Abstract
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.
Highlights
Endogenous small RNAs contribute to gene regulation and genome homeostasis, but their activities and functions are incompletely known
The small fraction of non-MIRNA sRNA loci that were stress responsive was mostly affected during drought stress, similar to the miRNAs
The expression of the RMR6 gene was not significantly altered by the treatments, and most RMR6-dependent small interfering RNAs (siRNAs) loci were unaffected by the stresses
Summary
Endogenous small RNAs (sRNAs) contribute to gene regulation and genome homeostasis, but their activities and functions are incompletely known. Plant endogenous small RNAs (sRNAs) range in length from 20 to 24 nucleotides (nts) and contribute to regulate gene expression through RNA-mediated transcriptional gene silencing (TGS) and post-TGS mechanisms Their activity is essential for the maintenance of genome integrity, the intrinsic normal growth of cells, and proper plant development. Pol IV-dependent siRNAs are often produced from transposable elements (TEs), TE-like sequences, and other repeats (Zhang et al, 2007; Mosher et al, 2008) They contribute to the reinforcement of TE silencing (Slotkin et al, 2005; Marí-Ordóñez et al, 2013; Nuthikattu et al, 2013) and in some cases are essential to control the expression of proteincoding genes in cis or in trans (Liu et al, 2004; Kinoshita et al, 2007; McCue et al, 2013). The available data suggest that Pol IV-dependent 24-nt siRNAs in maize primarily serve to mark and enforce boundaries between areas of transcriptionally active euchromatin and transcriptionally repressed heterochromatin
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