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| Status |
Public on Nov 01, 2016 |
| Title |
small RNA profiling of WT, ros1-4, nrpd1 single mutants and ros1-4/nrpd1doubble mutant [small RNA-seq] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Arabidopsis ROS1 is the first genetically characterized DNA demethylase in eukaryotes. Dysfunction of ROS1 leads to increase in DNA methylation level at thousands of genomic loci. However, the features of ROS1 targets are not well understood. In this study, we identified and characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. Most ROS1 targets are transposable elements (TEs) and intergenic regions. Compared to other TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting a role for ROS1 in preventing the spreading of DNA methylation from highly methylated TEs to nearby genes. Interestingly, we found that unlike general TEs, ROS1 targets are associated with an enrichment of H3K18ac and H3K27me3, and depletion of H3K27me and H3K9me2. We investigated the antagonism between ROS1 and RNA-directed DNA methylation (RdDM) by identifying and characterizing thousands of genomic regions regulated by both ROS1 and RdDM. Unexpectedly, we uncovered thousands of previously unidentified RdDM targets by analyzing the DNA methylome of ros1/nrpd1 double mutant plants. In addition, we show that ROS1 also antagonizes RdDM-independent DNA methylation at more than a thousand genomic loci. Our results provide significant insights into the genome-wide effects of both ROS1-mediated active DNA demethylation and RNA-directed DNA methylation as well as their interaction in plants.
Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of WT, ros1-4, nrpd1 single mutants and ros1-4/nrpd1doubble mutant
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| Overall design |
4 samples examined: WT, ros1-4 single mutant, nrpd1-3 single mutatn, and ros1-4/nrpd1-3 double mutant. Each sample has two replicates.
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| Contributor(s) |
Tang K, Lang Z, Zhu J |
| Citation(s) |
27797352 |
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| Submission date |
Jun 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian-Kang Zhu |
| E-mail(s) |
zhu132@purdue.edu
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| Organization name |
Purdue University
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| Department |
Department of Horticulture and Landscape Architecture
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| Street address |
625 Agriculture Mall Dr.
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| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
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| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE83802 |
The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications |
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| Relations |
| BioProject |
PRJNA327041 |
| SRA |
SRP077467 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE83800_RAW.tar |
85.0 Mb |
(http)(custom) |
TAR (of BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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