Plant microRNAs （miRNAs） regulate gene expression mainly by guiding cleavage of target mRNAs. In this study, a degradome library constructed from different soybean （Glycine max （L.） Merr.） tissues was deep-seque...Plant microRNAs （miRNAs） regulate gene expression mainly by guiding cleavage of target mRNAs. In this study, a degradome library constructed from different soybean （Glycine max （L.） Merr.） tissues was deep-sequenced. 428 potential targets of small interfering RNAs and 25 novel miRNA families were identified. A total of 211 potential miRNA targets, including 174 conserved miRNA targets and 37 soybean- specific miRNA targets, were identified. Among them, 121 targets were first discovered in soybean. The signature distribution of soybean primary miRNAs （pri-miRNAs） showed that most pri-miRNAs had the characteristic pattern of Dicer processing. The biogenesis of TAS3 small interfering RNAs （siRNAs） was conserved in soybean, and nine Auxin Response Factors were identified as TAS3 siRNA targets. Twenty- three miRNA targets produced secondary small interfering RNAs （siRNAs） in soybean. These targets were guided by five miRNAs： gma-miR393, gma-miR1508, gma-miR1510, gma-miR1514, and novel-11. Multiple targets of these secondary siRNAs were detected. These 23 miRNA targets may be the putative novel TAS genes in soybean. Global identification of miRNA targets and potential novel TAS genes will nnntrihnltp, tn r~__~nrP.h nn th~ f, mP.tinn_~ nf miRNA~ in ~nvh^n展开更多
Circular RNAs(circRNAs)are endogenous non-coding RNAs with covalently closed structures,which have important functions in plants.However,their biogenesis,degradation,and function upon treatment with gibberellins(GAs)a...Circular RNAs(circRNAs)are endogenous non-coding RNAs with covalently closed structures,which have important functions in plants.However,their biogenesis,degradation,and function upon treatment with gibberellins(GAs)and auxins(1-naphthaleneacetic acid,NAA)remain unknown.Here,we systematically identified and characterized the expression patterns,evolutionary conservation,genomic features,and internal structures of circRNAs using RNase R-treated libraries from moso bamboo(Phyllostachys edulis)seedlings.Moreover,we investigated the biogenesis of circRNAs dependent on both cis-and trans-regulation.We explored the function of circRNAs,including their roles in regulating microRNA(miRNA)-related genes and modulating the alternative splicing of their linear counterparts.Importantly,we developed a customized degradome sequencing approach to detect miRNA-mediated cleavage of circRNAs.Finally,we presented a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with GA and NAA.Collectively,our study provides insights into the biogenesis,function,and miRNA-mediated degradation of circRNAs in moso bamboo.展开更多
Carotenoids,as natural tetraterpenes,play a pivotal role in the yellow coloration of peaches and contribute to human dietary health.Despite a relatively clear understanding of the carotenoid biosynthesis pathway,the r...Carotenoids,as natural tetraterpenes,play a pivotal role in the yellow coloration of peaches and contribute to human dietary health.Despite a relatively clear understanding of the carotenoid biosynthesis pathway,the regulatory mechanism of miRNAs involved in carotenoid synthesis in yellow peaches remain poorly elucidated.This study investigated a total of 14 carotenoids and 40 xanthophyll lipids,including six differentially accumulated carotenoids:violaxanthin,neoxanthin,lutein,zeaxanthin,cryptoxanthin,and(E/Z)-phytoene.An integrated analysis of RNA-seq,miRNA-seq and degradome sequencing revealed that miRNAs could modulate structural genes such as PSY2,CRTISO,ZDS1,CHYB,VDE,ZEP,NCED1,NCED3 and the transcription factors NAC,ARF,WRKY,MYB,and bZIP,thereby participating in carotenoid biosynthesis and metabolism.The authenticity of miRNAs and target gene was corroborated through quantitative real-time PCR.Moreover,through weighted gene coexpression network analysis and a phylogenetic evolutionary study,coexpressed genes and MYB transcription factors potentially implicated in carotenoid synthesis were identified.The results of transient expression experiments indicated that mdm-miR858 inhibited the expression of PpMYB9 through targeted cleavage.Building upon these findings,a regulatory network governing miRNA-mediated carotenoid synthesis was proposed.In summary,this study comprehensively identified miRNAs engaged in carotenoid biosynthesis and their putative target genes,thus enhancing the understanding of carotenoid accumulation and regulatory mechanism in yellow peach peel and expanding the gene regulatory network of carotenoid synthesis.展开更多
MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in eukaryotes.Plant miRNAs modulate their targets mainly via messenger RNA(mRNA)cleavage.Small RNA(sRNA)targets have been extensively investi...MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in eukaryotes.Plant miRNAs modulate their targets mainly via messenger RNA(mRNA)cleavage.Small RNA(sRNA)targets have been extensively investigated in Arabidopsis using computational prediction,experimental validation,and degradome sequencing.However,small RNA targets are largely unknown in rice(Oryza sativa).Here,we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11(Oryza sativa L.ssp.indica).One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified.Of targets for the conserved miRNAs between Arabidopsis and rice,transcription factors comprise around 70%(58 in 82),indicating that these miRNAs act as masters of gene regulatory nodes in rice.In contrast,non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks.In addition,5 AUXIN RESPONSE FACTORs(ARFs)cleaved by the TAS3 derived ta-siRNAs were also detected.A total of 40 sRNA targets were further validated via RNA ligasemediated 5′rapid amplification of cDNA ends(RLM 5′-RACE).Our degradome results present a detailed sRNAtarget interaction atlas,which provides a guide for the study of the roles of sRNAs and their targets in rice.展开更多
supported by the Specialized Research Fund for the Doctoral Program of Higher Education of China （20134320120013）;the Natural Science Foundation of Hunan Province, China （14JJ3095）
The mesocotyl,a structure located between the basal part of the seminal root and the coleoptile node of seedlings,contributes to pushing the shoot tip through the soil surface,a function that is essential for the unif...The mesocotyl,a structure located between the basal part of the seminal root and the coleoptile node of seedlings,contributes to pushing the shoot tip through the soil surface,a function that is essential for the uniform emergence of direct-seeded rice.Its elongation is inhibited by light and induced in darkness.This investigation of an indica rice(P25)with vigorous mesocotyl elongation was aimed at identifying the"omics"basis of its lightinduced growth inhibition.A transcriptomic comparison between mesocotyl tissues that had developed in the dark and then been exposed to light identified many differentially expressed genes(DEGs)and differentially abundant micro RNAs(mi RNAs).Degradome sequencing analysis revealed 27 negative mi RNA-target pairs.A co-expression regulatory network was constructed based on the mi RNAs,their corresponding targets,and DEGs with a common Gene Ontology term.It suggested that auxin and light,probably antagonistically,affect mesocotyl elongation by regulating polyamine oxidase activity.展开更多
Plant species produce different types of allelopathic chemicals in nature;however,little is known about the differential regulation of plant allelopathy.Because allelopathy caused by p-hydroxybenzoic acid(pHBA)is one ...Plant species produce different types of allelopathic chemicals in nature;however,little is known about the differential regulation of plant allelopathy.Because allelopathy caused by p-hydroxybenzoic acid(pHBA)is one of the main obstacles to continuous cropping of Populus×euramericana ‘Neva’,we examined gene expression dynamics in Neva leaves induced by pHBA.The expression of genes related to photosynthesis and respiration changed,while mRNA involved in regulating gene expression during allelopathy was degraded.Some miRNAs that are involved in plant allelopathy target crucial genes for regulating reactive oxygen species.Moreover,coexpression regulatory networks were constructed based on profiles of the identified miRNA-target interactions and the differentially expressed miRNA-target pairs.These findings provide a mechanistic framework for understanding allelopathy in plants.展开更多
MicroRNAs （miRNAs）, a class of ～20-24 nt long non-coding RNAs, have critical roles in diverse biological processes including devel- opment, proliferation, stress response, etc. With the development and availability...MicroRNAs （miRNAs）, a class of ～20-24 nt long non-coding RNAs, have critical roles in diverse biological processes including devel- opment, proliferation, stress response, etc. With the development and availability of experimental technologies and computational approaches, the field of miRNA biology has advanced tremendously over the last decade. By sequence complementarity, miRNAs have been estimated to regulate certain mRNA transcripts. Although it was once thought to be simple and straightforward to find plant miR NA targets, this viewpoint is being challenged by genetic and biochemical studies. In this review, we summarize recent progress in plant miRNA target recognition mechanisms, principles of target prediction, and introduce current experimental and computational tools for plant miRNA target prediction. At the end, we also present our thinking on the outlook for future directions in the development of plant miRNA target finding methods.展开更多
基金supported by the National High-Tech Research and Development Program of China (2007AA10Z139)
文摘Plant microRNAs （miRNAs） regulate gene expression mainly by guiding cleavage of target mRNAs. In this study, a degradome library constructed from different soybean （Glycine max （L.） Merr.） tissues was deep-sequenced. 428 potential targets of small interfering RNAs and 25 novel miRNA families were identified. A total of 211 potential miRNA targets, including 174 conserved miRNA targets and 37 soybean- specific miRNA targets, were identified. Among them, 121 targets were first discovered in soybean. The signature distribution of soybean primary miRNAs （pri-miRNAs） showed that most pri-miRNAs had the characteristic pattern of Dicer processing. The biogenesis of TAS3 small interfering RNAs （siRNAs） was conserved in soybean, and nine Auxin Response Factors were identified as TAS3 siRNA targets. Twenty- three miRNA targets produced secondary small interfering RNAs （siRNAs） in soybean. These targets were guided by five miRNAs： gma-miR393, gma-miR1508, gma-miR1510, gma-miR1514, and novel-11. Multiple targets of these secondary siRNAs were detected. These 23 miRNA targets may be the putative novel TAS genes in soybean. Global identification of miRNA targets and potential novel TAS genes will nnntrihnltp, tn r~__~nrP.h nn th~ f, mP.tinn_~ nf miRNA~ in ~nvh^n
基金supported by the National Natural Science Foundation of China(Grant Nos.31971734 and 31800566)the National Key R&D Program of China(Grant No.2021YFD2200505)+2 种基金the Distinguished Young Scholar Program of Fujian Agriculture and Forestry University(Grant No.xjq202017)the Scientific Research Foundation of Graduate School of Fujian Agriculture and Forestry University(Grant No.324-1122yb061)the Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University(Grant No.72202200205),China。
文摘Circular RNAs(circRNAs)are endogenous non-coding RNAs with covalently closed structures,which have important functions in plants.However,their biogenesis,degradation,and function upon treatment with gibberellins(GAs)and auxins(1-naphthaleneacetic acid,NAA)remain unknown.Here,we systematically identified and characterized the expression patterns,evolutionary conservation,genomic features,and internal structures of circRNAs using RNase R-treated libraries from moso bamboo(Phyllostachys edulis)seedlings.Moreover,we investigated the biogenesis of circRNAs dependent on both cis-and trans-regulation.We explored the function of circRNAs,including their roles in regulating microRNA(miRNA)-related genes and modulating the alternative splicing of their linear counterparts.Importantly,we developed a customized degradome sequencing approach to detect miRNA-mediated cleavage of circRNAs.Finally,we presented a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with GA and NAA.Collectively,our study provides insights into the biogenesis,function,and miRNA-mediated degradation of circRNAs in moso bamboo.
基金Open access funding provided by Shanghai Jiao Tong UniversityOpen access funding provided by Shanghai Jiao Tong University+3 种基金supported by the National Natural Science Foundation of China(No.32201603)the Open Fund of the Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region(No.SYFMR2022011Z)the Open Fund of State Key Laboratory of Tree Genetics and Breeding(Chinese Academy of Forestry)(No.TGB2021008)the Scientific Research Program of Hubei Provincial Department of Education(No.B2021044).
文摘Carotenoids,as natural tetraterpenes,play a pivotal role in the yellow coloration of peaches and contribute to human dietary health.Despite a relatively clear understanding of the carotenoid biosynthesis pathway,the regulatory mechanism of miRNAs involved in carotenoid synthesis in yellow peaches remain poorly elucidated.This study investigated a total of 14 carotenoids and 40 xanthophyll lipids,including six differentially accumulated carotenoids:violaxanthin,neoxanthin,lutein,zeaxanthin,cryptoxanthin,and(E/Z)-phytoene.An integrated analysis of RNA-seq,miRNA-seq and degradome sequencing revealed that miRNAs could modulate structural genes such as PSY2,CRTISO,ZDS1,CHYB,VDE,ZEP,NCED1,NCED3 and the transcription factors NAC,ARF,WRKY,MYB,and bZIP,thereby participating in carotenoid biosynthesis and metabolism.The authenticity of miRNAs and target gene was corroborated through quantitative real-time PCR.Moreover,through weighted gene coexpression network analysis and a phylogenetic evolutionary study,coexpressed genes and MYB transcription factors potentially implicated in carotenoid synthesis were identified.The results of transient expression experiments indicated that mdm-miR858 inhibited the expression of PpMYB9 through targeted cleavage.Building upon these findings,a regulatory network governing miRNA-mediated carotenoid synthesis was proposed.In summary,this study comprehensively identified miRNAs engaged in carotenoid biosynthesis and their putative target genes,thus enhancing the understanding of carotenoid accumulation and regulatory mechanism in yellow peach peel and expanding the gene regulatory network of carotenoid synthesis.
基金This work was supported by National Basic Research Program of China(Nos.2009CB941500 and 2005CB522400 to X.C.)by National Natural Science Foundation of China(Grant Nos.30870534 and 30621001 to X.C.).
文摘MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in eukaryotes.Plant miRNAs modulate their targets mainly via messenger RNA(mRNA)cleavage.Small RNA(sRNA)targets have been extensively investigated in Arabidopsis using computational prediction,experimental validation,and degradome sequencing.However,small RNA targets are largely unknown in rice(Oryza sativa).Here,we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11(Oryza sativa L.ssp.indica).One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified.Of targets for the conserved miRNAs between Arabidopsis and rice,transcription factors comprise around 70%(58 in 82),indicating that these miRNAs act as masters of gene regulatory nodes in rice.In contrast,non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks.In addition,5 AUXIN RESPONSE FACTORs(ARFs)cleaved by the TAS3 derived ta-siRNAs were also detected.A total of 40 sRNA targets were further validated via RNA ligasemediated 5′rapid amplification of cDNA ends(RLM 5′-RACE).Our degradome results present a detailed sRNAtarget interaction atlas,which provides a guide for the study of the roles of sRNAs and their targets in rice.
基金supported by the Specialized Research Fund for the Doctoral Program of Higher Education of China (20134320120013)the Natural Science Foundation of Hunan Province, China (14JJ3095)
文摘supported by the Specialized Research Fund for the Doctoral Program of Higher Education of China （20134320120013）;the Natural Science Foundation of Hunan Province, China （14JJ3095）
基金financially supported by the National S&T Major Project of China(2016ZX08001006)the National Key Research and Development Program of China(2016YFD0101801 and 2017YFD0100300)the Agricultural Science and Technology Innovation Program of CAAS。
文摘The mesocotyl,a structure located between the basal part of the seminal root and the coleoptile node of seedlings,contributes to pushing the shoot tip through the soil surface,a function that is essential for the uniform emergence of direct-seeded rice.Its elongation is inhibited by light and induced in darkness.This investigation of an indica rice(P25)with vigorous mesocotyl elongation was aimed at identifying the"omics"basis of its lightinduced growth inhibition.A transcriptomic comparison between mesocotyl tissues that had developed in the dark and then been exposed to light identified many differentially expressed genes(DEGs)and differentially abundant micro RNAs(mi RNAs).Degradome sequencing analysis revealed 27 negative mi RNA-target pairs.A co-expression regulatory network was constructed based on the mi RNAs,their corresponding targets,and DEGs with a common Gene Ontology term.It suggested that auxin and light,probably antagonistically,affect mesocotyl elongation by regulating polyamine oxidase activity.
基金the National Public Welfare Industry Research Project of China(201504406)National Natural Science Foundation of China(31770706)+1 种基金National Natural Science Foundation of China(31870379)Science Research Projects of Facility Horticulture Laboratory of Universities in Shandong(2018YY031)。
文摘Plant species produce different types of allelopathic chemicals in nature;however,little is known about the differential regulation of plant allelopathy.Because allelopathy caused by p-hydroxybenzoic acid(pHBA)is one of the main obstacles to continuous cropping of Populus×euramericana ‘Neva’,we examined gene expression dynamics in Neva leaves induced by pHBA.The expression of genes related to photosynthesis and respiration changed,while mRNA involved in regulating gene expression during allelopathy was degraded.Some miRNAs that are involved in plant allelopathy target crucial genes for regulating reactive oxygen species.Moreover,coexpression regulatory networks were constructed based on profiles of the identified miRNA-target interactions and the differentially expressed miRNA-target pairs.These findings provide a mechanistic framework for understanding allelopathy in plants.
基金supported by Major State Basic Research and Development Program of China (973 Program) (Grant No. 2010CB126604)NSFC (Grant No. 61272380)+1 种基金supported by NSFC (Grant No. 61173118)the Shuguang Program of Shanghai Education Foundation
文摘MicroRNAs （miRNAs）, a class of ～20-24 nt long non-coding RNAs, have critical roles in diverse biological processes including devel- opment, proliferation, stress response, etc. With the development and availability of experimental technologies and computational approaches, the field of miRNA biology has advanced tremendously over the last decade. By sequence complementarity, miRNAs have been estimated to regulate certain mRNA transcripts. Although it was once thought to be simple and straightforward to find plant miR NA targets, this viewpoint is being challenged by genetic and biochemical studies. In this review, we summarize recent progress in plant miRNA target recognition mechanisms, principles of target prediction, and introduce current experimental and computational tools for plant miRNA target prediction. At the end, we also present our thinking on the outlook for future directions in the development of plant miRNA target finding methods.
