Location: Plant, Soil and Nutrition ResearchTitle: Genome-wide characterization of maize miRNA genes Author
Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/12/2009
Publication Date: 11/20/2009
Citation: Zhang, L., Chia, J., Kumari, S., Stein, J.C., Liu, Z., Narechania, A., Maher, C.A., Guill, K., Mcmullen, M.D., Ware, D. 2009. Genome-wide characterization of maize miRNA genes. PLoS Genetics. 5(11): e1000716. DOI: 10.1371/journal.pgen.1000716. Interpretive Summary: MicroRNAs (miRNAs) are small (20 to 24 nucleotide) non-coding RNAs that are derived from longer transcripts. These non-coding genes have been identified in the last 10 years to play essential roles in plant growth and development. The miRNA is known to regulate other transcripts through complementary binding, which allows the transcript to either be cleaved or functions to inhibit the translation of proteins. Here we describe genome-wide computational prediction of this class of non-coding genes and maize and their corresponding protein-coding target genes. To evaluate if these genes are expressed we looked for sequencing tags that represent miRNAs in small RNA libraries. In addition we also evaluated the size of the longer gene transcript using molecular approaches. Using the available sorghum gene sequence and annotations we were able to identify putative Sorghum bicolor orthologs for the maize microRNA based on computational analysis that made use of conserved order of protein coding genes for context. Our work provides insight into the number of non-coding genes in maize and the function of maize miRNA genes and their roles in maize.
Technical Abstract: MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in plant growth and development. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with ~35% of duplicate homeologous miRNA genes retained. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated a bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.