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Plant Physiol. 2016 Mar;170(3):1535-48. doi: 10.1104/pp.15.01205. Epub 2016 Jan 8.

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.

Author information

1
Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.).
2
Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.) serena.varotto@unipd.it.

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.

PMID:
26747286
PMCID:
PMC4775107
DOI:
10.1104/pp.15.01205
[Indexed for MEDLINE]
Free PMC Article

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