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| Status |
Public on Jul 26, 2023 |
| Title |
A DNA adenine demethylase impairs PRC2-mediated repression of genes marked by a specific chromatin signature |
| Organism |
Oryza sativa Japonica Group |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The Fe(II)- and α-ketoglutarate-dependent AlkB family dioxygenases are implicated in nucleotide demethylation. AlkB homolog1 (ALKBH1) is shown to demethylate DNA adenine methylation (6mA) preferentially from single-stranded or unpaired DNA, while its demethylase activity and function in the chromatin context are unclear. In this work we found that loss-of-function of the rice ALKBH1 gene led to increased 6mA in R-loop regions of the genome but had a limited effect on the overall 6mA level. However, the ALKBH1 mutation or over-expression mainly affected the expression of genes with a specific combination of chromatin modifications in the body region marked with H3K4me3 and H3K27me3 but depleted of DNA CG methylation. Further analysis revealed that the ALKBH1 protein preferentially binds to genes marked by the chromatin signature and has a function to maintain a high H3K4me3/H3K27me3 ratio by impairing the binding of Polycomb Repressive Complex2 (PRC2) to the targets, which is required for both the basal and stress-induced expression of the genes.These results unravel a function of ALKBH1 to control the balance between the antagonistic histone methylations for gene activity and provide insight into the regulatory mechanism of PRC2-mediated H3K27me3 deposition within the gene body region.
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| Overall design |
We used rice demethylase ALKBH1 mutant and overexpression materials to carry out 6mA-seq, RNA-seq and ChIP-seq, the dynamic regulation of 6mA and the mechanism of its influence on gene expression and the relationship between other chromatin modifications were analyzed.
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| Contributor(s) |
Jia Q, Zhang X, Zhou D |
| Citation(s) |
37649077 |
| Submission date |
Jan 12, 2023 |
| Last update date |
Sep 04, 2023 |
| Contact name |
Qingxiao Jia |
| Organization name |
HZAU
|
| Lab |
National Key Laboratory of Crop Genetic Improvement
|
| Street address |
No.1,Shizishan Street
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430000 |
| Country |
China |
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| Platforms (1) |
| GPL18525 |
Illumina HiSeq 2500 (Oryza sativa Japonica Group) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA923281 |
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