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Series GSE166887 Query DataSets for GSE166887
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
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.
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)
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
Lab Jacobsen lab
Street address 4045 Terasaki Life Sciences Building
City Los Angeles
State/province CA
ZIP/Postal code 90095-7239
Country USA
Platforms (1)
GPL21785 Illumina HiSeq 4000 (Arabidopsis thaliana)
Samples (8)
GSM5087601 WT_R1_SxaQSEQsYB052L8_index_22
GSM5087602 WT_R2_SxaQSEQsYB052L8_index_23
GSM5087603 WT_R3_SxaQSEQsYB052L8_index_25
This SubSeries is part of SuperSeries:
GSE166897 The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis
BioProject PRJNA702181
SRA SRP306739

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE166887_RAW.tar 6.6 Mb (http)(custom) TAR (of FPKM_TRACKING)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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