Transcriptional enhancers in animal development and evolution

Abstract

Regulatory DNAs serve as templates to bring weakly interacting transcription factors into close proximity so they can work synergistically to switch genes on and off in time and space. Most of these regulatory DNAs are enhancers that can work over long distances--a million base pairs or more in mammals--to control gene expression. Critical enhancers are sometimes even found within the introns of neighboring genes. This review summarizes well-defined examples of enhancers controlling key processes in animal development. Potential mechanisms of transcriptional synergy are discussed with regard to enhancer structure and contemporary ChIP-sequencing assays, whereby just a small fraction of the observed binding sites represent bona fide regulatory DNAs. Finally, there is a discussion of how enhancer evolution can produce novelty in animal morphology and of the prospects for reconstructing transitions in animal evolution by introducing derived enhancers in basal ancestors.

Figure 1. Activator synergy

Several nonexclusive mechanisms can be envisioned by which two transcriptional activators augment each other’s function. (A) Activators A and B cooperatively bind to linked sites. (B) A and B coordinately bind a third protein, X, which stabilizes the binding of A and B. (C) A recruits a histone remodeling protein that facilitates the binding of B. (D) A leads to ‘slippage’ of the nucleosome and thereby uncovers the B binding site. Reproduced with permission from [125].

Figure 2. Coordinate recruitment of co-activators at the β-interferon enhanceosome

HMG bends the enhanceosome and facilitates the binding of NF-κB, IRF, and Jun/ATF to linked sites. The three activator complexes form an extended surface for the recruitment of co-activators such as CBP. Reproduced with permission from [125].

Figure 3. Long-range enhancer–promoter interactions

(A) The T1 enhancer bypasses the ftz locus to activate Scr within the Antennapedia gene complex of Drosophila. Reproduced with permission from [58]. (B) The primary enhancer controlling Shh expression in the developing vertebrate limb bud is located within the intron of the Lmbr1 locus (unfilled box), which maps nearly one megabase from the Shh transcription start site. Reproduced with permission from [63].

Figure 4. Overlapping activators define the organizer

(A) Xenopus blastula. Xnrs (Xenopus Nodal-related signaling molecules) and pSmads are expressed in vegetal regions of the embryo. The homeobox gene Siamois is selectively expressed along the presumptive dorsal surface of the embryo. The two activators, pSmads and Siamois, are co-expressed in the region of the presumptive organizer where they activate the expression of the Goosecoid (Gsc) gene. (B) Summary of Gsc regulation in the organizer. The Smads and Siamois interact with Gsc regulatory sequences and activate expression. Reproduced with permission from [125].

Figure 5. Redirecting a conserved enhancer

In Drosophila melanogaster, 3′ enhancers (blue) activate ladybird expression (both the lbl and lbe genes) in the developing cardiac mesoderm. The lbe promoter contains paused Pol II, and has an enhancer blocking activity, preventing the activation of the neighboring C15 gene. In the flour beetle (Tribolium castaneum) the single ladybird gene is inverted relative to the orientation of the C15 locus. As a result the 3′ cardiac enhancer is able to activate C15 expression. Reproduced with permission from [118].

Figure 6. Reconstructing the past

Ancestral stickleback populations contain pelvic fins (A,C). Certain freshwater populations have reduced fins (B; arrowhead). The fins are restored in these populations upon expression of a transgene containing 2.5 kb of the 5′ flanking region of the Pitx1 locus from a population with pelvic fins. This regulatory sequence was attached to the coding region of Pitx1 derived from a population lacking pelvic fins. Expression of this transgene restores the pelvic fins in populations normally lacking them — compare (C) with transgene to (D) lacking the transgene. Reproduced with permission from [122].