|
| Status |
Public on Dec 15, 2017 |
| Title |
A small RNA pathway mediates allelic dosage in endosperm [sRNA-seq] |
| Organisms |
Arabidopsis thaliana; Arabidopsis lyrata |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Balance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of endosperm genes are expressed in a 2:1 maternal:paternal ratio, reflecting genomic DNA content. Here we find that the 2:1 transcriptional ratio is, unexpectedly, actively regulated. In A. thaliana and A. lyrata, endosperm 24 nt small RNAs are reduced in TEs and enriched in genes compared to the embryo. We find an inverse relationship between the parent-of-origin of sRNAs and mRNAs, with genes more likely to be associated with maternally than paternally biased sRNAs. Disruption of the Pol IV sRNA pathway causes a shift toward maternal allele mRNA expression for many genes. Furthermore, paternal inheritance of an RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. Thus, RNA Pol IV mediates transcriptional balance between maternally and paternally inherited genomes in endosperm.
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| Overall design |
Sequencing of 34 small RNA samples from A. thaliana dissected seed tissues (embryo, endosperm, and seed coat) 6 days after pollination and 15 small RNA samples from A. lyrata dissected seed tissues 15 days after pollination.
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| Contributor(s) |
Gehring M, Erdmann R, Klosinska M |
| Citation(s) |
29262317 |
| Submission date |
Feb 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Mary Gehring |
| Organization name |
Whitehead Institute for Biomedical Research
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
| GPL19447 |
Illumina HiSeq 2000 (Arabidopsis lyrata) |
|
| Samples (49)
|
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| This SubSeries is part of SuperSeries: |
| GSE94792 |
A small RNA pathway mediates allelic dosage in endosperm |
|
| Relations |
| BioProject |
PRJNA374333 |
| SRA |
SRP099231 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE94787_At_emb_v_endo_24nt_300bp_stats.txt.gz |
53.3 Mb |
(ftp)(http) |
TXT |
| GSE94787_CLN_allele_specific_24_300bp_values_2reps.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
| GSE94787_CVN_allele_specific_24_300bp_values_3reps.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
| GSE94787_KME_24_overallavg_comp_singlebase.bed.gz |
1.1 Gb |
(ftp)(http) |
BED |
| GSE94787_KME_allele_specific_24_300bp_values_3reps.txt.gz |
3.8 Mb |
(ftp)(http) |
TXT |
| GSE94787_KMN_24_overallavg_comp_singlebase.bed.gz |
1.1 Gb |
(ftp)(http) |
BED |
| GSE94787_KMN_allele_specific_24_300bp_values_3reps.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| GSE94787_KMS1_24_singlebase.bed.gz |
1.0 Gb |
(ftp)(http) |
BED |
| GSE94787_KM_emb_v_endo_24nt_300bp_stats.txt.gz |
61.6 Mb |
(ftp)(http) |
TXT |
| GSE94787_LCN_allele_specific_24_300bp_values_3reps.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
| GSE94787_MME_24_overallavg_comp_singlebase.bed.gz |
1.1 Gb |
(ftp)(http) |
BED |
| GSE94787_MMN2_3_24_overallavg_comp_singlebase.bed.gz |
1.0 Gb |
(ftp)(http) |
BED |
| GSE94787_MMS_24_overallavg_comp_singlebase.bed.gz |
1.0 Gb |
(ftp)(http) |
BED |
| GSE94787_MM_emb_v_endo_24nt_300bp_stats.txt.gz |
44.3 Mb |
(ftp)(http) |
TXT |
| GSE94787_TAIR10+Cvi1.fa.gz |
69.1 Mb |
(ftp)(http) |
FA |
| GSE94787_VCN_allele_specific_24_300bp_values_2reps.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
| GSE94787_singlebasecompilation.embryo.24.overallaverage.bed.gz |
692.3 Mb |
(ftp)(http) |
BED |
| GSE94787_singlebasecompilation.endosperm.24.overallaverage.bed.gz |
711.5 Mb |
(ftp)(http) |
BED |
| GSE94787_singlebasecompilation.seedcoat.24.overallaverage.bed.gz |
582.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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