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 Stresses  

Abstract

(A.L., M.J.A.) 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.

Small RNAs reflect grandparental environments in apomictic dandelion

“…In contrast, 21 nt sRNA showed a peak density toward the center of gene bodies. The distributional patterns reported here resemble previously reported genic signatures of sRNA abundance in well-annotated genomes such as maize (Gent et al 2013;Lunardon et al 2016), A. thaliana (Dowen et al 2012) and rice (Li et al 2012). The relative decrease in transcript-associated 24 nt sRNA after stress exposure may suggests a loss of methylation in gene flanking regions (and possibly also in TE sequences within genes) and consequent gene expression upregulation.…”

“…The most pronounced changes occurred for sRNAs of size 24nt whose relative abundance in the total sRNA population was markedly reduced in both of the stress conditions compared to the control. Relative loss of TE-associated 24nt sRNA has been reported for a variety of biotic and abiotic stressors (Dowen et al 2012;Lunardon et al 2016;McCue et al 2012). These changes appear to be mainly the result of hypomethylation and loss of RdDM targeting of transposable element (TE) sequences (McCue et al 2013;Tran et al 2005).…”

Epigenetic signatures of stress adaptation and flowering regulation in response to extended drought and recovery in Zea mays

“…Since it is well known that leaf‐derived floral molecular signals regulate flowering in maize (Dong et al, ), it could be speculated that their drought‐induced mis‐regulation alters inflorescence development. By investigating drought stress induced changes in maize small RNA accumulation (Lunardon, Forestan, Farinati, Axtell, & Varotto, ), we observed the upregulation of miR156, which is involved in floral transition in Arabidopsis as negative regulator of SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL; Wu & Poethig, ). In maize, miRNA156 negatively regulates the expression of TSH4 , UB2 , and UB3 (Chuck et al, ; Chuck et al, ; Chuck, Meeley, Irish, Sakai, & Hake, ; Wei et al, ), three SPL floral regulators which expression is altered after drought stress.…”

Natural antisense transcripts are significantly involved in regulation of drought stress in maize

“…The remaining reads were used to identify and annotate smRNA (in nostitch mode) using ShortStack version 3.4 (60,61). For each sample, the number of reads per million (RPM) was calculated using the number of mapped reads in gene regions (including 1 kb flanking sequences), which was then normalized to the total count of genome-mapped reads.…”