Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer

Abstract

Enhancers integrate spatiotemporal information to generate precise patterns of gene expression. How complex is the regulatory logic of a typical developmental enhancer, and how important is its internal organization? Here, we examine in detail the structure and function of sparkling, a Notch- and EGFR/MAPK-regulated, cone cell-specific enhancer of the Drosophila Pax2 gene, in vivo. In addition to its 12 previously identified protein-binding sites, sparkling is densely populated with previously unmapped regulatory sequences, which interact in complex ways to control gene expression. One segment is essential for activation at a distance, yet dispensable for other activation functions and for cell type patterning. Unexpectedly, rearranging sparkling's regulatory sites converts it into a robust photoreceptor-specific enhancer. Our results show that a single combination of regulatory inputs can encode multiple outputs, and suggest that the enhancer's organization determines the correct expression pattern by facilitating certain short-range regulatory interactions at the expense of others.

Figure 1. The Known Regulators of spa Are Insufficient for Transcription in Cone Cells

(A) Summary of the known regulatory inputs of the sparkling (spa) cone cell enhancer of dPax2. Defined TF binding sites (TFBSs) are shown as colored bars; uncharacterized sequences are grey. The enhancer is placed 846 bp upstream of the transcription start site in all transgenic constructs, except those in Figure 4. (B–D) Expression of a GFP transgene under the control of spa. (B) Eye-antennal imaginal disc from a spa-GFP transgenic larva. (C) The posterior of an eye disc, corresponding approximately to the boxed area in (B). Posterior is to the top. (D) Eye of a 24-hour pupa carrying spa(wt)-GFP, stained with antibodies against GFP (green) and the cone cell nuclear marker Cut (magenta). (E) spa(synth^NS), in which the previously uncharacterized sequences have been altered (black), but the 12 defined TFBSs are present in their native arrangement and spacing. (F) spa(synth^CS), containing the 12 TFBSs in compressed spacing.

Figure 2. Sequence and/or Spacing Constraints Apply to Multiple Segments of spa

(A) Diagrams of spa enhancer constructs and summary of their cone cell activity in larval eye discs. Dotted lines indicate deletions; black bars indicate mutations that preserve native spacing (NS). In each case, the 12 known TFBSs are preserved. +++, wild-type levels and pattern of expression in cone cells; ++, moderately reduced; +, severely reduced; +/−, detectable in very few cells;−, no detectable expression; ++++, augmented levels of expression. (B–K) GFP expression in eye imaginal discs driven by the wild-type spa enhancer (B) and mutant enhancers (C–K) carrying deletions or NS mutations in previously uncharacterized sequences, numbered 1 through 6.

Figure 3. Most of spa Is Composed of Critical Regulatory Sequences

(A–E) Diagrams of mutated spa enhancer constructs. Blue, yellow and red bars indicate defined binding sites for Lz, Pnt/Yan, and Su(H), respectively. Dotted lines indicate deletions; black bars indicate mutations that preserve native spacing (NS). GFP expression in larval cone cells is summarized as in Figure 2.

Figure 4. Region 1 Is Required for Activation at a Distance, But Not for Patterning

(A–E) Transgenic larval eye discs. In this figure, all enhancers are proximal to the minimal Hsp70 promoter, at position −121 from the transcription start site, compared to −846 in all other figures. Because spa drives stronger expression from a promoter-proximal position, these images were collected at a lower exposure setting than those in other figures.

Figure 5. Cell-Type Specificity of spa Is Controlled by the Arrangement of Its Regulatory Sites

(A–D) GFP expression driven by spa enhancer constructs in larval eye discs. All constructs shown here are placed at −846 bp. (A) spa(wt). (B) spa(KO), in which all 12 Lz/Ets/Su(H) sites are mutated. (C) A rearranged version of spa, in which spa(KO) is placed next to the 12 TFBSs to create spa(KO+synth^CS). (D) spa(KO+synth^NS), in which the TFBSs are placed in their native spacing next to spa(KO). (E and F) spa(KO+synth^CS) is expressed specifically in photoreceptors (PRs), but not in cone cells, in 24-hour pupae. (E) Confocal images at two different planes, in retinas stained with antibodies against GFP (green) and the cone cell nuclear marker Cut (magenta), show GFP in two nuclei per ommatidium, located basally to cone cells. Posterior is to the top. (F) GFP driven by spa(KO+synth^CS) co-localizes with the PR marker Elav (red). (G–J) Organization of regulatory elements within spa is critical for both transcriptional activity and cell-type specificity. (G) Effects of relocating region 1 (the remote control element or RCE), or of scrambling the locations of the known TFBSs, on enhancer function. (H) Rearranging the regulatory sites of spa converts its cell-type specificity. (I) Creation of a minimal synthetic R1/R6-specific element. (J) 2Xsynth^CS and 2Xsynth^NS, both of which contain two copies of all known TFBSs. (K) Region 5 of spa mediates repression in PRs, as well as activation in cone cells.

Figure 6. spa Enhancer Function Is Evolutionarily Conserved, Despite Rapid Sequence Divergence

(A) Alignment of the spa enhancer of D. melanogaster (mel) and orthologous sequences from D. yakuba (yak), D. erecta (ere), D. ananassae (ana), and D. pseudoobscura (pse). Binding sites for Lz, Pnt/Yan, and Su(H), and predicted orthologous sites, are highlighted in color. Regions 1 through 6 are labeled with black bars. TAAT motifs are underlined. Conserved bases are indicated with asterisks. (B) The 409-bp D. pseudoobscura sequence shown in panel A drives robust cone cell-specific gene expression in eye discs of transgenic D. melanogaster from −846 bp. (C) Summary of spa regulation: at least two functionally distinct classes of regulatory sites govern the enhancer activity of spa in vivo. spa requires the presence and proper arrangement of many regulatory sub-elements for its transcriptional activity and cell-type specificity. Region 1 appears to be required for remote enhancer activity, but dispensable for patterning. In addition, proper cell-type patterning of spa in the developing eye is considerably more complex than previously thought, and depends on short-range interactions among many regulatory sites. Green arrows indicate activation mediated by sites within spa; red bars indicate cell-type-specific repression activities. (D) A simple “combinatorial code” model is insufficient to explain the cell type specificity of spa, as the same regulatory elements can be rearranged to generate transcription in either cone cells or photoreceptors. Thus any model describing cone cell-specific transcriptional activation by spa must also incorporate rules of spatial organization.