|
| Status |
Public on May 01, 2019 |
| Title |
Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitizes Arabidopsis endosperm to paternal dosage [Bisulfite-seq] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
Seed development is sensitive to parental dosage, with excess maternal or paternal genomes creating reciprocal phenotypes. Paternal genomic excess results in extensive endosperm proliferation without cellularization and eventual seed abortion. We previously showed that loss of the RNA POL IV gene nrpd1 in tetraploid fathers represses seed abortion in paternal excess crosses. Here we show genetically that RNA-directed DNA methylation (RdDM) pathway activity in the paternal parent is sufficient to determine the viability of paternal excess seeds. The status of the RdDM pathway in paternal excess endosperm does not impact seed viability. Comparison of endosperm transcriptomes, DNA methylation, and small RNAs from balanced and paternal excess endosperm demonstrates that paternal excess seed abortion is unlikely to be dependent on either transposable element or imprinted gene mis-regulation. We suggest instead that loss of paternal RdDM modulates expression at a small subset of genes and desensitizes endosperm to paternal excess. Finally, using allele-specific transcription data, we present evidence of a transcriptional buffering system that up37 regulates maternal alleles and represses paternal alleles in response to excess paternal genomic dosage. These findings prompt reconsideration of models for dosage sensitivity in endosperm.
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| |
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| Overall design |
Sequencing of two replicates of bisulfite treated DNA from Balanced endosperm (Ler x Col), Lethal paternal excess endosperm (Ler x 4N Col), and Viable paternal excess endosperm (Ler x 4N nrpd1)
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| |
|
| Contributor(s) |
Gehring M, PRV S |
| Citation(s) |
31064867 |
| |
| Submission date |
Feb 22, 2019 |
| Last update date |
Jul 30, 2019 |
| Contact name |
satyaki P Rajavasireddy |
| E-mail(s) |
satyaki@wi.mit.edu
|
| Phone |
6072290279
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Gehring Lab
|
| Street address |
455 Main Street
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
|
| Samples (6)
|
| GSM3618290 |
Lethal_paternal_excess_2 [Bisulfite-seq] |
| GSM3618291 |
Viable_paternal_excess_1 [Bisulfite-seq] |
| GSM3618292 |
Viable_paternal_excess_2 [Bisulfite-seq] |
|
| This SubSeries is part of SuperSeries: |
| GSE126932 |
Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitizes Arabidopsis endosperm to paternal dosage |
|
| Relations |
| BioProject |
PRJNA523800 |
| SRA |
SRP186588 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE126929_Balanced_CG.tdf |
8.7 Mb |
(ftp)(http) |
TDF |
| GSE126929_Balanced_CHG.tdf |
8.8 Mb |
(ftp)(http) |
TDF |
| GSE126929_Balanced_CHH.tdf |
50.9 Mb |
(ftp)(http) |
TDF |
| GSE126929_CG_Balanced_greater_than_Lethal_paternal_excess.bed.gz |
3.9 Kb |
(ftp)(http) |
BED |
| GSE126929_CG_Balanced_greater_than_Viable_paternal_excess.bed.gz |
6.8 Kb |
(ftp)(http) |
BED |
| GSE126929_CG_Balanced_less_than_Lethal_paternal_excess.bed.gz |
11.4 Kb |
(ftp)(http) |
BED |
| GSE126929_CG_Balanced_less_than_Viable_paternal_excess.bed.gz |
13.5 Kb |
(ftp)(http) |
BED |
| GSE126929_CG_Balanced_vs_Lethal_paternal_excess_stats_all.txt.gz |
17.5 Mb |
(ftp)(http) |
TXT |
| GSE126929_CG_Balanced_vs_Viable_paternal_excess_stats_all.txt.gz |
18.2 Mb |
(ftp)(http) |
TXT |
| GSE126929_CG_Lethal_greater_than_Viable_paternal_excess.bed.gz |
9.8 Kb |
(ftp)(http) |
BED |
| GSE126929_CG_Lethal_less_than_Viable_paternal_excess.bed.gz |
8.1 Kb |
(ftp)(http) |
BED |
| GSE126929_CG_Lethal_vs_Viable_paternal_excess_stats_all.txt.gz |
18.1 Mb |
(ftp)(http) |
TXT |
| GSE126929_CHG_Balanced_greater_than_Lethal_paternal_excess.bed.gz |
30.0 Kb |
(ftp)(http) |
BED |
| GSE126929_CHG_Balanced_greater_than_Viable_paternal_excess.bed.gz |
17.0 Kb |
(ftp)(http) |
BED |
| GSE126929_CHG_Balanced_less_than_Lethal_paternal_excess.bed.gz |
261 b |
(ftp)(http) |
BED |
| GSE126929_CHG_Balanced_less_than_Viable_paternal_excess.bed.gz |
243 b |
(ftp)(http) |
BED |
| GSE126929_CHG_Balanced_vs_Lethal_paternal_excess_stats_all.txt.gz |
16.0 Mb |
(ftp)(http) |
TXT |
| GSE126929_CHG_Balanced_vs_Viable_paternal_excess_stats_all.txt.gz |
16.3 Mb |
(ftp)(http) |
TXT |
| GSE126929_CHG_Lethal_greater_than_Viable_paternal_excess.bed.gz |
412 b |
(ftp)(http) |
BED |
| GSE126929_CHG_Lethal_less_than_Viable_paternal_excess.bed.gz |
983 b |
(ftp)(http) |
BED |
| GSE126929_CHG_Lethal_vs_Viable_paternal_excess_stats_all.txt.gz |
15.9 Mb |
(ftp)(http) |
TXT |
| GSE126929_CHH_Balanced_greater_than_Lethal_paternal_excess.bed.gz |
75.7 Kb |
(ftp)(http) |
BED |
| GSE126929_CHH_Balanced_greater_than_Viable_paternal_excess.bed.gz |
57.5 Kb |
(ftp)(http) |
BED |
| GSE126929_CHH_Balanced_less_than_Lethal_paternal_excess.bed.gz |
2.5 Kb |
(ftp)(http) |
BED |
| GSE126929_CHH_Balanced_less_than_Viable_paternal_excess.bed.gz |
1.2 Kb |
(ftp)(http) |
BED |
| GSE126929_CHH_Balanced_vs_Lethal_paternal_excess_stats_all.txt.gz |
24.4 Mb |
(ftp)(http) |
TXT |
| GSE126929_CHH_Balanced_vs_Viable_paternal_excess_stats_all.txt.gz |
24.3 Mb |
(ftp)(http) |
TXT |
| GSE126929_CHH_Lethal_greater_than_Viable_paternal_excess.bed.gz |
3.4 Kb |
(ftp)(http) |
BED |
| GSE126929_CHH_Lethal_less_than_Viable_paternal_excess.bed.gz |
24.9 Kb |
(ftp)(http) |
BED |
| GSE126929_CHH_Lethal_vs_Viable_paternal_excess_stats_all.txt.gz |
24.2 Mb |
(ftp)(http) |
TXT |
| GSE126929_Lethal_paternal_excess_CG.tdf |
8.6 Mb |
(ftp)(http) |
TDF |
| GSE126929_Lethal_paternal_excess_CHG.tdf |
8.8 Mb |
(ftp)(http) |
TDF |
| GSE126929_Lethal_paternal_excess_CHH.tdf |
49.3 Mb |
(ftp)(http) |
TDF |
| GSE126929_Viable_paternal_excess_CG.tdf |
9.5 Mb |
(ftp)(http) |
TDF |
| GSE126929_Viable_paternal_excess_CHG.tdf |
9.6 Mb |
(ftp)(http) |
TDF |
| GSE126929_Viable_paternal_excess_CHH.tdf |
55.6 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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