Patterns and evolution of ACGT repeat cis-element landscape across four plant genomes

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.

Comparative analysis of MIR168 promoters in three plant species

“…It is reported that these G-boxes are differentially regulated by the distance between two copies of the motif (Mehrotra and Mehrotra, 2010). Moreover, the G-box copy number in a promoter, and the distance from the transcriptional start site, also result in drastically altered gene expression, causing changes in the pattern of expression and even in resistance (Mehrotra et al, 2005(Mehrotra et al, , 2013. Thus, the degree of conservation of different regulatory elements may decrease depending on the motif in monocots and dicots.…”

“…However, the most interesting results relate to the copy number of the G-box (CACGTG) of MIR168 promoters from different species were different. G-box (CACGTG) is the most prevalent G-box in all ACGT classes ACGT classes (Figure 1 and S1 Figure) (Mehrotra et al, 2013). The MIR168 promoter of A. thaliana contains three G-box motifs (CACGTG) (Gazzani et al, 2009).…”

“…The relative position of the ACGT core motif, and its copy number upstream of the promoter, affects the recognition of transcription factors and therefore, affects development and the response to different environments, such as flower development and pathogen defense (Chuang et al, 1999;Zhou et al, 2000;Mehrotra et al, 2005). Multiple ACGT motifs, which bind synergistically to transcription factors, can form enhancer elements (Mehrotra et al, 2013). Our data suggest that there are no G-box motifs in the rice MIR168 promoter, whereas two and three G-boxes can be found in the grape and Arabidopsis MIR168 promoters, respectively.…”

Osmolality/salinity-responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fish

“…Our reporter assays demonstrate that even subtle sequence variation within the OSRE1 consensus itself alters enhancer activity, and such alterations could be important for tuning the degree of salinity induction of different genes. Another evolutionary mechanism for tuning environmental responsiveness of gene expression pertains to alteration of copy number for a particular CRE (84,85). Thus, the difference in the number of OSRE1 motifs in the MIPS of O. mossambicus and O. niloticus (Fig.…”

Cis Regulatory Elements in Regulation of Plant Gene Expression: An Overview

“…Using gene expression databases we also observed trends suggesting that co occuring 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 [1].…”