Title : Understanding the Drought Mediated Regulon of miRNA Biogenesis Machinery in Oryza sativa
Abstract:
Mi RNAs are integral nodes of regulation in plant development and stress responses. Their biogenesis process is an intricate and complex event consisting of many genes/TFs that work in an equally complicated and regulated fashion so as to give rise to mature functional forms of miRNAs under ever changing conditions of development and stress. Most of these genes have been studied in Arabidopsis however, their orthologs and functions have not been explored in other plant species. In the present study, we have manually curated all the information present in the literature domain regarding these genes and compiled the knowledge of the biogenesis process based on experimentally veri?ed direct evidences only. As many as 98 genes are found to be involved in miRNA biogenesis machinery, out of which 19 are TFs. Altogether 28 genes are in the ?rst step (transcription), 46 genes in the second step (processing) and in the ?nal step there are 23 genes. Most of these genes are found to be directly or indirectly interacting with the core-components of miRNA biogenesis – AGO1, DCL1, HYL1, HEN1, HST, Pol II and SE. Few of the genes regulate via interaction with other genes as partners. Further, the conservation pattern of these genes in other plant species ranging from dicots to monocots and lower organisms was identi?ed. Orthologs for 13 and 8 genes appears to be absent in lower organisms and monocots respectively. Subsequently, an attempt was made to characterize the orthologs identi?ed in Oryza sativa on the basis of comparative genomics including sequence variations (SNPs/Indels), transcriptome and epigenomics - DNA methylation and histone modi?cations. A total of 16 gene orthologs were absent in Oryza sativa and 42 genes were signi?cantly di?erentially expressed (DEGs) in either of the three tissues (?ag leaf, in?orescence and root) under drought stress in two cultivars, Nagina22 (drought tolerant) and IR64 (drought sensitive). Likewise, several genes have DMRs (Di?erentially Methylated Regions) under drought stress in all the tissues and in both the varieties and are marked with various histone modi?cations like H3K4me3, H3K9ac, H3K27me3. Furthermore, we found that many biogenesis proteins including HST, HYL1 and AGO1 intersect with many QTL (Quantitative Trait Loci) related to yield and agronomic traits in rice. Interestingly, apart from yield related traits, AGO1 is part of several other development and stress related QTL traits. Eventually we again manually curate all the physical interactions of the biogenesis core proteins in order to create a regulatory network consisting of these biogenesis proteins with all their physical interactors and targeting miRNAs. We found that as many as 96 and 50 miRNAs in Oryza sativa and Arabidopsis respectively, are targeting these miRNA biogenesis genes out of which 10 miRNAs in Oryza sativa are of high con?dence. The study enhances our understanding of the evolution of the miRNA biogenesis and its integration with the molecular schema of the cell. It also highlights avenues for further investigations in plant systems beyond Arabidopsis.
