The Role of Insulators in Genome Organization and Gene Expression

Abstract

Transcription of eukaryotic genomes is regulated by enhancer and silencer input at a gene promoter. These regulatory elements act over large distances and demonstrate limited target specificity, suggesting that constraints exist to increase specificity. Insulators are deoxyribonucleic acid (DNA) elements that limit enhancer and silencer action, establishing independent transcriptional domains. Eukaryotic genomes contain a variety of widely distributed insulators. The best characterized are the Drosophila Su(Hw)‐dependent insulators and the vertebrate CCCTC‐binding factor (CTCF)‐dependent insulators. Emerging evidence suggests that insulators are not impassable barriers, but are active players in many nuclear functions. Insulator action depends on the organization and properties of local enhancers, promoters and insulators. Two models describing insulator action include (1) formation of independent structural domains that have a global impact on transcription and (2) direct participation in transcriptional regulation that confers specificity to regulatory interactions. Further studies of insulators will provide a richer understanding of transcriptional regulation in eukaryotes.

Keywords: insulators; suppressor of hairy‐wing; CTCF; transcription regulation; genome organization

Figure 1.

Insulator effectiveness is altered by local insulators, enhancers and promoters. (a) An insulator (black inverted triangle) located upstream of an enhancer (circle marked E) and gene promoter (white rectangle with arrow) has no effect on enhancer‐activated transcription. Two insulators, flanking an enhancer, block enhancer‐activated transcription. Two insulators, located between the enhancer and promoter, permit insulator pairing and allow enhancer‐activated transcription. Three insulators placed between the enhancer and promoter restores the enhancer block. The (+) and (−) symbols refer to the level of enhancer‐activated transcription. (b) The shared enhancer (black circle marked E) is located between a gene with a weak promoter (white rectangle with thin bent arrow) and a gene with a strong promoter (black rectangle with bold bent arrow). The amount of enhancer‐activated transcription from each promoter is designated on either side. (I) The level of enhancer‐activated transcription is determined by promoter strength. (II) An insulator placed between the enhancer and weak promoter blocks enhancer‐activated transcription of the weak promoter, with no effect on the strong promoter. (III) A strong promoter overcomes the enhancer block when the insulator is placed between the enhancer–promoter pair. (IV) Increasing the strength of the adjacent promoter improves the effectiveness of the insulator block. (V) Increasing enhancer strength (larger circle marked E) overcomes an insulator block of the weak promoter.

Figure 2.

The endogenous 1A‐2 locus. 1A‐2 is located between yellow (yellow rectangles) and the downstream yellow‐achaete intergenic RNA (yar) gene (blue rectangles). 1A‐2 is bound by Su(Hw) protein (red octagon). The yellow gene is controlled by four tissue‐specific enhancers (ovals marked W for wing, B for body, Br for bristle and Tc for tarsal claw). The yellow2 allele contains an insertion of the gypsy retrotransposon (raised white inverted triangle) that blocks the upstream wing and body enhancers. The gypsy retrotransposon is flanked by long‐terminal repeats (LTRs; grey rectangles with black arrows) and contains a Su(Hw)‐binding region in the 5′ UTR. The region removed in Δ1A‐2 flies is shown by the brackets.

Figure 3.

The chicken β‐globin locus. It contains four globin genes (ρ, βH, βA and ɛ, yellow rectangles), an enhancer (β/ɛ, yellow circle) and the upstream LCR (arrows). The LCR contains four DNase I hypersensitive sites (DHS; arrows), the fourth constitutive site is 5′HS4 (blue arrow). 5′HS4 is comprised of binding sites for CTCF and USF. The 3′ boundary of the locus is marked by a DHS, 3′HS1 (red arrow). The β‐globin locus is flanked upstream by a 16‐kb region of condensed chromatin (grey ovals) and the folate receptor gene (FR, white rectangle), and downstream by the odorant receptor gene (OR, black rectangle).

Figure 4.

The imprinted mammalian insulin‐like growth factor2 (Igf2)/H19 locus. (a) The differentially methylated domain (DMD; inverted white triangle) is located in the intergenic region between Igf2 (white rectangle) and H19 (blue rectangle). Expression of Igf2 and H19 is controlled by shared downstream enhancers (black ovals). The DMD contains four CTCF‐binding sites (black rectangles) that are bound on the maternally inherited chromosome, blocking activation of Igf2 and while directing enhancers to H19. (b) On the paternally inherited chromosome, methylation (black circles) prevents CTCF binding to the DMD and silences the H19 promoter, allowing enhancer activation of Igf2. (c) Deletion of the DMD results in bi‐allelic expression of Igf2 and H19.

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Baxley, Ryan M, and Geyer, Pamela K(Sep 2009) The Role of Insulators in Genome Organization and Gene Expression. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001157.pub2]