Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts

Abstract

The elucidation of principles governing evolution of gene regulatory sequence is critical to the study of metazoan diversification. We are therefore exploring the structure and organizational constraints of regulatory sequences by studying functionally equivalent cis-regulatory modules (CRMs) that have been evolving in parallel across several loci. Such an independent dataset allows a multi-locus study that is not hampered by nonfunctional or constrained homology. The neurogenic ectoderm enhancers (NEEs) of Drosophila melanogaster are one such class of coordinately regulated CRMs. The NEEs share a common organization of binding sites and as a set would be useful to study the relationship between CRM organization and CRM activity across evolving lineages. We used the D. melanogaster transgenic system to screen for functional adaptations in the NEEs from divergent drosophilid species. We show that the individual NEE modules across a genome in any one lineage have independently evolved adaptations to compensate for lineage-specific developmental and/or genomic changes. Specifically, we show that both the site composition and the site organization of NEEs have been finely tuned by distinct, lineage-specific selection pressures in each of the three divergent species that we have examined: D. melanogaster, D. pseudoobscura, and D. virilis. Furthermore, by precisely altering the organization of NEEs with different morphogen gradient threshold readouts, we show that CRM organizational evolution is sufficient for explaining changes in enhancer activity. Thus, evolution can act on CRM organization to fine-tune morphogen gradient threshold readouts over a wide dynamic range. Our study demonstrates that equivalence classes of CRMs are powerful tools for detecting lineage-specific adaptations by gene regulatory sequences.

Modularity of CHIP/LDB transcription complexes regulates cell differentiation

“…21 these observations suggest that the transcription factors that bind these CrMs may function as part of a yet undefined transcription complex. thus, the location and spacing of the binding sites reflect the positioning of the transcription factors within the transcription complex.…”

The evolution of dorsal–ventral patterning mechanisms in insects

“…Dorsal cooperates with other maternal factorssuch as Zelda, basic helix-loop-helix (bHLH) proteins, and at least one unidentified factor-to achieve the most dorsally extending expression domains (Crocker et al 2008;). In addition, Dorsal cooperates with its ventral targets twist (twi) and snail (sna) to pattern the mesoderm and ventral neurectoderm.…”

Multiple layers of complexity in cis‐regulatory regions of developmental genes

“…Over many years, these analyses have shed light on the logic of cis-regulation (Istrail and Davidson, 2005). Furthermore, they have provided invaluable insights into the structural rules (Erives and Levine, 2004;Panne et al, 2007;Swanson et al, 2010) and evolutionary histories (Ludwig and Kreitman, 1995;Crocker et al, 2008) of enhancers. Nevertheless, it is widely recognized in the cis-regulation community that, often, small enhancer elements do not faithfully recapitulate native expression patterns (Barolo, 2012).…”