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| Status |
Public on Nov 23, 2021 |
| Title |
The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq-12_13] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. How loss of ATXR5/6 and H3K27me1 leads to these phenotypes remains unclear. Here we provide extensive characterization of the atxr5/6 hypomorphic mutant by comprehensively examining gene expression and epigenetic changes in the mutant. We found that the tissue-specific phenotypes of TE derepression and excessive DNA in this atxr5/6 mutant correlated with residual ATXR6 expression from the hypomorphic ATXR6 allele. However, upregulation of DNA damage genes occurred regardless of ATXR6 levels and thus appears to be a separable process. We also isolated an atxr6 null allele which showed that ATXR5 and ATXR6 are required for female germline development. Finally, we characterize three previously reported suppressors of the hypomorphic atxr5/6 mutant and show that these rescue atxr5/6 via distinct mechanisms, two of which involve increasing H3K27me1 levels.
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| Overall design |
Total RNA was extracted from two-week-old roots grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype.Each replicate conisted of ~ 10 roots from individual plants. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
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| Contributor(s) |
Potok ME, Jacobsen SE |
| Citation(s) |
35027454, 37980416 |
| |
| Submission date |
Feb 16, 2021 |
| Last update date |
Dec 08, 2023 |
| Contact name |
magdalena ewelina potok |
| Organization name |
UCLA
|
| Department |
MCDB
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| Lab |
Jacobsen lab
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| Street address |
4045 Terasaki Life Sciences Building
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7239 |
| Country |
USA |
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| Platforms (1) |
| GPL21785 |
Illumina HiSeq 4000 (Arabidopsis thaliana) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE166897 |
The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis |
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| Relations |
| BioProject |
PRJNA702181 |
| SRA |
SRP306739 |
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