A Comparison of Transcriptomes Between Germinating Seeds and Growing Axillary Buds of Arabidopsis

Plant growth is constrained by developmental and environmental cues. This growth constraint is strategic and determines plant’s architecture and competence of environmental adaptation. Dormancy is one form of growth arrest that commonly occurs in seeds and axillary buds. Transcriptomes of germinating seeds and axillary buds display some characteristic features in over-represented cis-acting elements in the promoters of genes whose expressions are associated with germination or axillary bud outgrowth. Two cis-acting elements, Up1 and Up2, are over-represented in the promoters of up-regulated genes during germination or axillary bud growth. Gene ontology classification indicated that genes containing Up1- or Up2-cis-acting elements are associated with protein synthesis and cell cycle. Interestingly, a significant proportion of the Up1- and Up2-containing genes expressed in growing axillary buds encode for protein synthesis- and cell cycle-related proteins, while those expressed in germinating seeds encode for protein synthesis, but not cell cycle-related proteins. Additionally, promoters of genes down-regulated during seed germination or axillary bud outgrowth contain a significant over-representation of abscisic acid-responsive elements (ABRE). The down-regulated genes containing ABRE promoter elements are enriched for processes related to metabolism and stress response in both seeds and axillary buds, although different sets of genes are expressed in each organ. This suggests that unidentified organ-specific cis-acting elements are involved in the transcriptional regulation of down-regulated genes.