Regulation of gene expression in the genomic context

Abstract

Metazoan life is dependent on the proper temporal and spatial control of gene expression within the many cells-essentially all with the identical genome-that make up the organism. While much is understood about how individual gene regulatory elements function, many questions remain about how they interact to maintain correct regulation globally throughout the genome. In this review we summarize the basic features and functions of the crucial regulatory elements promoters, enhancers, and insulators and discuss some of the ways in which proper interactions between these elements is realized. We focus in particular on the role of core promoter sequences and propose explanations for some of the contradictory results seen in experiments aimed at understanding insulator function. We suggest that gene regulation depends on local genomic context and argue that more holistic in vivo investigations that take into account multiple local features will be necessary to understand how genome-wide gene regulation is maintained.

Figure 1

Genomic region showing promoters, enhancers, and insulators. Pictured is a 100 kb fragment of the Drosophila genome (chr2L:12,593,026..12,693,025), based on the FlyBase v.FB2013_04 genome annotation [102]. Transcripts for the genes nub, Ref2, pdm2, and CG15485 are shown along the top of the figure. Each promoter is highlighted with a vertical black dashed arrow. Insulators are depicted by orange dashed lines and enhancers by yellow circles containing upward-pointing arrows; the arrows connote that while the time when enhancers become active is known, how long they remain active generally has not been described. Enhancer names are drawn from the REDfly database [103]. Developmental time is portrayed vertically on the y-axis; not all stages are shown and the axis is not to scale. Blue circles and lines depict gene expression from each promoter based on RNA-seq data provided as part of the genome annotation. Circles represent the onset of expression and lines continued expression, which sometimes must be inferred as it is not always possible to determine from which promoter the later expression originates. Note that of the seven promoters located between the two insulators, only three appear to be co-regulated, potentially by the nub_CE8011 enhancer (red text). Promoter pdm2-RB/RC may be regulated by the pdm2_CE8012 enhancer, but the other nearby transcripts are not expressed at the time when this enhancer becomes active (blue text). Interestingly, enhancer pdm2_CRM6 is active exactly when promoter pdm2-RA is inactive, raising the possibility that it engages in insulator bypass to activate one of the other pdm2 promoters or that its native role is as a negative regulatory element and its classification as an enhancer is due to experimental artifact (green text).

Figure 2

Promoter competition experiments (adapted from [66, 81]). Arrows represent promoters, with key core promoter motifs listed below. Blue boxes represent enhancers, ovals insulators. (A) The enhancer is able to activate a TATA-containing promoter as well as (B) an INR/DPE-containing promoter, when either is the only promoter present in proximity. (C) When both promoters are placed equidistant from the enhancer, only the TATA promoter is activated. (D) Placement of an insulator between the enhancer and TATA promoter blocks activation of this promoter and restores the ability of the enhancer to activate the INR/DPE promoter. (E) A different promoter, which does not contain any known core promoter motifs, does not compete effectively with the TATA promoter and (F) allows it to be activated even in the presence of an intervening insulator. The strength of the activation (degree of insulator bypass) may depend on how strongly the other promoter is able to compete for the enhancer.