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| Status |
Public on Jan 26, 2021 |
| Title |
Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [DNA methylation] |
| Sample organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by high throughput sequencing
Third-party reanalysis
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| Summary |
Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements, which is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. In contrast, the global loss of H3K27me3 in the haploid form shapes a chromatin accessibility landscape that is poised to re-initiate the transition back to diploid life after fertilization. These distinct epigenetic reprogramming events rewire transcription through major reorganization of the regulatory epigenome to guide the alternation of generations in flowering plants.
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| Overall design |
Re-analysis of published pollen dme-2/+ DNA methylomes
third-party reanalysis
SRR516179, SRR516180, SRR534177
Adapter trimming was performed using TrimGalore version 0.6.2.
Reads were aligned to the Arabidopsis genome (TAIR10) using the Bismark version 0.22.2
BAM files containing clonal deduplicated and uniquely mapped reads were then used as substrate for Methylpy software version 1.2.9
Bisulfite conversion rates were calculated using the unmethylated chloroplast genome. Differentially methylated regions (DMRs) were defined using Methylpy. Differentially methylated cytosines (DMCs) with coverage ≥4 overlapping reads were identified by root mean square tests and a false discovery rate ≤ 0.05.
Differentially methylated sites within 250 bp were collapsed into DMRs. DMRs were further filtered by discarding regions with < 5 DMCs.
TAIR10 cDNA sequences (Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz)
*.DMC_fdr0.05.bed: Differentially methylated cystosines (DMCs) in dme-2/+ pollen compared to WT that pass the FDR threshold < 0.05
*.DMR.bed: Differentially methylated regions (DMRs) in dme-2/+ pollen compared to WT that pass the FDR threshold < 0.05
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| Contributor(s) |
Borg M, Papareddy RK |
| Citation(s) |
33491647, 38816386 |
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| Submission date |
Jul 29, 2020 |
| Last update date |
Jun 12, 2024 |
| Contact name |
Michael Borg |
| E-mail(s) |
borgmichael@gmail.com
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| Organization name |
Gregor Mendel Institute
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| Lab |
Berger Lab
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| Street address |
Dr. Bohr-Gasse 3
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| This SubSeries is part of SuperSeries: |
| GSE155369 |
Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis |
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| Relations |
| Reanalysis of |
GSM952446 |
| Reanalysis of |
GSM952447 |
| Reanalysis of |
GSM980986 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE155367_Processed_data_description.xlsx |
13.6 Kb |
(ftp)(http) |
XLSX |
| GSE155367_WT_dme2.CG_rms_results_collapsed.tsv.DMR.bed.gz |
64.8 Kb |
(ftp)(http) |
BED |
| GSE155367_WT_dme2.CHG_rms_results_collapsed.tsv.DMR.bed.gz |
6.7 Kb |
(ftp)(http) |
BED |
| GSE155367_WT_dme2.CHH_rms_results_collapsed.tsv.DMR.bed.gz |
27.7 Kb |
(ftp)(http) |
BED |
| GSE155367_col0_leaf_WT_CG.bw |
24.9 Mb |
(ftp)(http) |
BW |
| GSE155367_col0_leaf_WT_CHG.bw |
25.3 Mb |
(ftp)(http) |
BW |
| GSE155367_col0_leaf_WT_CHH.bw |
93.5 Mb |
(ftp)(http) |
BW |
| GSE155367_dme2_CGhyper_DMC_fdr0.05.bed.gz |
1.0 Mb |
(ftp)(http) |
BED |
| GSE155367_dme2_CHGhyper_DMC_fdr0.05.bed.gz |
456.4 Kb |
(ftp)(http) |
BED |
| GSE155367_dme2_CHHhyper_DMC_fdr0.05.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE155367_dme2_VN.CNN.bw |
200.5 Mb |
(ftp)(http) |
BW |
| GSE155367_dme2_sperm.CNN.bw |
197.1 Mb |
(ftp)(http) |
BW |
| GSE155367_wt_VN.CNN.bw |
194.1 Mb |
(ftp)(http) |
BW |
| GSE155367_wt_sperm.CNN.bw |
189.9 Mb |
(ftp)(http) |
BW |
| Processed data are available on Series record |
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