The Regulatory Code for Transcriptional Response Diversity and Its Relation to Genome Structural Properties in A. thaliana

Abstract

Regulation of gene expression via specific cis-regulatory promoter elements has evolved in cellular organisms as a major adaptive mechanism to respond to environmental change. Assuming a simple model of transcriptional regulation, genes that are differentially expressed in response to a large number of different external stimuli should harbor more distinct regulatory elements in their upstream regions than do genes that only respond to few environmental challenges. We tested this hypothesis in Arabidopsis thaliana using the compendium of gene expression profiling data available in AtGenExpress and known cis-element motifs mapped to upstream gene promoter regions and studied the relation of the observed breadth of differential gene expression response with several fundamental genome architectural properties. We observed highly significant positive correlations between the density of cis-elements in upstream regions and the number of conditions in which a gene was differentially regulated. The correlation was most pronounced in regions immediately upstream of the transcription start sites. Multistimuli response genes were observed to be associated with significantly longer upstream intergenic regions, retain more paralogs in the Arabidopsis genome, are shorter, have fewer introns, and are more likely to contain TATA-box motifs in their promoters. In abiotic stress time series data, multistimuli response genes were found to be overrepresented among early-responding genes. Genes involved in the regulation of transcription, stress response, and signaling processes were observed to possess the greatest regulatory capacity. Our results suggest that greater gene expression regulatory complexity appears to be encoded by an increased density of cis-regulatory elements and provide further evidence for an evolutionary adaptation of the regulatory code at the genomic layout level. Larger intergenic spaces preceding multistimuli response genes may have evolved to allow greater regulatory gene expression potential.

The protein expression landscape of the Arabidopsis root

“…2D and SI Appendix, Table S10). A small possibility exists that these data support a previously reported suggestion that RNA expression is less variable and often tissue specific for long CDS (40)(41)(42), which might lead to more consistent protein expression. However, a more likely explanation for our results is that low-molecularweight proteins are sampled less frequently in GeLC-MS/MS experiments (43), and these proteins thus seem to be poorly correlated with transcript levels in our binary comparisons.…”

Cloning and Functional Characterization of Three Branch Point Oxidosqualene Cyclases from Withania somnifera (L.) Dunal

“…cis-Acting regulatory elements and their corresponding transcription factors constitute one of the transcriptional regulatory mechanisms induced by different environmental and extracellular conditions to help the plants in adaptive strategies (52). Therefore, the presence of numerous putative cis-regulatory motifs in the three OSC promoters suggests control over their transcriptional activity being mediated in response to various signals.…”

The significance of genome-wide transcriptional regulation in the evolution of stress tolerance

“…Transcriptional initiation requires assembly of this polymerase to a core promoter structure such as the TATA box which is present in about 20% of Saccharomyces cerevisiae genes (Basehoar et al 2004). Remarkably, TATA-containing genes seem to be enriched in stress response genes, a notion that applies to plants (Walther et al 2007) and humans (Yang et al 2007), and suggests that TATA motifs are associated with rapid and variable regulation. Indeed, it was shown that stress-related proteins expressed from genes with a TATA box exhibit a high level of intrinsic variability (Newman et al 2006).…”