title: Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis.
abstract: BACKGROUND
  In Arabidopsis, a large number of genes involved in the accumulation of seed storage reserves during seed development have been characterized, but the relationship of gene expression and regulation underlying this physiological process remains poorly understood. A more holistic view of this molecular interplay will help in the further study of the regulatory mechanisms controlling seed storage compound accumulation.
  
  
  RESULTS
  We identified gene coexpression networks in the transcriptome of developing Arabidopsis (Arabidopsis thaliana) seeds from the globular to mature embryo stages by analyzing publicly accessible microarray datasets. Genes encoding the known enzymes in the fatty acid biosynthesis pathway were found in one coexpression subnetwork (or cluster), while genes encoding oleosins and seed storage proteins were identified in another subnetwork with a distinct expression profile. In the triacylglycerol assembly pathway, only the genes encoding diacylglycerol acyltransferase 1 (DGAT1) and a putative cytosolic "type 3" DGAT exhibited a similar expression pattern with genes encoding oleosins. We also detected a large number of putative cis-acting regulatory elements in the promoter regions of these genes, and promoter motifs for LEC1 (LEAFY COTYLEDON 1), DOF (DNA-binding-with-One-Finger), GATA, and MYB transcription factors (TF), as well as SORLIP5 (Sequences Over-Represented in Light-Induced Promoters 5), are overrepresented in the promoter regions of fatty acid biosynthetic genes. The conserved CCAAT motifs for B3-domain TFs and binding sites for bZIP (basic-leucine zipper) TFs are enriched in the promoters of genes encoding oleosins and seed storage proteins.
  
  
  CONCLUSIONS
  Genes involved in the accumulation of seed storage reserves are expressed in distinct patterns and regulated by different TFs. The gene coexpression clusters and putative regulatory elements presented here provide a useful resource for further experimental characterization of protein interactions and regulatory networks in this process.
authors.affiliation: Agricultural Lipid Biotechnology Program, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.
authors.forename: Fred Y
authors.initials: FY
authors.lastname: Peng
authors.forename: Randall J
authors.initials: RJ
authors.lastname: Weselake
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D001483:Base Sequence; D005227:Fatty Acids / Q000096:biosynthesis; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D017343:Genes, Plant / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012639:Seeds / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism
chemical_list: D005227:Fatty Acids; D010940:Plant Proteins