Evolution of Regulated Transcription

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.

Subunits of the PBAP Chromatin Remodeler Are Capable of Mediating Enhancer-Driven Transcription in Drosophila

“…There is a model of enhancer–promoter connection where the base of a chromatin loop is directly formed between the elements via protein–protein interactions. However, a loop can arise via its progressive extrusion as well [ 64 , 65 ]. The SWI/SNF remodeler acts as a directional DNA translocase [ 66 ] and has an intrinsic property to generate DNA loops on nucleosomes [ 67 , 68 ].…”

Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogenAgrobacterium fabrum

“…This separation distance is compatible with DNA loop formation ( 45 ) allowing the simultaneous binding of two distant palindromes (190 bp apart) within the intergenic region of atu1418–1419 . Thus, Atu1419 tetramer could repress gene expression via DNA looping, such as several negative regulators in prokaryotes ( 46 ) such as the extensively studied tetrameric lac operon repressor ( 47 ).…”

Quantifying the regulatory role of individual transcription factors inEscherichia coli

“…To build a predictive understanding of gene regulation, we need to understand not just where and when TFs bind but also learn the function and magnitude of the mechanisms of regulation at work by each TF [41, 42, 43]. Often, it is difficult to separate the contributing factors of regulation, such as the TF binding affinity, copy number and interactions with other TFs, from the regulatory role of the TF that is characterized by its interactions with RNA polymerase at the promoter [44].…”

“…To build a predictive understanding of gene regulation, we need to understand not just where and when TFs bind but also learn the function and magnitude of the mechanisms of regulation at work by each TF [63,64,65].…”