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

Alice Lunardon, Cristian Forestan, Silvia Farinati, Michael Axtell, Serena Varotto

Research output: Contribution to journalArticle

12 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1535-1548
Number of pages14
JournalPlant physiology
Volume170
Issue number3
DOIs
StatePublished - Mar 1 2016

Fingerprint

abiotic stress
Zea mays
small interfering RNA
Small Interfering RNA
Genome
RNA
mutants
loci
genome
corn
Genes
genes
Nucleotides
nucleotides
RNA Sequence Analysis
DNA Transposable Elements
Droughts
DNA-Directed RNA Polymerases
DNA-directed RNA polymerase
MicroRNAs

All Science Journal Classification (ASJC) codes

  • Physiology
  • Genetics
  • Plant Science

Cite this

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title = "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 = "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.",
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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. / Lunardon, Alice; Forestan, Cristian; Farinati, Silvia; Axtell, Michael; Varotto, Serena.

In: Plant physiology, Vol. 170, No. 3, 01.03.2016, p. 1535-1548.

Research output: Contribution to journalArticle

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