title: Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.
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 data sets as an essential resource for the study of seed biology.
authors: Department of Plant Biology, University of California, Davis, CA 95616, USA.
authors: Mark F
authors: MF
authors: Belmonte
authors: Ryan C
authors: RC
authors: Kirkbride
authors: Sandra L
authors: SL
authors: Stone
authors: Julie M
authors: JM
authors: Pelletier
authors: Anhthu Q
authors: AQ
authors: Bui
authors: Edward C
authors: EC
authors: Yeung
authors: Meryl
authors: M
authors: Hashimoto
authors: Jiong
authors: J
authors: Fei
authors: Corey M
authors: CM
authors: Harada
authors: Matthew D
authors: MD
authors: Munoz
authors: Brandon H
authors: BH
authors: Le
authors: Gary N
authors: GN
authors: Drews
authors: Siobhan M
authors: SM
authors: Brady
authors: Robert B
authors: RB
authors: Goldberg
authors: John J
authors: JJ
authors: Harada
mesh_terms: D017360:Arabidopsis / Q000033:anatomy & histology / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000145:classification / Q000235:genetics*; D016000:Cluster Analysis; D056625:Endosperm / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D008856:Microscopy, Fluorescence; D020411:Oligonucleotide Array Sequence Analysis; D030821:Plants, Genetically Modified; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000033:anatomy & histology / Q000235:genetics* / Q000254:growth & development
chemical_list: D029681:Arabidopsis Proteins; D049452:Green Fluorescent Proteins