Edible plant derived exosome-like nanoparticles(ELNs)have been shown to have multiple nutraceutical functions.However,the diversity of plant materials makes the plant derived ELN study challenging.More efforts are sti...Edible plant derived exosome-like nanoparticles(ELNs)have been shown to have multiple nutraceutical functions.However,the diversity of plant materials makes the plant derived ELN study challenging.More efforts are still needed to explore the feasible isolation methods of edible plant derived ELNs and the possible roles of food-derived ELNs in improving human health.In this study,a size exclusion chromatography based method was compared with the traditional ultracentrifugation method to isolate blueberry derived ELNs(B-ELNs),and the miRNA profile of B-ELNs was analyzed by high-throughput sequencing.A total of 36 miRNAs were found to be enriched in B-ELNs compared with berry tissue,and their potential cross-kingdom human gene targets were further predicted.Results showed that size exclusion chromatography was effective for B-ELN isolation.The most abundant miRNAs in B-ELNs mainly belonged to the miR166 family and miR396 family.Target gene prediction indicated that B-ELNs could potentially regulate pathways related to the human digestive system,immune system and infectious diseases.展开更多
以高耐热玉米品种郑单958、低耐热玉米品种先玉335为材料,以正常生长条件为对照,在花期进行高温胁迫,通过miRNA高通量测序筛选玉米花粉中的差异表达miRNA,然后预测其靶基因,并对靶基因的本体特征和代谢通路进行富集分析。结果表明,共筛...以高耐热玉米品种郑单958、低耐热玉米品种先玉335为材料,以正常生长条件为对照,在花期进行高温胁迫,通过miRNA高通量测序筛选玉米花粉中的差异表达miRNA,然后预测其靶基因,并对靶基因的本体特征和代谢通路进行富集分析。结果表明,共筛选到818个miRNA前体序列。在郑单958高温胁迫花粉与对照花粉对比组(HT958 vs CK958)中共筛选到19个显著差异表达miRNA序列,其中15个miRNA序列上调表达,4个下调表达,3个miRNA序列达到极显著水平(P<0.01)。对这19个显著差异表达miRNA的靶基因进行预测,共获得了503个基因转录本,其富集较多的GO生物学过程条目分别为转录调控DNA-模板、微管生物学过程、磷酸化作用、RNA聚合酶Ⅱ正向调控转录过程、甲基化作用等,KEGG富集较显著的代谢通路分别是谷胱甘肽代谢、碳代谢、花生四烯酸代谢、糖酵解/糖异生、叶酸生物合成等。在先玉335高温胁迫花粉与对照花粉对比组(HT335 vs CK335)中共筛选到15个显著差异表达miRNA序列,其中7个miRNA序列上调表达,8个下调表达,1个miRNA序列达到了极显著水平(P<0.01)。对这15个显著差异表达miRNA的靶基因进行预测,共获得了454个基因转录本,其富集较多的GO生物学过程条目分别为转录调控DNA-模板、磷酸化作用、蛋白质磷酸化作用、蛋白质水解、DNA修复等,富集较显著的KEGG代谢通路分别是其他多糖降解、亚油酸代谢、代谢通路、硫胺素代谢、内质网内蛋白质加工过程等。在郑单958高温胁迫花粉与先玉335高温胁迫花粉对比组(HT985 vs HT335)中共筛选到85个显著差异表达miRNA序列,其中35个miRNA序列为上调表达,50个为下调表达,24个miRNA序列达到了极显著水平(P<0.01)。对这85个显著差异表达miRNA的靶基因进行预测,共获得了2 286个基因转录本,其富集较多的GO生物学过程条目分别为转录调控DNA-模板、磷酸化作用、蛋白质磷酸化、蛋白质水解、跨膜转运等,富集较显著的代谢通路分别是鞘脂类代谢、淀粉和蔗糖代谢、其他多糖降解、代谢通路、半胱氨酸及甲硫氨酸代谢等。在HT958 vs CK958与HT335 vs CK335对比组中共筛选到94个显著差异表达miRNA序列,其中(预测全新)PC-3p-10069_1143、(预测全新)PC-3p-18335_646、(玉米)zma-miR164f-5p等28个miRNA序列达到了极显著水平(P<0.01)。对这94个显著差异表达miRNA的靶基因进行预测,共获得了4 569个基因转录本,其富集较多的GO生物学过程条目分别为转录调控DNA-模板、磷酸化作用、蛋白质磷酸化、蛋白质转运、蛋白质水解等,其富集较显著的KEGG代谢通路分别是内质网内蛋白质加工过程、真核生物核糖体生物合成、剪接体、鞘脂类代谢、内吞作用等。展开更多
Computational prediction of potential microRNAs （miRNAs） and their target genes was performed to identify the miRNAs and genes associated with temperature response in rice. The data of temperature-responsive miRNAs ...Computational prediction of potential microRNAs （miRNAs） and their target genes was performed to identify the miRNAs and genes associated with temperature response in rice. The data of temperature-responsive miRNAs of Arabidopsis, and miRNAs and the whole genome data of rice were used to predict potential miRNAs in Oryza sativa involved in temperature response. A total of 55 miRNAs were common in both the species, and 27 miRNAs were predicted at the first time in rice. Target genes were searched for these 27 miRNAs in rice genome following stringent criteria. Real time PCR based on expression analysis of nine miRNAs showed that majority of the miRNAs were down regulated under heat stress for rice cultivar Nagina 22. Furthermore, miR169, miR1884 and miR160 showed differential expression in root and shoot tissues of rice. Identification and expression studies of miRNAs during heat stress will advance the understanding of gene regulation under stress in rice.展开更多
MicroRNAs （miRNAs） are a group of regulatory RNAs that regulate gene expression post-transcriptionally by the degradation or translational inhibition of their target messenger RNAs （mRNAs）. Regulation is accomplis...MicroRNAs （miRNAs） are a group of regulatory RNAs that regulate gene expression post-transcriptionally by the degradation or translational inhibition of their target messenger RNAs （mRNAs）. Regulation is accomplished when the 22-25 nucleotide miRNAs bind to complementary sequences in the 3＇-untranslated regions （UTR）. One barrier to miRNA research is to find target genes. Although computational target predictions have shed light on important aspects of microRNA target recognition, questions remain concerning the rates of false positives. In addition, we do not completely understand how microRNAs can recognize and regulate their targets. As such, experimental positive predictions and allow for an unbiased stu ap dy proaches are required, which can reflect in vivo processes, eliminating false of microRNA target recognition. In this review, we summarized experimental approaches that have been described for the identification and validation of mRNA targets associated with specific miRNAs.展开更多
为鉴定不同饲养方式下牦牛皮下脂肪组织中差异表达的微小RNAs(miRNAs),本试验采用高通量测序对不同饲养方式下牦牛皮下脂肪组织中的miRNAs进行筛选,运用DESeq分别鉴定出自然放牧18月龄(G18) vs (从自然放牧18月龄开始舍饲育肥6个月至24...为鉴定不同饲养方式下牦牛皮下脂肪组织中差异表达的微小RNAs(miRNAs),本试验采用高通量测序对不同饲养方式下牦牛皮下脂肪组织中的miRNAs进行筛选,运用DESeq分别鉴定出自然放牧18月龄(G18) vs (从自然放牧18月龄开始舍饲育肥6个月至24月龄)F24、G18 vs (自然放牧至24月龄)G24和F24 vs G24皮下脂肪组织中差异表达的miRNAs,对差异表达的miRNAs进行靶基因预测分析。在9个牦牛皮下脂肪组织中共鉴定出1158个miRNAs,其中已知miRNAs 731个,新预测miRNAs 427个。在G18 vs F24中有43个差异miRNAs,预测到的靶基因2436个;在G18 vs G24中有68个差异miRNAs,预测到的靶基因3559个,在F24 vs G24中有31个差异miRNAs,预测到的靶基因1456个。对预测到的基因进行GO和KEGG富集分析,其主要富集到了脂肪酸代谢过程、脂肪酸生物合成过程、脂肪酸生物氧化、不饱和脂肪酸代谢过程和脂肪细胞分化调节等。因此,枯草期对牦牛进行补饲有利于牦牛皮下脂肪组织沉积。展开更多
Recently, the identification of miRNA targets has received much attention. The strategies to determine miRNA targets include bioinformatic prediction and experimental assays. The bioinformatic prediction methods are m...Recently, the identification of miRNA targets has received much attention. The strategies to determine miRNA targets include bioinformatic prediction and experimental assays. The bioinformatic prediction methods are mainly based on the confirmed rules of interaction between miRNAs and their targets, and are carried out by programs, such as miRanda, TargetScan, TargetScanS, RNAhybrid, DIANA-microT, PicTar, RNA22 and FindTar, which follow well-known principles. The experimental assays to find miRNA targets employ immunoprecipitation of AGO proteins to identify interacting mRNAs, or the analysis of mRNA or protein levels to identify genes which can be regulated by miRNAs. The improvement of current bioinformatic and experimental assays and the development of novel assays will enable greater efficiency in the identification of miRNA targets and thus facilitate miRNA research. This paper describes progress in the prediction and identification of miRNA targets.展开更多
基金supported by the National Natural Science Foundation of China(31701561)。
文摘Edible plant derived exosome-like nanoparticles(ELNs)have been shown to have multiple nutraceutical functions.However,the diversity of plant materials makes the plant derived ELN study challenging.More efforts are still needed to explore the feasible isolation methods of edible plant derived ELNs and the possible roles of food-derived ELNs in improving human health.In this study,a size exclusion chromatography based method was compared with the traditional ultracentrifugation method to isolate blueberry derived ELNs(B-ELNs),and the miRNA profile of B-ELNs was analyzed by high-throughput sequencing.A total of 36 miRNAs were found to be enriched in B-ELNs compared with berry tissue,and their potential cross-kingdom human gene targets were further predicted.Results showed that size exclusion chromatography was effective for B-ELN isolation.The most abundant miRNAs in B-ELNs mainly belonged to the miR166 family and miR396 family.Target gene prediction indicated that B-ELNs could potentially regulate pathways related to the human digestive system,immune system and infectious diseases.
文摘以高耐热玉米品种郑单958、低耐热玉米品种先玉335为材料,以正常生长条件为对照,在花期进行高温胁迫,通过miRNA高通量测序筛选玉米花粉中的差异表达miRNA,然后预测其靶基因,并对靶基因的本体特征和代谢通路进行富集分析。结果表明,共筛选到818个miRNA前体序列。在郑单958高温胁迫花粉与对照花粉对比组(HT958 vs CK958)中共筛选到19个显著差异表达miRNA序列,其中15个miRNA序列上调表达,4个下调表达,3个miRNA序列达到极显著水平(P<0.01)。对这19个显著差异表达miRNA的靶基因进行预测,共获得了503个基因转录本,其富集较多的GO生物学过程条目分别为转录调控DNA-模板、微管生物学过程、磷酸化作用、RNA聚合酶Ⅱ正向调控转录过程、甲基化作用等,KEGG富集较显著的代谢通路分别是谷胱甘肽代谢、碳代谢、花生四烯酸代谢、糖酵解/糖异生、叶酸生物合成等。在先玉335高温胁迫花粉与对照花粉对比组(HT335 vs CK335)中共筛选到15个显著差异表达miRNA序列,其中7个miRNA序列上调表达,8个下调表达,1个miRNA序列达到了极显著水平(P<0.01)。对这15个显著差异表达miRNA的靶基因进行预测,共获得了454个基因转录本,其富集较多的GO生物学过程条目分别为转录调控DNA-模板、磷酸化作用、蛋白质磷酸化作用、蛋白质水解、DNA修复等,富集较显著的KEGG代谢通路分别是其他多糖降解、亚油酸代谢、代谢通路、硫胺素代谢、内质网内蛋白质加工过程等。在郑单958高温胁迫花粉与先玉335高温胁迫花粉对比组(HT985 vs HT335)中共筛选到85个显著差异表达miRNA序列,其中35个miRNA序列为上调表达,50个为下调表达,24个miRNA序列达到了极显著水平(P<0.01)。对这85个显著差异表达miRNA的靶基因进行预测,共获得了2 286个基因转录本,其富集较多的GO生物学过程条目分别为转录调控DNA-模板、磷酸化作用、蛋白质磷酸化、蛋白质水解、跨膜转运等,富集较显著的代谢通路分别是鞘脂类代谢、淀粉和蔗糖代谢、其他多糖降解、代谢通路、半胱氨酸及甲硫氨酸代谢等。在HT958 vs CK958与HT335 vs CK335对比组中共筛选到94个显著差异表达miRNA序列,其中(预测全新)PC-3p-10069_1143、(预测全新)PC-3p-18335_646、(玉米)zma-miR164f-5p等28个miRNA序列达到了极显著水平(P<0.01)。对这94个显著差异表达miRNA的靶基因进行预测,共获得了4 569个基因转录本,其富集较多的GO生物学过程条目分别为转录调控DNA-模板、磷酸化作用、蛋白质磷酸化、蛋白质转运、蛋白质水解等,其富集较显著的KEGG代谢通路分别是内质网内蛋白质加工过程、真核生物核糖体生物合成、剪接体、鞘脂类代谢、内吞作用等。
基金Financial support received from NICRA (National Initiative of Climate and Resilient Agriculture) project is acknowledged.
文摘Computational prediction of potential microRNAs （miRNAs） and their target genes was performed to identify the miRNAs and genes associated with temperature response in rice. The data of temperature-responsive miRNAs of Arabidopsis, and miRNAs and the whole genome data of rice were used to predict potential miRNAs in Oryza sativa involved in temperature response. A total of 55 miRNAs were common in both the species, and 27 miRNAs were predicted at the first time in rice. Target genes were searched for these 27 miRNAs in rice genome following stringent criteria. Real time PCR based on expression analysis of nine miRNAs showed that majority of the miRNAs were down regulated under heat stress for rice cultivar Nagina 22. Furthermore, miR169, miR1884 and miR160 showed differential expression in root and shoot tissues of rice. Identification and expression studies of miRNAs during heat stress will advance the understanding of gene regulation under stress in rice.
基金Supported by the National Natural Science Foundation of China (30570990, 30471059, 31171578)the "863" project (2008AA10Z153)+2 种基金the Key Research Plan of Heilongjiang Province (GA06B103-3)the Innovation Research Group of NEAU (CXT004)the Research Fund for the Doctoral Program of Higher Education of China (20102325120002)
文摘MicroRNAs （miRNAs） are a group of regulatory RNAs that regulate gene expression post-transcriptionally by the degradation or translational inhibition of their target messenger RNAs （mRNAs）. Regulation is accomplished when the 22-25 nucleotide miRNAs bind to complementary sequences in the 3＇-untranslated regions （UTR）. One barrier to miRNA research is to find target genes. Although computational target predictions have shed light on important aspects of microRNA target recognition, questions remain concerning the rates of false positives. In addition, we do not completely understand how microRNAs can recognize and regulate their targets. As such, experimental positive predictions and allow for an unbiased stu ap dy proaches are required, which can reflect in vivo processes, eliminating false of microRNA target recognition. In this review, we summarized experimental approaches that have been described for the identification and validation of mRNA targets associated with specific miRNAs.
文摘为鉴定不同饲养方式下牦牛皮下脂肪组织中差异表达的微小RNAs(miRNAs),本试验采用高通量测序对不同饲养方式下牦牛皮下脂肪组织中的miRNAs进行筛选,运用DESeq分别鉴定出自然放牧18月龄(G18) vs (从自然放牧18月龄开始舍饲育肥6个月至24月龄)F24、G18 vs (自然放牧至24月龄)G24和F24 vs G24皮下脂肪组织中差异表达的miRNAs,对差异表达的miRNAs进行靶基因预测分析。在9个牦牛皮下脂肪组织中共鉴定出1158个miRNAs,其中已知miRNAs 731个,新预测miRNAs 427个。在G18 vs F24中有43个差异miRNAs,预测到的靶基因2436个;在G18 vs G24中有68个差异miRNAs,预测到的靶基因3559个,在F24 vs G24中有31个差异miRNAs,预测到的靶基因1456个。对预测到的基因进行GO和KEGG富集分析,其主要富集到了脂肪酸代谢过程、脂肪酸生物合成过程、脂肪酸生物氧化、不饱和脂肪酸代谢过程和脂肪细胞分化调节等。因此,枯草期对牦牛进行补饲有利于牦牛皮下脂肪组织沉积。
基金Supported by the National Basic Research Program of China (Grant No. 2005CB724600)the National Natural Science Foundation of China (Grant No. 30600110)
文摘Recently, the identification of miRNA targets has received much attention. The strategies to determine miRNA targets include bioinformatic prediction and experimental assays. The bioinformatic prediction methods are mainly based on the confirmed rules of interaction between miRNAs and their targets, and are carried out by programs, such as miRanda, TargetScan, TargetScanS, RNAhybrid, DIANA-microT, PicTar, RNA22 and FindTar, which follow well-known principles. The experimental assays to find miRNA targets employ immunoprecipitation of AGO proteins to identify interacting mRNAs, or the analysis of mRNA or protein levels to identify genes which can be regulated by miRNAs. The improvement of current bioinformatic and experimental assays and the development of novel assays will enable greater efficiency in the identification of miRNA targets and thus facilitate miRNA research. This paper describes progress in the prediction and identification of miRNA targets.
