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| Status |
Public on May 15, 2019 |
| Title |
Methylome of the Arabidopsis mRNA export mutant aly1 and associated controls |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
RNA-directed DNA methylation (RdDM) is a set of mechanisms by which transcriptionally-repressive DNA methylation and histone modifications are targeted de novo to transposable element and transgene regions of the genome. We identified a mutant in which all forms of RdDM are deficient, leading to the transcriptional activation of some transposable elements and the complete inability to initiate transgene silencing. The mutated gene, ALY1, encodes an RNA-binding nuclear export protein belonging to a family of four ALY proteins in Arabidopsis. ALY proteins function together to export a large number of mRNAs from the nucleus for translation, but we found that ALY1 is unique in its ability to enable RdDM. We sequenced methylomes (via MethylC-seq) to identify the genome-wide loss of CHH methylation targeted by RdDM in aly1 mutants. We sequenced small RNAs and determined that ALY1 functions in RdDM downstream of small RNA production and export. We sequenced total, nuclear and cytoplasmic mRNAs to determine that ALY1 functions in the nuclear export directly or indirectly on 2,612 mRNAs. Additionally, we sequenced RNAs bound to the ALY1 protein using RNA-immunoprecipitation followed by high throughput sequencing.
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| |
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| Overall design |
Examination of whole genome methylation in three replicates of wild-type Columbia and eleven mutants.
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| |
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| Contributor(s) |
Cuerda-Gil D, Panda K, Slotkin RK |
| Citation(s) |
30814259 |
| Submission date |
Aug 17, 2018 |
| 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 |
| |
|
| Platforms (1) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
|
| Samples (11)
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| This SubSeries is part of SuperSeries: |
| GSE118709 |
Methylome, transcriptome, RIP-seq and small RNA-seq of the Arabidopsis mRNA export mutant aly1 and associated controls |
|
| Relations |
| BioProject |
PRJNA486504 |
| SRA |
SRP158256 |
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