Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses1[OPEN]

• Published in: Plant physiology (Bethesda) 2016-01, Vol.170 (3), p.1535-1548
• Main Authors: Lunardon, Alice, Forestan, Cristian, Farinati, Silvia, Axtell, Michael J., Varotto, Serena
• Format: Article
• Language: English
• ISSN: 0032-0889; 1532-2548
• DOI: 10.1104/pp.15.01205

Agronomically realistic, long-term drought stress mis-regulates some miRNAs and induces the down-regulation of a set of small RNA loci in the maize leaf. Endogenous small RNAs ( sRNAs ) contribute to gene regulation and genome homeostasis, but their activities and functions are incompletely known. The maize genome has a high number of transposable elements ( TEs ; almost 85%), some of which spawn abundant sRNAs . We performed sRNA and total RNA sequencing from control and abiotically stressed B73 wild-type plants and rmr6-1 mutants. RMR6 encodes the largest subunit of the RNA polymerase IV complex and is responsible for accumulation of most 24-nucleotide (nt) small interfering RNAs ( siRNAs ). We identified novel MIRNA loci and verified miR399 target conservation in maize. RMR6 -dependent 23-24 nt siRNA loci were specifically enriched in the upstream region of the most highly expressed genes. Most genes misregulated in rmr6-1 did not show a significant correlation with loss of flanking siRNAs , but we identified one gene supporting existing models of direct gene regulation by TE-derived siRNAs . Long-term drought correlated with changes of miRNA and sRNA accumulation, in particular inducing down-regulation of a set of sRNA loci in the wild-typeleaf.