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Series GSE108527 Query DataSets for GSE108527
Status Public on Jun 06, 2018
Title DDM1 represses noncoding RNA expression and RNA-directed DNA methylation in heterochromatin
Organism Oryza sativa Japonica Group
Experiment type Methylation profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary In this work, we studied function of rice DDM1 in coordinating DNA methylation, expression of small (sRNA) and long noncoding (lncRNA) RNAs, and nucleosome positioning by high throughput approaches.We show that the ddm1a/1b mutation resulted in ectopic CHH methylation of transposable elements (TE) and repeats. The ectopicCHH methylationwas dependent on DRM2, a DNA methyltransferase involved in sRNA-dependent DNA-methylation (RdDM). The ddm1a/1b mutation resulted in increases of heterochromatic sRNA but decreases of euchromatic sRNA production,induced expression of a set of developmentally regulated heterochromatic lncRNA , and increased nucleosome occupancy of TE-related or silent genes including heterochromatic lncRNA loci. In particular,DDM1-mediated repression ofCentromericRetrotransposons of Rice1 (CRR1) was essential for centromere function.
Overall design BS-seq of ddm1a/1b/drm2 triple mutant; two replicates for smRNA-seq of wt and ddm1a/1b double mutant.
Contributor(s) Tan F, Lu Y
Citation(s) 29794169
Submission date Dec 26, 2017
Last update date Jun 06, 2018
Contact name Feng Tan
Organization name National Key Lab of Crop Genetic Improvement
Street address No.1 Shizishan street
City Wuhan
State/province Hubei
ZIP/Postal code 430070
Country China
Platforms (1)
GPL13834 Illumina HiSeq 2000 (Oryza sativa Japonica Group)
Samples (3)
GSM2902811 ddm1a/1b/drm2 BS-seq
GSM2902812 ddm1a/1b smRNA-seq
GSM2902813 wt smRNA-seq
BioProject PRJNA427582
SRA SRP127576

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Supplementary file Size Download File type/resource
GSE108527_RAW.tar 755.5 Mb (http)(custom) TAR (of BW)
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Processed data provided as supplementary file
Raw data are available in SRA

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