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| 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
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| 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.
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| Overall design |
BS-seq of ddm1a/1b/drm2 triple mutant; two replicates for smRNA-seq of wt and ddm1a/1b double mutant.
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| Contributor(s) |
Tan F, Lu Y |
| Citation(s) |
29794169 |
| Submission date |
Dec 26, 2017 |
| Last update date |
Jun 06, 2018 |
| Contact name |
Feng Tan |
| E-mail(s) |
tanfeng19880807@126.com
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| Organization name |
National Key Lab of Crop Genetic Improvement
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| Street address |
No.1 Shizishan street
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platforms (1) |
| GPL13834 |
Illumina HiSeq 2000 (Oryza sativa Japonica Group) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA427582 |
| SRA |
SRP127576 |
