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| Status |
Public on Dec 31, 2018 |
| Title |
Maternal siRNAs mediate spatial and temporal regulation of gene expression and seed development in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
In Arabidopsis seed development involves maternal small interfering RNAs (siRNAs) that induce RNA-directed DNA methylation (RdDM) through the NRPD1 pathway. To investigate their biological functions we characterized siRNAs in the endosperm and seed coat that were separated by laser capture microdissection (LCM) in reciprocal genetic crosses with an nrpd1 mutant. We also monitored the spatio-temporal activity of the NRPD1 pathway on seed development using AGO4:GFP::AGO4 (promoter:GFP::protein) reporter and promoter:GUS sensors of siRNA-mediated silencing. From these approaches we identified four distinct groups of siRNA loci that were dependent on or independent of the maternal NRPD1 allele in the endosperm or seed coat. A group of maternally expressed NRPD1-siRNA loci targets endosperm-preferred genes, including those encoding AGAMOUS-LIKE (AGL) transcription factors. Using the sensor AGL40:GUS and AGL91:GUS constructs we demonstrate that spatial and temporal expression patterns of these genes in the endosperm were regulated by the NRPD1-mediated pathway irrespective of complete silencing (AGL91) or incomplete silencing (AGL40) of these target genes. Modified expression of these siRNA-targeted genes affects seed size and we propose that the corresponding maternal siRNAs could account for parent-of-origin effects on the endosperm in interploidy and hybrid crosses. These analyses reconcile previous studies on siRNAs and imprinted gene expression during seed development.
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| Overall design |
1. Examination of small RNAs in embryo, endosperm and seed coat of Arabidopsis seeds. 2. Examiniation of small RNAs in reciprocal crosses between wild type and nrpd1a mutant as well as rdr2 mutant. 7 crosses were made including 3 self pollination of parent strains.
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| Contributor(s) |
Kirkbride RC, Lu J, Zhang C, Mosher RA, Baulcombe DC, Chen ZJ |
| Citation(s) |
30692258 |
| |
| Submission date |
Jun 06, 2013 |
| Last update date |
Mar 11, 2019 |
| Contact name |
Z Jeffrey Jeffrey Chen |
| E-mail(s) |
zjchen@austin.utexas.edu
|
| Phone |
512-475-9327
|
| Organization name |
The University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Lab |
Polyploidy, Hybrid Vigor, and Epigenetics
|
| Street address |
2506 Speedway NMS 3.122 Stop A500
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712-1597 |
| Country |
USA |
| |
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| Platforms (3) |
| GPL9302 |
Illumina Genome Analyzer II (Arabidopsis thaliana) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
| GPL21785 |
Illumina HiSeq 4000 (Arabidopsis thaliana) |
|
| Samples (18)
|
| GSM1155403 |
small RNA-seq of wild type x wild type seeds |
| GSM1155404 |
small RNA-seq of nrpd1a x nrpd1a seeds |
| GSM1155405 |
small RNA-seq of nrpd1a x wild type seeds |
| GSM1155406 |
small RNA-seq of wild type x nrpd1a seeds |
| GSM1155407 |
small RNA-seq of rdr2 x rdr2 seeds |
| GSM1155408 |
small RNA-seq of rdr2 x wild type |
| GSM1155409 |
small RNA-seq of wild type x rdr2 seeds |
| GSM1155410 |
small RNA-seq of embryo |
| GSM1155411 |
small RNA-seq of endosperm |
| GSM1155412 |
small RNA-seq of seed coat |
| GSM3581786 |
CxN_ES1: Col x nrpd1 LCM Endsoperm Replicate 1 |
| GSM3581787 |
CxN_ES4: Col x nrpd1 LCM Endsoperm Replicate 4 |
| GSM3581788 |
CxN_SC1: Col x nrpd1 LCM Seed Coat Replicate 1 |
| GSM3581789 |
CxN_SC4: Col x nrpd1 LCM Seed Coat Replicate 4 |
| GSM3581790 |
NxC_ES1: nrpd1 x Col LCM Endsoperm Replicate 1 |
| GSM3581791 |
NxC_ES4: nrpd1 x Col LCM Endsoperm Replicate 4 |
| GSM3581792 |
NxC_SC1: nrpd1 x Col LCM Seed Coat Replicate 1 |
| GSM3581793 |
NxC_SC4: nrpd1 x Col LCM Seed Coat Replicate 4 |
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| Relations |
| BioProject |
PRJNA207397 |
| SRA |
SRP024279 |
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