceedings of the National Academy of Sciences USA,2012,109(31):12817-12821.
[36]Qiao Y,Shi J,Zhai Y,et al.Phytophthora effector targets a novel component of small RNA pathway in plants to promote infection[J].Proceedings of the National Academy of Sciences USA,2015,112(18):5850-5855.
[37]Wu H J,Wang Z M,Wang M,et al.Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants[J].Plant Physiology,2013,161(4):1875-1884.
[38]郭红媛,贾举庆,段娜,等.燕麦microRNAs及其靶基因的生物信息学预测[J].山西农业科学,2014,42(5):428-431.
[39]Jha A,Shankar R.Employing machine learning for reliable miRNA target identification in plants[J].BMC Genomics,2011,12:636.
[40]Wu H J,Ma Y K,Chen T,et al.PsRobot:A web-based plant small RNA meta-analysis toolbox[J].Nucleic Acids Research,2012,40:22-28.
[41]Zhang Y J.miRU:An automated plant miRNA target prediction server[J].Nucleic Acids Research,2005,33:701-704.
[42]Dai X B,Zhao P X.psRNATarget:A plant small RNA target analysis server[J].Nucleic Acids Research,2011,39:155-159.
[43]Kiebasa S M,Blüthgen N,Fhling M,et al.Targetfinder.org:A resource for systematic discovery of transcription factor target genes[J].Nucleic Acids Research,2010,38:233-238.
[44]Xie F L,Zhang B H.Target-align:A tool for plant microRNA target identification[J].Bioinformatics,2010,26(23):3002-3003.
[45]Sun X,Dong B Q,Yin L J,et al.PMTED:A plant microRNA target expression database[J].BMC Bioinformatics,2010,14:1-7.
[46]Singh N K.MiRNAs target databases:Developmental methods and target identification techniques with functional annotations[J].Cellular and Molecular Life Sciences,2017,74(12):2239-2261.
[47]Li Y F,Zheng Y,Addo-Quaye C,et al.Transcriptomewide identification of microRNA targets in rice[J].Plant Journal,2010,62(5):742-759.
[48]Llave C,Xie Z,Kasschau K D,et al.Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA[J].Science,2002,297(5589):2053-2056.
[49]Addo-Quaye C,Eshoo T W,Bartel D P.Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome[J].Current Biology,2008,8(10):758-762.
[50]German M A,Luo S,Schroth G,et al.Construction of parallel analysis of RNA ends(PARE)libraries for the study of cleaved miRNA targets and the RNA degradome[J].Nature Protocols,2008,4(8):356-362.
[51]Liu Q K,Micheal J A.Quantitating plant microRNA-mediated target repression using a dual-luciferase translent expression system[J].Methods in Molecular Biology,2015,1284:287-303.
[52]Sunkar R,Kapoor A,Zhu J K.Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance[J].The Plant Cell,2006,18(8):2051-2065.
[53]Ding J,Zhou S,Guan J.Finding microRNA targets in plants:Current status and perspectives[J].Genomics Proteomics Bioinformatics,2012,10(5):264-275.
[54]Zhai J,Arikit S,Simon S A,et al.Rapid construction of parallel analysis of RNA end(PARE)libraries for Illumina sequencing[J].Methods,2014,67(1):84-90.
[55]Addo-Quaye C,Miller W,Axtell M J.Cleave Land:A pipeline for using degradome data to find cleaved small RNA targets[J].Bioinformatics,2009,25(1):130-131.
[56]Zheng Y,Li Y F,Sunkar R,et al.Seq Tar:An effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants[J].Nucleic Acids Research,2012,40(4):1-18.
[57]Liu H,Qin C,Chen Z,et al.Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing[J].BMC Genomics,2014,15(25):1-18.
[58]Zhang Y,Zhu X,Chen X,et al.Identification and characterization of cold-responsive microRNAs in tea plant(Camellia sinensis)and their targets using high-throughput sequencing and degradome analysis[J].BMC Plant Biology,2014,14(271):1-18.
[59]Sun Z,He Y,Li J,et al.Genome-wide characterization of rice black streaked dwarf virus-responsive microRNAs in rice leaves and roots by small RNA and degradome sequencing[J].Plant&Cell Physiology,2015,56(4):688-699.
[60]Wang Y,Li L,Tang S,et al.Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet[J].BMC Genetics,2016,17(57):1-16.
[61]Brodersen P,Sakvarelidze-Achard L,Bruun-Rasmussen M,et al.Widespread translational inhibition by plant miRNAs and siRNAs[J].Science,2008,320(5880):1185-1190.
[62]Grentzmann G,Ingram J A,Kelly P J,et al.A dual-luciferase reporter system for studying recoding signals[J].RNA,1998,4(4):479-486.
[63]贾小云,刘慧,沈洁,等.MicroRNA828负调控缺磷胁迫诱导的番茄花青素生物合成[J].中国农业科学,2015,48(15):2911-2924.
[64]Chuck G S,Tobias C,Sun L,et al.Overexpression of the maize Corngrass1 microRNA prevents flowering,improves digestibility,and increases starch content of switchgrass[J].Proceedings of the National Academy of Sciences USA,2011,108(42):17550-17555.
[2]Sunkar R,Li Y F,Jagadeeswaran G.Functions of microRNAs in plant stress responses[J].Trends in Plant Science,2012,17(4):196-203.
[3]Law J A,Jacobsen S E.Establishing,maintaining and modifying DNA methylation patterns in plants and animals[J].Nature Reviews Genetics,2010,11(3):204-220.
[4]Yu B,Bi L,Zheng B,et al.The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis[J].Proceedings of the National Academy of Sciences USA,2008,105(29):10073-10078.
[5]Xie M,Zhang S,Yu B.MicroRNA biogenesis,degradation and activity in plants[J].Cellular and Molecular Life Science,2015,72(1):87-99.
[6]Reinhart B J,Weinstein E G,Rhoades M W,et al.MicroRNAs in plants[J].Genes&Development,2002,16(13):1616-1626.
[7]Kurihara Y,Watanabe Y.Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions[J].Proceedings of the National Academy of Sciences USA,2004,101(34):12753-12758.
[8]Fukudome A,Fukuhara T.Plant dicer-likeproteins:Double-stranded RNA cleaving enzymes for small RNA biogenesis[J].Journal of Plant Research,2017,130(1):33-44.
[9]Yu B,Yang Z,Li J,et al.Methylation as a crucial step in plant microRNA biogenesis[J].Science,2005,307(5711):932-935.
[10]Park M Y,Wu G,Gonzalez-Sulser A,et al.Nuclear processing and export of microRNAs in Arabidopsis[J].Proceedings of the National Academy of Sciences USA,2005,102(10):3691-3696.
[11]Chen X.A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development[J].Science,2004,303(5666):2022-2025.
[12]Schwab R,Palatnik J F,Riester M,et al.Specific effects of microRNAs on the plant transcriptome[J].Developmental Cell,2005,8(4):517-527.
[13]Bartel D P.MicroRNAs:Genomics,biogenesis,mechanism and function[J].Cell,2004,116(2):281-297.
[14]Gao F,Nan F,Feng J,et al.Identification and characterization of microRNAs in Eucheuma denticulatum by high-throughput sequencing and bioinformatics analysis[J].RNA Biology,2015,13(3):343-352.
[15]Okamura K,Phillips M D,Tyler D M,et al.The regulatory activity of microRNA*species has substantial influence on microRNA and 3'UTR evolution[J].Nature Structural&Molecular Biology,2008,15(4):354-363.
[16]Devers E,Branscheid A,May P,et al.Stars and symbiosis:MicroRNA and microRNA*-mediated transcript cleavage involved in arbuscular mycorrhizal symbiosis[J].Plant Physiol,2011,156(4):1990-2010.
[17]Zhang J,Huang M,Liang J,et al.Genome-wide mining for microRNAs and their targets in Betula luminifera using high-throughput sequencing and degradome analyses[J].Tree Genet Genomes,2016,12(5):99.
[18]Srivastava S,Zheng Y,Kudapa H,et al.High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea[J].Plant Science,2015,235:46-57.
[19]Kang M,Zhao Q,Zhu D,et al.Characterization of microRNAs expression during maize seed development[J].BMC Genomics,2012,13(1):360.
[20]Kim Y J,Zheng B,Yu Y,et al.The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana[J].The EMBO Journal,2011,30(5):814-822.
[21]Wang L,Song X,Gu L,et al.NOT2 proteins promote polymeraseⅡ-dependent transcription and interact with multiple microRNA biogenesis factors in Arabidopsis[J].The Plant Cell,2013,25(2):715-727.
[22]Fang X,Cui Y,Li Y,et al.Transcription and processing of primary microRNAs are coupled by Elongator complex in Arabidopsis[J].Nature Plants,2015,1(16):15075.
[23]Laubinger S,Sachsenberg T,Zeller G,et al.Dual roles of the nuclear cap-binding complex and SERRATE in premRNA splicing and microRNA processing in Arabidopsis thaliana[J].Proceedings of the National Academy of Sciences USA,2008,105(25):8795-8800.
[24]Hajheidari M,Farrona S,Huettel B,et al.CDKF;1 and CDKD protein kinases regulate phosphorylation of serine residues in the C-terminal domain of Arabidopsis RNA polymeraseⅡ[J].The Plant Cell,2012,24(4):1626-1642.
[25]Manavella P A,Hagmann J,Ott F,et al.Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1[J].Cell,2012,151(4):859-870.
[26]Su C,Li Z,Cheng J,et al.The protein phosphatase 4 and SMEK1 complex dephosphorylates HYL1 to promote miRNA biogenesis by antagonizing the MAPK cascade in Arabidopsis[J].Developmental Cell,2017,41(5):527-539.
[27]Karlsson P,Christie M D,Seymour D K,et al.KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1[J].Proceedings of the National Academy of Sciences USA,2015,112(45):14096-14101.
[28]Raghuram B,Sheikh A H,Rustagi Y,et al.MicroRNA biogenesis factor DRB1 is a phosphorylation target of mitogen activated protein kinase MPK3 in both rice and Arabidopsis[J].The FEBS Journal,2015,282(3):521-536.
[29]Yan J,Wang P,Wang B,et al.The SnRK2 kinases modulate miRNA accumulation in Arabidopsis[J].PLo S Genetics,2017,13(4):e1006753.
[30]Cho S K,Ben Chaabane S,Shah P,et al.COP1 E3 ligase protects HYL1 to retain microRNA biogenesis[J].Nature Communications,2014,5:5867.
[31]Yu Y,Jia T,Chen X.The‘how’and‘where’of plant microRNAs[J].New Phytologist,2017,216(4):1002-1017.
[32]Ben Chaabane S,Liu R,Chinnusamy V,et al.STA1,an Arabidopsis pre-mRNA processing factor 6 homolog,is a new player involved in miRNA biogenesis[J].Nucleic Acids Research,2013,4141(3):1984-1997.
[33]Zhan X,Wang B,Li H,et al.Arabidopsis proline-rich protein important for development and abiotic stress tolerance is involved in microRNA biogenesis[J].Proceedings of the National Academy of Sciences USA,2012,109(44):18198-18203.
[34]K9ster T,Meyer K,Weinholdt C,et al.Regulation of primiRNA processing by the hnRNP-like protein At GRP7in Arabidopsis[J].Nucleic Acids Research,2014,42(15):9925-9936.
[35]Ren G,Xie M,Dou Y,et al.Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis[J].Proceedings of the National Academy of Sciences USA,2012,109(31):12817-12821.
[36]Qiao Y,Shi J,Zhai Y,et al.Phytophthora effector targets a novel component of small RNA pathway in plants to promote infection[J].Proceedings of the National Academy of Sciences USA,2015,112(18):5850-5855.
[37]Wu H J,Wang Z M,Wang M,et al.Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants[J].Plant Physiology,2013,161(4):1875-1884.
[38]郭红媛,贾举庆,段娜,等.燕麦microRNAs及其靶基因的生物信息学预测[J].山西农业科学,2014,42(5):428-431.
[39]Jha A,Shankar R.Employing machine learning for reliable miRNA target identification in plants[J].BMC Genomics,2011,12:636.
[40]Wu H J,Ma Y K,Chen T,et al.PsRobot:A web-based plant small RNA meta-analysis toolbox[J].Nucleic Acids Research,2012,40:22-28.
[41]Zhang Y J.miRU:An automated plant miRNA target prediction server[J].Nucleic Acids Research,2005,33:701-704.
[42]Dai X B,Zhao P X.psRNATarget:A plant small RNA target analysis server[J].Nucleic Acids Research,2011,39:155-159.
[43]Kiebasa S M,Blüthgen N,Fhling M,et al.Targetfinder.org:A resource for systematic discovery of transcription factor target genes[J].Nucleic Acids Research,2010,38:233-238.
[44]Xie F L,Zhang B H.Target-align:A tool for plant microRNA target identification[J].Bioinformatics,2010,26(23):3002-3003.
[45]Sun X,Dong B Q,Yin L J,et al.PMTED:A plant microRNA target expression database[J].BMC Bioinformatics,2010,14:1-7.
[46]Singh N K.MiRNAs target databases:Developmental methods and target identification techniques with functional annotations[J].Cellular and Molecular Life Sciences,2017,74(12):2239-2261.
[47]Li Y F,Zheng Y,Addo-Quaye C,et al.Transcriptomewide identification of microRNA targets in rice[J].Plant Journal,2010,62(5):742-759.
[48]Llave C,Xie Z,Kasschau K D,et al.Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA[J].Science,2002,297(5589):2053-2056.
[49]Addo-Quaye C,Eshoo T W,Bartel D P.Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome[J].Current Biology,2008,8(10):758-762.
[50]German M A,Luo S,Schroth G,et al.Construction of parallel analysis of RNA ends(PARE)libraries for the study of cleaved miRNA targets and the RNA degradome[J].Nature Protocols,2008,4(8):356-362.
[51]Liu Q K,Micheal J A.Quantitating plant microRNA-mediated target repression using a dual-luciferase translent expression system[J].Methods in Molecular Biology,2015,1284:287-303.
[52]Sunkar R,Kapoor A,Zhu J K.Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance[J].The Plant Cell,2006,18(8):2051-2065.
[53]Ding J,Zhou S,Guan J.Finding microRNA targets in plants:Current status and perspectives[J].Genomics Proteomics Bioinformatics,2012,10(5):264-275.
[54]Zhai J,Arikit S,Simon S A,et al.Rapid construction of parallel analysis of RNA end(PARE)libraries for Illumina sequencing[J].Methods,2014,67(1):84-90.
[55]Addo-Quaye C,Miller W,Axtell M J.Cleave Land:A pipeline for using degradome data to find cleaved small RNA targets[J].Bioinformatics,2009,25(1):130-131.
[56]Zheng Y,Li Y F,Sunkar R,et al.Seq Tar:An effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants[J].Nucleic Acids Research,2012,40(4):1-18.
[57]Liu H,Qin C,Chen Z,et al.Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing[J].BMC Genomics,2014,15(25):1-18.
[58]Zhang Y,Zhu X,Chen X,et al.Identification and characterization of cold-responsive microRNAs in tea plant(Camellia sinensis)and their targets using high-throughput sequencing and degradome analysis[J].BMC Plant Biology,2014,14(271):1-18.
[59]Sun Z,He Y,Li J,et al.Genome-wide characterization of rice black streaked dwarf virus-responsive microRNAs in rice leaves and roots by small RNA and degradome sequencing[J].Plant&Cell Physiology,2015,56(4):688-699.
[60]Wang Y,Li L,Tang S,et al.Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet[J].BMC Genetics,2016,17(57):1-16.
[61]Brodersen P,Sakvarelidze-Achard L,Bruun-Rasmussen M,et al.Widespread translational inhibition by plant miRNAs and siRNAs[J].Science,2008,320(5880):1185-1190.
[62]Grentzmann G,Ingram J A,Kelly P J,et al.A dual-luciferase reporter system for studying recoding signals[J].RNA,1998,4(4):479-486.
[63]贾小云,刘慧,沈洁,等.MicroRNA828负调控缺磷胁迫诱导的番茄花青素生物合成[J].中国农业科学,2015,48(15):2911-2924.
[64]Chuck G S,Tobias C,Sun L,et al.Overexpression of the maize Corngrass1 microRNA prevents flowering,improves digestibility,and increases starch content of switchgrass[J].Proceedings of the National Academy of Sciences USA,2011,108(42):17550-17555.