Abstract
BackgroundTranscription factor binding is regulated by several interactions, primarily involving cis-element binding. These binding sites maintain specificity by means of their sequence, and other additional factors such as inter-motif distance and spacer specificity. The ACGT core sequence has been established as a functionally important cis-element which frequently regulates gene expression in synergy with other cis-elements. In this study, we used two monocotyledonous – Oryza sativa and Sorghum bicolor, and two dicotyledonous species – Arabidopsis thaliana and Glycine max to analyze the conservation of co-occurring ACGT core elements in plant promoters with respect to spacer distance between them. Using data generated from Arabidopsis thaliana and Oryza sativa, we also identified conserved regions across all spacers and possible conditions regulating gene promoters with multiple ACGT cis-elements.ResultsOur data indicated specific predominant spacer lengths between co-occurring ACGT elements, but these lengths were not universally conserved across all species under analysis. However, the frequency distribution indicated local regions of high correlation among monocots and dicots. Sequence specificity data clearly revealed a preference for G at the first and C at the terminal position of a spacer sequence, suggesting that the G-box motif is the most prevalent for the ACGT class of promoters. Using gene expression databases, we also observed trends suggesting that co-occurring ACGT elements are responsible for gene regulation in response to exogenous stress. Conservation in patterns of ACGT (N) ACGT among orthologous genes also indicated the possibility that emergence of functional significance across species was a result of parallel evolution of these cis-elements.ConclusionsAlthough the importance of ACGT elements has been acknowledged for several plant species, ours is the first study that attempts to compare their occurrence across four species and analyze conservation among them. The apparent preference for particular spacer distances suggest that these motifs might be implicated in important physiological functions which are yet to be identified. Variations in correlation patterns among monocots and dicots might arise out of differences in transcriptional regulation in the two classes. In accordance with literature, we established the involvement of co-occurring ACGT elements in stress responses and showed how this regulation differs with variation in the ACGT (N) ACGT motif. We believe that our study will be an essential resource in determining optimum spacer length and spacer sequence between ACGT elements for promoter design in future.
Highlights
Transcription factor binding is regulated by several interactions, primarily involving cis-element binding
As it has been previously seen that cooperatively binding transcription factors are usually spaced within 25 bp, we limited our analysis to a spacer distance of 30 bp
Attempting to identify conservation between monocots and dicots, we identified potential peaks at spacer lengths of 0, 14 and 26 for dicots (Figure 1A) and lengths of 0, 2, 4 and 26 (Figure 1B) across monocots
Summary
Transcription factor binding is regulated by several interactions, primarily involving cis-element binding. Regulation of gene transcription relies on interactions among transcription factors (TFs) which bind to specific DNA cis sites to form a conglomeration of proteins which guide the polymerase binding [1] These cis sites include enhancers, core promoters, matrix or scaffold attachment regions, insulators and silencers. Unless helical phasing is conserved to provide allowance for protein binding, even a change in spacer length by one base pair can drastically alter gene expression levels [12] This implies that conserved sequences (conforming to the various spatial and positional constraints) occurring in higher numbers as compared to what is probabilistically expected may be of specific functional significance
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