| Base on the next generation sequencing technology, this thesis, focusing on plant transcriptome, predicted natural antisense transcripts (NATs) and competing endogenous RNAs (ceRNAs) using the bioinformatic methods in plants. We analyzed natural antisense transcripts in arabidopsis and discovered a series features of NATs.The results are summarized as follows:1. Natural antisense transcripts (NATs), as one type of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and pathological processes. We constructed a plant NAT database (PlantNATsDB) involving approximately 2 million NAT pairs in 70 plant species. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. PlantNATsDB provides variously user-friendly web interfaces to facilitate the presentation of NATs and an integrated, graphical network browser to display the complex networks formed by different NATs. Moreover, a "Gene Set Analysis" module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. The PlantNATsDB is freely available at http://bis.zju.edu.cn/pnatdb/.2. Natural antisense transcripts (NATs) are endogenous transcripts that can form double-stranded RNA structures. Many protein coding genes (PCs) and non-protein coding genes (NPC) tend to form cis-NATs and trans-NATs, respectively. In this work, we identified 4,080 cis-NATs and 2,491 trans-NATs genome-widely in Arabidopsis. Of these,5,385 NAT-siRNAs were detected from the small RNA sequencing data. NAT-siRNAs are typically 21nt, and are processed by Dicer-like 1 (DCL1)/DCL2 and RDR6 and function in epigenetically activated situations, or 24nt, suggesting these are processed by DCL3 and RDR2 and function in environment stress. NAT-siRNAs are significantly derived from PC/PC pairs of trans-NATs and NPC/NPC pairs of c/s-NATs. Furthermore, NAT pair genes typically have similar pattern of epigenetic status. Cis-NATs tend to be marked by euchromatic modifications whereas trans-’NATs tend to be marked by heterochromatic modifications.3. Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for microRNA (miRNA) binding, thereby regulating the abundance of other RNA transcripts which share the same microRNA response elements (MREs). Although this type of RNA cross talk was first described in Arabidopsis, and was subsequently shown to be active in animal models, there is no database collating potential ceRNA data for plants. We have developed a comprehensive Plant ceRNA database (PceRBase) which predicts 672 000 potential ceRNA target-target, and 165000 ceRNA target-mimic pairs from 26 plant species. Predicted pairing structure between miRNAs and their target mRNA transcripts, expression levels of ceRNA pairs and associated GO annotations are also stored in the database. A web interface provides convenient browsing and searching for specific genes of interest. Tools are available for gene set enrichment analysis and network visualization. Moreover, we have developed a web-tool to help user to predict ceRNA pairs from their own data. PceRBase is freely accessible at http://bis.zju.edu.cn/pcemadb/index.jsp. |
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