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| Status |
Public on Jan 20, 2016 |
| 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 |
| Organism |
Zea mays |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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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 (wt) plants and rmr6-1 mutants. RMR6 encodes the largest subunit of the RNA polymerase IV (Pol IV) complex, and is responsible for accumulation of most 24 nucleotide (nt) small interfering RNA (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 mis-regulated 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 wt leaf.
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| Overall design |
sRNA profile of maize leaf and shoot apical meristematic area, of wt and rmr6-1 mutant plants grown under 1) control conditions 2) salt stress 3) drought stress 4) salt+drought stress. Each condition was replicated two/three times, after 10 days of treatment and after 7 days of recovery.
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| Contributor(s) |
Lunardon A, Forestan C, Farinati S, Axtell MJ, Varotto S |
| Citation(s) |
26747286 |
| |
| Submission date |
Jul 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael J Axtell |
| Organization name |
Penn State University
|
| Department |
Department of Biology
|
| Street address |
University Park
|
| City |
State College |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| Platforms (1) |
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| Samples (50)
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| Relations |
| BioProject |
PRJNA288808 |
| SRA |
SRP060265 |
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