|
| Status |
Public on Mar 04, 2022 |
| Title |
RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm [bisulfite_sequencing] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
Gene expression in endosperm – a seed tissue that mediates transfer of maternal resources to offspring – is under complex epigenetic control. We show here that plant-specific RNA Polymerase IV mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs, DNA methylation, and mRNAs in A. thaliana endosperm from reciprocal heterozygotes produced by crossing wild-type plants to Pol IV mutants. We find that maternally and paternally acting Pol IV have divergent effects on endosperm. Losses of maternal and paternal Pol IV impact sRNAs and DNA methylation at distinct genomic sites. Strikingly, maternally and paternally-acting Pol IV have antagonistic impacts on gene expression at some loci, divergently promoting or repressing endosperm gene expression. Antagonistic parent-of origin effects have only rarely been described and are consistent with a gene regulatory system evolving under parental conflict
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| |
|
| Overall design |
Sequencing of two replicates of bisulfite treated DNA from WT (Ler x Col-0 F1), mat nrpd1+/- (Ler nrpd1-/- x Col-0 F1), and pat nrpd1+/- (Ler x Col-0 nrpd1-/- F1)
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| |
|
| Contributor(s) |
Gehring M, Satyaki P |
| Citation(s) |
35389984 |
| |
| Submission date |
Mar 01, 2022 |
| Last update date |
Jun 03, 2022 |
| Contact name |
Satyaki PRV |
| E-mail(s) |
satyaki@wi.mit.edu
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Gehring
|
| Street address |
455 Main street, Room number 549
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
|
| Samples (6)
|
|
| This SubSeries is part of SuperSeries: |
| GSE197717 |
RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm |
|
| Relations |
| BioProject |
PRJNA811628 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE197712_CG_DMRs_pat_nrpd1_mat_nrpd1_het.txt.gz |
12.2 Kb |
(ftp)(http) |
TXT |
| GSE197712_CG_DMRs_wild-type_mat_nrpd1_het.txt.gz |
6.4 Kb |
(ftp)(http) |
TXT |
| GSE197712_CG_DMRs_wild-type_pat_nrpd1_het.txt.gz |
7.4 Kb |
(ftp)(http) |
TXT |
| GSE197712_CG_WT.bedgraph.gz |
18.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE197712_CG_mat_nrpd1.bedgraph.gz |
21.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE197712_CG_pat_nrpd1.bedgraph.gz |
18.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE197712_CHH_DMRs_pat_nrpd1_mat_nrpd1_het.txt.gz |
21.7 Kb |
(ftp)(http) |
TXT |
| GSE197712_CHH_DMRs_wild-type_mat_nrpd1_het.txt.gz |
22.4 Kb |
(ftp)(http) |
TXT |
| GSE197712_CHH_DMRs_wild-type_pat_nrpd1_het.txt.gz |
21.7 Kb |
(ftp)(http) |
TXT |
| GSE197712_CHH_WT.bedgraph.gz |
82.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE197712_CHH_mat_nrpd1.bedgraph.gz |
11.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE197712_CHH_pat_nrpd1.bedgraph.gz |
82.2 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE197712_percent_mat_filter_WT.bed.gz |
1.5 Kb |
(ftp)(http) |
BED |
| GSE197712_percent_mat_filter_mat_nrpd1.bed.gz |
1.8 Kb |
(ftp)(http) |
BED |
| GSE197712_percent_mat_filter_pat_nrpd1.bed.gz |
1.5 Kb |
(ftp)(http) |
BED |
| GSE197712_variable_CG_WT.bed.gz |
959 b |
(ftp)(http) |
BED |
| GSE197712_variable_CG_mat_nrpd1.bed.gz |
5.9 Kb |
(ftp)(http) |
BED |
| GSE197712_variable_CG_pat_nrpd1.bed.gz |
1.6 Kb |
(ftp)(http) |
BED |
| GSE197712_variable_CHH_WT.bed.gz |
32.9 Kb |
(ftp)(http) |
BED |
| GSE197712_variable_CHH_mat_nrpd1.bed.gz |
45.0 Kb |
(ftp)(http) |
BED |
| GSE197712_variable_CHH_pat_nrpd1.bed.gz |
36.6 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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