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| Status |
Public on May 08, 2023 |
| Title |
DDT-RELATED PROTEIN4-IMITATION SWITCH alters nucleosome distribution to relieve transcriptional silencing in Arabidopsis [Bisulfite-seq] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
DNA methylation is a conserved epigenetic modification that usually functions to repress gene expression. However, not all DNA methylated loci are faithfully silenced, and genes bearing promoter DNA methylation often show varying levels of transcription. The flexibility in transcription allows for greater adaptability in response to environmental and developmental cues, the mechanisms of which are not fully understood. In this work, we demonstrate that a plant-specific ISWI complex, consisting of CHR11, CHR17, DDR4, and DDR5, functions to partially de-repress DNA methylated genes and TEs through chromatin relaxation. This action requires the known transcriptional activator DNAJ proteins, providing a mechanistic link between nucleosome remodeling and transcriptional activation. We also show that the anti-silencing effects of enhanced chromatin accessibility can be genetically uncoupled from that of DNA demethylation, and is antagonized by the chromatin compactor, MORC proteins. Our work reveals a mechanism for balancing between the needs of transcriptional flexibility and faithful silencing of DNA methylated loci. As both ISWI and MORC family genes are distributed widely across plant and animal species, the findings may represent a conserved eukaryotic mechanism for fine-tuning gene expression under epigenetic repression.
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| Overall design |
The dataset contain 37 RNAseq samples, 7 ChIPseq samples, 4 WGBS samples, 10 MNase-seq samples and 58BSPCR samples. Plants are of different genetic backgrounds, which include col-0, morc1 mutant, morc1/ddr4 mutant, ZF-DDR4 mutant, met1 mutant, drm3/cmt3 mutant, drm2/cmt3/ddr4 mutant, ZF-DDR4/chr11/17 mutant.
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| Contributor(s) |
Wang Z, Liu Q, Zhang Q |
| Citation(s) |
37208763 |
| BioProject |
PRJNA834847 |
| Submission date |
May 05, 2022 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Zejia Wang |
| E-mail(s) |
wangzj@stu.pku.edu.cn
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| Organization name |
Peking University
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| Street address |
Yanyuan Street
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platforms (2) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (62)
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| GSM6107560 |
GFP-morc1, region2, bspcr |
| GSM6107561 |
GFP-morc1/ddr4, region1, bspcr |
| GSM6107562 |
GFP-morc1/ddr4, region2, bspcr |
| GSM6107563 |
GFP-drm2/cmt3, region1, bspcr |
| GSM6107564 |
GFP-drm2/cmt3, region2, bspcr |
| GSM6107565 |
GFP-drm2/cmt3/ddr4, region1, bspcr |
| GSM6107566 |
GFP-drm2/cmt3/ddr4, region2, bspcr |
| GSM6107567 |
Col0, region1, bspcr |
| GSM6107568 |
Col0, region2, bspcr |
| GSM6107569 |
met1, region1, bspcr |
| GSM6107570 |
met1, region2, bspcr |
| GSM6107571 |
DDR4-ZF, region1, rep1, bspcr |
| GSM6107572 |
DDR4-ZF, region2, rep1, bspcr |
| GSM6107573 |
DDR4-ZF, region1, rep2, bspcr |
| GSM6107574 |
DDR4-ZF, region2, rep2, bspcr |
| GSM6107575 |
DDR4-ZF/chr11/17, region1, rep1, bspcr |
| GSM6107576 |
DDR4-ZF/chr11/17, region2, rep1, bspcr |
| GSM6107577 |
DDR4-ZF/chr11/17, region1, rep2, bspcr |
| GSM6107578 |
DDR4-ZF/chr11/17, region2, rep2, bspcr |
| GSM7091024 |
6wt_AT1G06993_region1_bspcr |
| GSM7091025 |
6wt_AT1G06993_region2_bspcr |
| GSM7091026 |
6wt_AT3G29639_region1_bspcr |
| GSM7091027 |
6wt_AT3G29639_region2_bspcr |
| GSM7091028 |
6wt_AT3G29639_region3_bspcr |
| GSM7091029 |
6wt_AT5G35490_region2_bspcr |
| GSM7091030 |
6wt_AT5G35490_region3_bspcr |
| GSM7091031 |
6wt_AT4TE09845_region1_bspcr |
| GSM7091032 |
6wt_AT4TE09845_region2_bspcr |
| GSM7091033 |
6wt_AT5TE46150_region2_bspcr |
| GSM7091034 |
6wt_AT5TE48725_region1_bspcr |
| GSM7091035 |
6wt_AT5TE48725_region2_bspcr |
| GSM7091036 |
6morc_AT1G06993_region1_bspcr |
| GSM7091037 |
6morc_AT1G06993_region2_bspcr |
| GSM7091038 |
6morc_AT3G29639_region1_bspcr |
| GSM7091039 |
6morc_AT3G29639_region2_bspcr |
| GSM7091040 |
6morc_AT3G29639_region3_bspcr |
| GSM7091041 |
6morc_AT5G35490_region2_bspcr |
| GSM7091042 |
6morc_AT5G35490_region3_bspcr |
| GSM7091043 |
6morc_AT4TE09845_region1_bspcr |
| GSM7091044 |
6morc_AT4TE09845_region2_bspcr |
| GSM7091045 |
6morc_AT5TE46150_region2_bspcr |
| GSM7091046 |
6morc_AT5TE48725_region1_bspcr |
| GSM7091047 |
6morc_AT5TE48725_region2_bspcr |
| GSM7091048 |
6morc/ddr4_AT1G06993_region1_bspcr |
| GSM7091049 |
6morc/ddr4_AT1G06993_region2_bspcr |
| GSM7091050 |
6morc/ddr4_AT3G29639_region1_bspcr |
| GSM7091051 |
6morc/ddr4_AT3G29639_region2_bspcr |
| GSM7091052 |
6morc/ddr4_AT3G29639_region3_bspcr |
| GSM7091053 |
6morc/ddr4_AT5G35490_region2_bspcr |
| GSM7091054 |
6morc/ddr4_AT5G35490_region3_bspcr |
| GSM7091055 |
6morc/ddr4_AT4TE09845_region1_bspcr |
| GSM7091056 |
6morc/ddr4_AT4TE09845_region2_bspcr |
| GSM7091057 |
6morc/ddr4_AT5TE46150_region2_bspcr |
| GSM7091058 |
6morc/ddr4_AT5TE48725_region1_bspcr |
| GSM7091059 |
6morc/ddr4_AT5TE48725_region2_bspcr |
| GSM7091060 |
ddr4_rep1_WGBS |
| GSM7091061 |
ddr4_rep2_WGBS |
| GSM7091062 |
Col0_rep1_WGBS |
| GSM7091063 |
Col0_rep2_WGBS |
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| This SubSeries is part of SuperSeries: |
| GSE202271 |
DDT-RELATED PROTEIN4-IMITATION SWITCH alters nucleosome distribution to relieve transcriptional silencing in Arabidopsis |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE202270_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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