Identification And Analysis Of Maize MiRNAs Targets And Mock Targets Across The Genome

In recent years, intricate interactions among diverse transcripts were described, including protein-coding messenger RNAs, long non-coding RNAs (IncRNAs) and pseudogenes. They can act as competing endogenous RNAs (ceRNAs), natural microRNA sponges or target mimics, and communicate with each other by competing for shared microRNA response elements (MREs). MicroRNAs (miRNAs) are a class of single-stranded small ncRNAs of approximately 21-24 nucleotides that are involved in transcriptional and post-transcriptional gene regulation in eukaryotes. Long intergenic noncoding RNAs (lincRNAs) are endogenous ncRNAs that transcribed from intergenic regions of the genome and play critical roles in regulating gene expression through multiple RNA-mediated mechanisms. LincRNAs are involved in a variety of biological processes such as cell cycle regulation, immune surveillance and embryonic stem cells differentiation in animals; however, the function of lincRNAs are participated in multiple biological processes, especially in reproductive development, flowering time and response to stress in plants. Pseudogene are considered as nonfunctional genomic sequences with sequence similarity to functional genes, and the knowledge of pseudogene can improve genome annotation and the understanding of genome evolution.Protein-coding genes are mainly transcripts in eukaryotes, but the ncRNAs are also important. Intensive studies on mRNAs as miRNA targets or miRNA decoys have widely demonstrated, while the research on other transcripts including lincRNAs and pseudogenes as miRNA targets or decoys is seldom explored, especially in plants. Maize (Zea mays L.) is one of most important crops worldwide for fundamental development and evolution. The data including miRNAs, lincRNAs, pseudogenes, cDNAs and degradomes are collected and intergrated, followed by bioinformation methods to predict the lincRNAs and pseudogenes potentially acting as miRNA targets and miRNA decoys. Then, the function of lincRNAs acting as miRNA targets are predicted and annotated via a co-expression network, and the function of lincRNAs as miRNA decoys are annotated according to the ceRNA hypothesis. Our results show that:1. We developed a computational method and systematically predicted 466 lincRNAs as 165 miRNA targets and 86 lincRNAs as 58 miRNA decoys in maize. Furthermore,34 lincRNAs predicted as 33 miRNA targets were validated based on degradome data.2. LincRNAs acting as miRNA targets or decoys are a common phenomenon, which indicates that the regulated networks of miRNAs also involve lincRNAs.3. To elucidate the function of lincRNAs, we reconstructed a miRNA-regulated network involving 78 miRNAs,117 lincRNAs and 8834 mRNAs. Based on the lincRNA-mRNA co-expression network and the competing endogenous RNA hypothesis, we predicted 34 lincRNAs function as miRNA targets and 86 lincRNAs function as miRNA decoys participate in cellular and metabolic processes, and play role in catalytic activity and molecular binding functions.4. Through the identification of degradome and filtering rules, there were 236 miRNA-pseudogene were comprised of 109 miRNAs and 203 pseudogene that as miRNA targets. Moreover, we found 348 may act as ceRNAs, which interact with miRNAs and sequester it to protect mRNAs from repression.Conclusion:This study employed a computational pipeline for the systematic analysis of putative miRNA-lincRNA, miRNA-pseudogene and miRNA-mRNA duplexes for miRNAs, lincRNAs, pseudogenes and mRNAs. We found that 42 miRNA-lincRNA and 236 miRNA-pseudogene duplexes remained after filtering based on degradome evidence, which were composed of miRNAs and potential miRNA targets. Furthermore,86 lincRNAs and 348 pseudogenes were predicted as miRNA decoys that may competitively bind to miRNAs. According to the obtained co-expression networks and the ceRNA hypothesis, we effectively predicted the function of lincRNAs as miRNA targets or decoys. This work provides a comprehensive view of miRNA-regulated networks and lays a solid foundation for elucidating the function of lincRNAs and pseudogenes.