Identification of cis-Elements That Regulate Gene Expression during Initiation of Axillary Bud Outgrowth in Arabidopsis

Abstract

Growth regulation associated with dormancy is an essential element in plant life cycles. To reveal regulatory mechanisms of bud outgrowth, we analyzed transcriptomes of axillary shoots before and after main stem decapitation in Arabidopsis (Arabidopsis thaliana). We searched for any enriched motifs among the upstream regions of up-regulated and down-regulated genes after decapitation. The promoters of down-regulated genes were enriched for TTATCC motifs that resemble the sugar-repressive element, whereas the promoters of up-regulated genes were enriched for GGCCCAWW and AAACCCTA, designated Up1 and Up2, respectively. Transgenic plants harboring a reporter gene driven by a tandem repeat of the elements were produced to analyze their function in vivo. Sugar-repressive element-mediated gene expression was down-regulated by the application of sugars but was unaffected after decapitation. In contrast, expression driven by the repeat containing both Up1 and Up2 was upregulated after decapitation, although the Up1 or Up2 repeat alone failed to induce reporter gene expression in axillary shoots. In addition, disruption of both Up1 and Up2 elements in a ribosomal protein gene abolished the decapitation-induced expression. Ontological analysis demonstrated that up-regulated genes with Up elements were disproportionately predicted to function in protein synthesis and cell cycle. Up1 is similar to an element known to be a potential target for TCP (TEOSINTE BRANCHED1, CYCLOIDEA, PCFs family) transcription factor(s), which regulate expression of cell cycle-related and ribosomal protein genes. Our data indicate that Up1-mediated transcription of protein synthesis and cell cycle genes is an important regulatory step during the initiation of axillary shoot outgrowth induced by decapitation.

A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks

“…The CATGCA motif in Figure 6c is part of the RY-repeat element that is specifically required during seed development [47]. The motif GGCCCA in Figure 6d matches the UP1ATMSD motif that is over-represented in a list of up-regulated genes after main stem decapitation in Arabidopsis, many of which are predicted to function in protein synthesis [48]. Finally, genes in Figure 6e are involved in cell cycle and are regulated by the CAACGG motif, which contains the myb core motif found in the promoter of Arabidopsis cell cycle regulating cyclin B1:1 gene [47].…”

Seed Production Affects Maternal Growth and Senescence in Arabidopsis

“…We explored the similarities between dormancy and GPA: gene expression changes from growing to arrested meristems and vice versa are consistent with the idea that GPA represents a shoot dormancy. For example, two of the genes with highest gene expression changes during GPA are the AtDRM1 and AtDRM2 genes, considered markers for dormant axillary buds (Tatematsu et al, 2005;Rae et al, 2014). Furthermore, genes responding to ABA, which have recently been proposed to regulate axillary bud growth (Yao and Finlayson, 2015), are strongly up-regulated during GPA.…”

“…Our data suggest that the meristem retained identity and functional properties throughout all experimental conditions, and responded to GPA largely by a reduction in cellular components necessary for mitotic activity. Tatematsu et al, 2005). Blue colors represent low, yellow colors represent high expression in our microarray dataset.…”

“…in axillary buds that are suppressed by apical dominance (Shimizu-Sato and Mori, 2001). Previous work has established patterns of gene expression changes in lateral buds upon release of apical dominance, and identified two expression markers that are highly expressed in dormant buds, the DORMANCY-ASSOCIATED PROTEIN1 and 2 (AtDRM1 and AtDRM2) genes (Tatematsu et al, 2005). Using our microarray dataset, we visualized the expression of genes that were previously determined to respond in axillary buds to the removal of dominant shoots (Fig.…”

Transcriptome Profiling of Tiller Buds Provides New Insights into PhyB Regulation of Tillering and Indeterminate Growth in Sorghum

“…Over-expression of AtE2FA in Arabidopsis induces mature leaf cells to reenter the cell cycle (Rossignol et al, 2002), and AtE2FA silencing reduces cotyledon and root growth and cell proliferation (Magyar et al, 2012). Decapitation increases cell cycle and ribosomal protein gene expression in dormant buds of Arabidopsis and pea and stimulates bud outgrowth (Devitt and Stafstrom, 1995;Tatematsu et al, 2005). Taken together, growth arrest at 6 DAP is not associated with decreased expression of genes involved in the cell cycle, but reduced expression of a sorghum homolog of AtE2F3 at 8 DAP and elevated expression of SbTB1 in phyB-1 buds may lead to reduced expression of genes involved in the cell cycle as the dormancy program becomes more fully established after 8 DAP.…”