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| Status |
Public on Sep 04, 2014 |
| Title |
Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
The mutagenic activity of transposable elements (TEs) is suppressed by epigenetic silencing and small interfering RNAs (siRNAs), especially in gametes that would transmit transposed elements to the next generation. In pollen from the model plant Arabidopsis, we show that TEs are unexpectedly reactivated and transpose, but only in the pollen vegetative nucleus, which accompanies the sperm cells but does not provide DNA to the fertilized zygote. TE expression coincides with down-regulation of the heterochromatin remodeler DECREASE IN DNA METHYLATION 1 and of most TE siRNAs. However, 21 nucleotide siRNA from Athila retrotransposons is generated in pollen and accumulates in sperm, indicating that siRNA from TEs activated in the vegetative nucleus can target silencing in gametes. We propose a conserved role for reprogramming in germline companion cells, such as nurse cells in insects and vegetative nuclei in plants, to reveal intact TEs in the genome and regulate their activity in gametes.
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| Overall design |
Mature pollen was collected from Columbia reference strain plants by vacuum filtration (Johnson-Brousseau and McCormick, 2004). DNA and RNA were isolated from a ddm1-2 plant in the Columbia reference background. Small RNAs of 19–28 nt were size selected by denaturing 15% PAGE, and cloned as in Brennecke et al. (2007). Additional details regarding the cloning of small RNAs are found in the Supplemental Data. The small RNA libraries were sequenced on Illumina 1G sequencer. The total number of sequences perfectly matching the Arabidopsis genome were as follows: WT inflorescence, 4,158,848 (2,286,133 unique); WT pollen, 1,034,665 (437,984 unique); ddm1 inflorescence, 4,098,772 (1,637,771 unique); and WT sperm, 760,651 (429,972 unique).
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| Contributor(s) |
Slotkin KR, Vaughn M, Borges F, Tanurdžić M, Becker JD, Feijó JA, Martienssen RA |
| Citation(s) |
19203581 |
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| Submission date |
Sep 03, 2014 |
| Last update date |
Jan 20, 2021 |
| Contact name |
Robert A Martienssen |
| E-mail(s) |
martiens@cshl.edu
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| Organization name |
Cold Spring Harbor Laboratory
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| Department |
Delbruck Bldg.
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| Lab |
Martienssen
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| Street address |
1 Bungtown Rd
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| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platforms (1) |
| GPL9062 |
Illumina Genome Analyzer (Arabidopsis thaliana) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA260113 |
| SRA |
SRP046256 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE61028_RAW.tar |
2.9 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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