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| Status |
Public on Apr 06, 2023 |
| Title |
Noncoding RNA-mediated DNA methylation directs nucleosome positioning |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We explored the mechanism by which RdDM affects nucleosome positioning in Arabidopsis thaliana. We showed that POLV has a direct effect on nucleosomes through the SWI/SNF complex. We found that the AGO4-siRNA complex is involved in nucleosome positioning via IDN2. Moreover, the SWI/SNF complex is not required for DNA methylation in positioned nucleosomes. Instead, we found that DNA methylation is needed for nucleosome positioning in differentially methylated regions. Taken together, we propose a model where the RdDM pathway directs nucleosome positioning through DNA methylation to establish transcriptional gene silencing.
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| Overall design |
14 samples of MNase-H3-ChIP-Seq with 6 different genotypes and 2 replicates of each (Col-0, nrpe1, swi3b, drm2, cmt3, met1-3)
6 samples of WGBS with 3 different genotypes and 2 replicates of each (Col-0, nrpe1, swi3b)
Please note that as processed data was generated from multiple samples (as indicated in the corresponding sample description field) and is linked to the Series records.
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| Contributor(s) |
Sethuraman S, Rothi H, Wierzbicki A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Apr 06, 2020 |
| Last update date |
Apr 06, 2023 |
| Contact name |
Shriya Sethuraman |
| Organization name |
University of Michigan
|
| Department |
Bioinformatics
|
| Lab |
Andrzej Wierzbicki lab
|
| Street address |
5164 Biological Sciences Building, 1105 N. University Ave.
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48105 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL21785 |
Illumina HiSeq 4000 (Arabidopsis thaliana) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA623375 |
| SRA |
SRP255431 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE148173_Col-0_MNase_readCount_cmt3_CG_DMR.csv.gz |
18.9 Kb |
(ftp)(http) |
CSV |
| GSE148173_Col-0_MNase_readCount_cmt3_CHG_DMR.csv.gz |
382.7 Kb |
(ftp)(http) |
CSV |
| GSE148173_Col-0_MNase_readCount_cmt3_CHH_DMR.csv.gz |
108.1 Kb |
(ftp)(http) |
CSV |
| GSE148173_Col-0_MNase_readCount_drm2_CG_DMR.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
| GSE148173_Col-0_MNase_readCount_drm2_CHG_DMR.csv.gz |
357.4 Kb |
(ftp)(http) |
CSV |
| GSE148173_Col-0_MNase_readCount_drm2_CHH_DMR.csv.gz |
275.0 Kb |
(ftp)(http) |
CSV |
| GSE148173_Col-0_MNase_readCount_met1_CG_DMR.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
| GSE148173_Col-0_MNase_readCount_met1_CHG_DMR.csv.gz |
591.9 Kb |
(ftp)(http) |
CSV |
| GSE148173_Col-0_MNase_readCount_met1_CHH_DMR.csv.gz |
1.1 Mb |
(ftp)(http) |
CSV |
| GSE148173_PolV_stabilized_Col-0_methylation.csv.gz |
85.6 Kb |
(ftp)(http) |
CSV |
| GSE148173_PolV_stabilized_nrpe1_methylation.csv.gz |
58.9 Kb |
(ftp)(http) |
CSV |
| GSE148173_PolV_stabilized_nucleosomes.bed.gz |
29.7 Kb |
(ftp)(http) |
BED |
| GSE148173_PolV_stabilized_swi3b_methylation.csv.gz |
80.9 Kb |
(ftp)(http) |
CSV |
| GSE148173_SWI3B_stabilized_Col-0_methylation.csv.gz |
757.8 Kb |
(ftp)(http) |
CSV |
| GSE148173_SWI3B_stabilized_nrpe1_methylation.csv.gz |
705.2 Kb |
(ftp)(http) |
CSV |
| GSE148173_SWI3B_stabilized_nucleosomes.bed.gz |
29.7 Kb |
(ftp)(http) |
BED |
| GSE148173_SWI3B_stabilized_swi3b_methylation.csv.gz |
746.0 Kb |
(ftp)(http) |
CSV |
| GSE148173_cmt3_MNase_readCount_cmt3_CG_DMR.csv.gz |
14.3 Kb |
(ftp)(http) |
CSV |
| GSE148173_cmt3_MNase_readCount_cmt3_CHG_DMR.csv.gz |
278.3 Kb |
(ftp)(http) |
CSV |
| GSE148173_cmt3_MNase_readCount_cmt3_CHH_DMR.csv.gz |
66.3 Kb |
(ftp)(http) |
CSV |
| GSE148173_drm2_MNase_readCount_drm2_CG_DMR.csv.gz |
1.7 Mb |
(ftp)(http) |
CSV |
| GSE148173_drm2_MNase_readCount_drm2_CHG_DMR.csv.gz |
381.6 Kb |
(ftp)(http) |
CSV |
| GSE148173_drm2_MNase_readCount_drm2_CHH_DMR.csv.gz |
262.6 Kb |
(ftp)(http) |
CSV |
| GSE148173_met13_MNase_readCount_met1_CG_DMR.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE148173_met13_MNase_readCount_met1_CHG_DMR.csv.gz |
339.9 Kb |
(ftp)(http) |
CSV |
| GSE148173_met13_MNase_readCount_met1_CHH_DMR.csv.gz |
802.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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