Variation in vertebrate cis-regulatory elements in evolution and disease

Abstract

Much of the genetic information that drives animal diversity lies within the vast non-coding regions of the genome. Multi-species sequence conservation in non-coding regions of the genome flags important regulatory elements and more recently, techniques that look for functional signatures predicted for regulatory sequences have added to the identification of thousands more. For some time, biologists have argued that changes in cis-regulatory sequences creates the basic genetic framework for evolutionary change. Recent advances support this notion and show that there is extensive genomic variability in non-coding regulatory elements associated with trait variation, speciation and disease.

Keywords: Non-coding conserved elements; archipelagos; enhancers; evolution; holoenhancers; regulatory mutations.

Figure 1. Composition of long-range acting regulatory landscapes. A-D represent four different organizational types of regulatory elements. (A) depicts the β-globin genes showing the two embryonic (yellow rectangles) and two adult (red rectangles) genes. The hypersensitive sites of the LCR (red ovals) contact either the embryonic or the adult genes and activates at different times during differentiation. (B) depicts the regulatory archipelago that regulates the HoxD cluster of genes during limb bud development. An array of regulatory components represented by the light blue ovals interact to coordinately regulate Hoxd13-d10 by coming into contact with the genes. This regulatory array also activates the bystander genes Evx2 and Lnp. (C) shows the composition of the holo-enhancer for the Fgf8 gene requiring a large number of regulators dispersed throughout neighboring genes. The expression of the neighboring genes are unaffected by the presence of these regulators. Several regulators (green ovals) act together to control expression in the AER and the ectopic expression is filtered to ensure tissue specificity of expression. (D) shows the composition of the Shh regulatory domain. This domain contains single enhancers, such as the ZRS (green oval) that appear to contain most of regulatory information for spatial expression. Other regions of expression such as the gut require the activity of two enhancers (red ovals). In A-D the open rectangles represent the active genes; black and shades of gray represent genes refractory to surrounding enhancer activity.

Figure 2. Evolutionary changes due to innovations in regulatory elements. (A) depicts some of the regulatory changes that have occurred in evolution of the vertebrate appendages. The lines do not represent evolutionary time scales, but depict some of the changes that have occurred between monkey and human, between mouse and bat and that have occurred in the transition from fins in fish to limbs in tetrapods. (B) depicts a change in the H1 enhancer of the Myf gene that may have increased the length of the rib cage in snakes. The length of the rib cage in the mouse is, at least in part, controlled by the Hox genes, with Hoxb6 being rib promoting and Hoxa10 rib suppressing. The loss of Hox10 binding to the Myf H1 promoter may be a crucial step in elongating the rib cage in snakes. Misproduction of HOXB6 in the mouse (even with the point mutation that inhibits protein/DNA binding) phenocopies the rib elongation seen in snakes.