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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      
dateReleased:
01-20-2016
description:
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. 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.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-70487
refinement:
raw
alternateIdentifiers:
70487
keywords:
functional genomics
dateModified:
01-23-2016
availability:
available
types:
gene expression
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-70487/E-GEOD-70487.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-70487/E-GEOD-70487.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70487
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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