Constrution And Analysis Of Plant Natural Antisense Transcripts Database

Natural anti sense transcripts (NATs) are RNAs that are complementary to other endogenous RNAs. This type of regulatory RNAs includes both protein-coding and non-coding RNAs (ncRNAs). NATs could potentially regulate gene expression at both the transcriptional and post-transcriptional levels through a variety of biological mechanisms. Experimental methods and computational predictions indicate that NATs occur prevalently in plant genomes and play significant roles in physiological and pathological processes. More and more examples of NATs have been shown to act together with endogenous siRNAs (small interfering RNAs) from the overlapping regions in both plant and animal species, suggesting the important biological roles of this type of siRNAs. Moreover, deep sequencing of small RNAs (sRNAs) together with bioinformatics analysis reveals that the overlap portions of NATs are the hotspots for siRNA generation, further indicating that NATs are an important biogenesis mechanism of endogenous siRNAs. This type of siRNAs is thus termed as nat-siRNAs (natural antisense transcript-derived siRNAs). Although their important biological functions have been reported widely, a comprehensive database related to plant NATs is lacking up to now. Besides, NAT information is still vacant in some plants. Bioinformatics prediction of NATs can assist the functional studies on these plants.Consequently, we constructed a plant NAT database (PlantNATsDB, Plant Natural Antisense Transcripts DataBase) involving approximately2million NAT pairs in69plant species. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. PlantNATsDB provides various 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.Furthermore, we performed a global survey on plant nat-siRNAs based on the NAT information from PlantNATsDB database. By utilizing the currently available sRNA high-throughput sequencing (HTS) data, the scene of sRNA generation within the overlapping regions of natural antisense transcript pairs was investigated. We found that the overlapping regions of trans-NAT pairs were indeed the hotspots of sRNA generation, but the situation is not consistent for the cis-NAT pairs from eight species. Interestingly, several examples of cis-NATs with phase-distributed sRNA loci in their overlapping regions were identified. Most nat-siRNAs in these cis-NATs were from reproductive organs, such as inflorescences, flower buds and siliques. By presenting these findings, I hope that my studies could partially expand the current understanding of plant sRNAs, especially nat-siRNAs, and could inspire further in-depth studies on the huge sRNA population in plants.The PlantNATsDB is freely available at http://bis.zju.edu.cn/pnatdb/.