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| Status |
Public on Nov 14, 2014 |
| Title |
Small RNA accumulation in Transposable Element-silent and Transposable Element-active epigenomes |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Background: The small RNAs that Transposable Elements generate are vastly different when they are transcriptionally silenced compared to when they are transcriptionally activated. We performed the deep sequencing of small RNAs in a number of small RNA biogenesis mutants in both Transposable Element-silenced and Transposable Element-active epigenome backgrounds.
Results: We found that Transposable Elements generate large amounts of 21-22nt siRNAs only when they are transcriptionally active. These 21-22nt siRNAs are incorporated into the AGO6 protein.
Conclusion: Ago6 is the key protein that bridges the post-transcriptional degradation of Transposable Element mRNAs and the establishment of DNA methylation.
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| |
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| Overall design |
Examination of flower bud small RNAs from wild type and 5 single or double mutant combinations, many of which have biological replicates. In addition, IP purification of the AGO6 protein (and mock no-antigen controls) followed by sequencing of the incorporated small RNAs.
Replicate A for Col and ddm1 are submitted in GSE41755
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| |
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| Contributor(s) |
Slotkin RK, McCue A, Panda K |
| Citation(s) |
25388951 |
| |
| Submission date |
Apr 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
R. Keith Slotkin |
| E-mail(s) |
kslotkin@danforthcenter.org
|
| Organization name |
Donald Danforth Plant Science Center
|
| Street address |
975 North Warson Road
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
|
| Samples (22)
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| Relations |
| BioProject |
PRJNA245874 |
| SRA |
SRP041575 |
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