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| Status |
Public on Apr 11, 2013 |
| Title |
Arabidopsis small RNAs associated with RDR6-dependent RNA-directed DNA Methylation |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Background: The majority of plant transposable elements (TEs) are found in a silenced state that is epigenetically propagated by the maintenance of symmetrical DNA methylation. TE methylation is established and reinforced by a mechanism of RNA-dependent DNA methylation, which is dependent on transcription of the PolIV RNA polymerase. Recently, a pathway has been described that initiates de novo DNA methylation dependent on components of the RNAi post-transcriptional silencing pathway, independent of PolIV. To define the function of this new pathway, we have focused on the RDR6 protein, which plays a central role in the pathway we refer to as RDR6-dependent RNA-directed DNA Methylation (RDR6-RdDM).
Methods: We have sequenced total small RNAs from wild-type and three mutant genotypes: ddm1, ddm1/rdr6, and rdr6.
Conclusions: We demonstrate that RDR6-RdDM utilizes 21 and 22 nucleotide siRNAs to de novo methylate actively transcribing TEs. In addition, we find that the RDR6-RdDM pathway functions in the efficient initiation and re-establishment of TE transcriptional silencing, while it is not necessary to maintain trans-generational epigenetic silencing.
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| Overall design |
Examination of flower bud small RNAs from wild-type and 3 mutant genotypes
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| Contributor(s) |
Slotkin RK, Panda K |
| Citation(s) |
25388951, 23542151 |
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| Submission date |
Oct 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard Keith Slotkin |
| E-mail(s) |
[email protected]
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| Organization name |
The Ohio State University
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| Department |
Molecular Genetics
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| Lab |
Slotkin Laboratory
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| Street address |
318 West 12th Ave.
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| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
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| Platforms (1) |
| GPL11221 |
Illumina Genome Analyzer IIx (Arabidopsis thaliana) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA178113 |
| SRA |
SRP016580 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE41755_RAW.tar |
15.2 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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