Abstract
The genomes of all organisms abound with various cis-regulatory elements, which control gene activity. Transcriptional enhancers are a key group of such elements in eukaryotes and are DNA regions that form physical contacts with gene promoters and precisely orchestrate gene expression programs. Here, we follow gradual evolution of this regulatory system and discuss its features in different organisms. In eubacteria, an enhancer-like element is often a single regulatory element, is usually proximal to the core promoter, and is occupied by one or a few activators. Activation of gene expression in archaea is accompanied by the recruitment of an activator to several enhancer-like sites in the upstream promoter region. In eukaryotes, activation of expression is accompanied by the recruitment of activators to multiple enhancers, which may be distant from the core promoter, and the activators act through coactivators. The role of the general DNA architecture in transcription control increases in evolution. As a whole, it can be seen that enhancers of multicellular eukaryotes evolved from the corresponding prototypic enhancer-like regulatory elements with the gradually increasing genome size of organisms.
Highlights
Gene expression is a complicated multistep process that requires tight control
Enhancers are one of the most important and best studied groups of regulatory elements. These specific DNA regions act as binding targets for transcription factors (TFs), which form DNA–protein complexes associated with transcription activation
The broadly accepted concept is that a transcriptional enhancer is an independent DNA sequence that is separated from the promoter by a distance in 1D
Summary
Gene expression is a complicated multistep process that requires tight control. Eukaryotes have the corresponding regulatory machinery containing multiple cis- and trans-elements. Enhancers are one of the most important and best studied groups of regulatory elements. These specific DNA regions act as binding targets for transcription factors (TFs), which form DNA–protein complexes associated with transcription activation. The origin of transcription regulation mechanisms of eukaryotes lies in the world of prokaryotes. It is of great interest to follow evolution of the mechanism whereby transcription is activated step by step. The evolutionary approach obviously allows us to better understand the origin of the transcription regulatory complexity of higher eukaryotes, to clarify the general details of regulation, and to highlight the specific mechanisms and features that are found in the regulation of eukaryotes and are shared with prokaryotes. We provide an overview of enhancer-like mechanisms in prokaryotes, describe similarities in these mechanisms shared by both eukaryotes and prokaryotes, and discuss the gradual increase in the complexity of regulation by enhancers in evolution from eubacteria and archaea to unicellular eukaryotes, further to multicellular invertebrates, and to vertebrates
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