Identification and validation of promoters and cis-acting regulatory elements

Abstract

Studies of promoters that largely regulate gene expression at the transcriptional level are crucial for improving our basic understanding of gene regulation and will expand the toolbox of available promoters for use in plant biotechnology. In this review, we present a comprehensive analysis of promoters and their underlying mechanisms in transcriptional regulation, including epigenetic marks and chromatin-based regulation. Large-scale prediction of promoter sequences and their contributing cis-acting elements has become routine due to recent advances in transcriptomic technologies and genome sequencing of several plants. However, predicted regulatory sequences may or may not be functional and demonstration of the contribution of the element to promoter activity is essential for confirmation of regulatory sequences. Synthetic promoters and introns provide useful approaches for functional validation of promoter sequences. The development and improvement of gene expression tools for rapid, efficient, predictable, and high-throughput analysis of promoter components will be critical for confirmation of the functional regulatory element sequences identified through transcriptomic and genomic analyses.

Cis-regulatory elements used to control gene expression in plants

“…PAT1 and B33 are most active in the vascular tissues during initial tuber development and later on in parenchyma. As they contain sucrose-inducible sequences, the expression efficiency may be boosted by supplementation with this sugar (Jefferson et al 1990;Liu et al 1990;Hernandez-Garcia and Finer 2014). application was observed, thus enabling early and easy localization of infected regions in plants in vivo.…”

Understanding the Mechanisms Involved in the Regulation of Cytochrome P450 Gene Expression in Drosophila melanogaster (Diptera: Drosophilidae)

“…This level of regulation consolidates the contribution of various types of cis-acting genomic elements, which are vital molecular switches involved in the transcriptional regulation of a productive chain of gene activities regulating numerous biological processes, including abiotic stress responses, developmental processes and hormone responses [30,31]. This transcriptional regulation transpires within a complex genomic milieu in which promoters, enhancers, and insulators are intimately connected both along the one-dimensional linear chromosome and within the three-dimensional nuclear chromatin environment [32][33][34].…”

“…The physical interplay between regulatory proteins and the basic transcriptional machinery is straight forward during initiation of transcription owing to the location of proximal elements to the core promoter [34].…”

Advances in Genetic Improvement for Tocotrienol Production: A Review

“…They regulate the level and tissue-specificity of gene expression (23). Different promoter sequences and their regulatory motifs can be identified from plant genomic sequences (24).…”