Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed
Open Access
- 14 January 2013
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 110 (5), E435-E444
- https://doi.org/10.1073/pnas.1222061110
Abstract
Seeds are complex structures that consist of the embryo, endosperm, and seed-coat regions that are of different ontogenetic origins, and each region can be further divided into morphologically distinct subregions. Despite the importance of seeds for food, fiber, and fuel globally, little is known of the cellular processes that characterize each subregion or how these processes are integrated to permit the coordinated development of the seed. We profiled gene activity genome-wide in every organ, tissue, and cell type of Arabidopsis seeds from fertilization through maturity. The resulting mRNA datasets offer the most comprehensive description of gene activity in seeds with high spatial and temporal resolution, providing unique insights into the function of understudied seed regions. Global comparisons of mRNA populations reveal unexpected overlaps in the functional identities of seed subregions. Analyses of coexpressed gene sets suggest that processes that regulate seed size and filling are coordinated across several subregions. Predictions of gene regulatory networks based on the association of transcription factors with enriched DNA sequence motifs upstream of coexpressed genes identify regulators of seed development. These studies emphasize the utility of these datasets as an essential resource for the study of seed biology.Keywords
This publication has 45 references indexed in Scilit:
- Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seedsProceedings of the National Academy of Sciences of the United States of America, 2012
- Genome-Wide Analysis Reveals Gene Expression and Metabolic Network Dynamics during Embryo Development in ArabidopsisPlant Physiology, 2011
- Regulation and Flexibility of Genomic Imprinting during Seed DevelopmentTHE PLANT CELL ONLINE, 2011
- Global analysis of gene activity duringArabidopsisseed development and identification of seed-specific transcription factorsProceedings of the National Academy of Sciences of the United States of America, 2010
- Establishing, maintaining and modifying DNA methylation patterns in plants and animalsNature Reviews Genetics, 2010
- A Role for Multiple Circadian Clock Genes in the Response to Signals That Break Seed Dormancy inArabidopsisTHE PLANT CELL ONLINE, 2009
- Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in PollenCell, 2009
- TheArabidopsisMYB5 Transcription Factor Regulates Mucilage Synthesis, Seed Coat Development, and Trichome MorphogenesisTHE PLANT CELL ONLINE, 2009
- Potential Sites of Bioactive Gibberellin Production during Reproductive Growth inArabidopsisTHE PLANT CELL ONLINE, 2008
- Genomic imprinting in endosperm: its effect on seed development in crosses between species, and its implications for the evolution of apomixisPhilosophical Transactions B, 1991