Project description:In plants, non-coding small RNAs play a vital role for plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate (JA) pathway, we compared the non-coding small RNAs between the JA-deficient aos mutant and the JA-treated wild type Arabidopsis via high-throughput sequencing. 30 new miRNAs and 27 new miRNA candidates were identified through a bioinformatics approach. 49 known miRNAs (belonging to 24 families), 15 new miRNAs and new miRNA candidates (belonging to 11 families) and 3 tasiRNA families were induced by JA, whereas 1 new miRNA, 1 tasiRNA family and 22 known miRNAs (belonging to 9 families) were repressed by JA.
Project description:In plants, non-coding small RNAs play a vital role for plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate (JA) pathway, we compared the non-coding small RNAs between the JA-deficient aos mutant and the JA-treated wild type Arabidopsis via high-throughput sequencing. 30 new miRNAs and 27 new miRNA candidates were identified through a bioinformatics approach. 49 known miRNAs (belonging to 24 families), 15 new miRNAs and new miRNA candidates (belonging to 11 families) and 3 tasiRNA families were induced by JA, whereas 1 new miRNA, 1 tasiRNA family and 22 known miRNAs (belonging to 9 families) were repressed by JA. 2 samples were examined: wild type treated with JA, and the JA-deficient aos mutant.
Project description:Small RNA sequences from Arabidopsis thaliana Col-0 inflorescence tissues of three biological replicates. The data were analyzed to identify non-templated nucleotides in Arabidopsis small RNAs.
Project description:MicroRNAs (miRNAs) are 21-24 nucleotide (nt) small non-coding RNAs that regulate a wide variety of biological processes at the posttranscriptional level. MiRNA expression often exhibits spatial and temporal specificity. However, genome-wide miRNA expression patterns in different Arabidopsis organs during plant development have not yet been fully investigated. In this study, we sequenced 59 small RNA libraries generated from different tissue types at different developmental stages of Arabidopsis. We then re-annotated Arabidopsis miRNAs based on the most recent criteria. Global analysis of miRNA expression patterns showed that most miRNAs are ubiquitously expressed in different organs or tissues. But a small set of miRNAs, either previously annotated or newly identified, show highly specific expression patterns. In addition, the expression of some miRNA members belonging to the same family is strictly regulated spatially and temporally. Unexpectedly, we found that quite a few miRNAs are produced from different arms of their hairpin precursors at different developmental stages, suggesting that arm switching could be a general and important mechanism in developmental regulation.
Project description:Brassinosteroids (BRs) are a class of class of phytohormones with important roles in regulating physiological and developmental processes. Small RNAs, including small interfering RNAs and microRNAs (miRNAs), are non-protein coding RNAs that regulate gene expression at the transcriptional and post-transcriptional levels. However, the roles of small RNAs in BR response have not been studied well. In this study, we aimed to identify BR-responsive small RNA clusters and miRNAs in Arabidopsis. In addition, the effect of BR-responsive small RNAs on their transcripts and target genes were examined. Small RNA libraries were constructed from control and epibrassinolide-treated seedlings. After sequencing the small RNA libraries, differentially expressed small RNA clusters were identified by examining the expression levels of small RNAs in 100-nt bins of Arabidopsis genome. To identify the BR-responsive miRNAs, the expression levels of all the annotated mature miRNAs, registered in miRBase, were analyzed. Previously published RNA-seq data were utilized to monitor the BR-responsive expression patterns of differentially expressed small RNA clusters and miRNA target genes. In results, 38 BR-responsive small RNA clusters, including 30 down-regulated and eight up-regulated clusters, were identified. These differentially expressed small RNA clusters were from miRNA loci, transposons, protein-coding genes, pseudo genes and others. Of these, a transgene, BRI1, accumulates small RNAs, which are not found in the wild type. Small RNAs in this transgene are up-regulated by BRs while BRI1 mRNA is down-regulated by BRs. By analyzing the expression patterns of mature miRNAs, we have identified BR-repressed miR398a-5p and BR-induced miR156g. Although miR398a-5p is down-regulated by BRs, its predicted targets were not responsive to BRs. However, SPL3, a target of BR-inducible miR156g, is down-regulated by BRs. BR-responsive small RNAs and miRNAs identified in this study will provide an insight into the role of small RNAs in BR responses in plants. Especially, we suggest that miR156g/SPL3 module might play a role in BR-mediated growth and development in Arabidopsis.