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

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...

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Published in:Plant physiology (Bethesda) 2016-03, Vol.170 (3), p.1535-1548
Main Authors: Lunardon, Alice, Forestan, Cristian, Farinati, Silvia, Axtell, Michael J., Varotto, Serena
Format: Article
Language:English
Subjects:
3' Untranslated Regions - genetics
Adaptation, Physiological - genetics
DNA-Directed RNA Polymerases - genetics
Droughts
Gene Expression Profiling - methods
Gene Expression Regulation, Plant
GENES, DEVELOPMENT AND EVOLUTION
Genome, Plant - genetics
High-Throughput Nucleotide Sequencing - methods
Meristem - genetics
MicroRNAs - genetics
Mutation
Plant Leaves - genetics
Plant Proteins - genetics
Plant Shoots - genetics
RNA, Plant - genetics
RNA, Small Interfering - genetics
RNA, Small Untranslated - genetics
Stress, Physiological
Time Factors
Zea mays - genetics
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Summary: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.
ISSN:0032-0889
1532-2548
1532-2548
DOI:10.1104/pp.15.01205