An ancient yet flexible cis-regulatory architecture allows localized Hedgehog tuning by patched/Ptch1

Abstract

The Hedgehog signaling pathway is part of the ancient developmental-evolutionary animal toolkit. Frequently co-opted to pattern new structures, the pathway is conserved among eumetazoans yet flexible and pleiotropic in its effects. The Hedgehog receptor, Patched, is transcriptionally activated by Hedgehog, providing essential negative feedback in all tissues. Our locus-wide dissections of the cis-regulatory landscapes of fly patched and mouse Ptch1 reveal abundant, diverse enhancers with stage- and tissue-specific expression patterns. The seemingly simple, constitutive Hedgehog response of patched/Ptch1 is driven by a complex regulatory architecture, with batteries of context-specific enhancers engaged in promoter-specific interactions to tune signaling individually in each tissue, without disturbing patterning elsewhere. This structure—one of the oldest cis-regulatory features discovered in animal genomes—explains how patched/Ptch1 can drive dramatic adaptations in animal morphology while maintaining its essential core function. It may also suggest a general model for the evolutionary flexibility of conserved regulators and pathways.DOI: http://dx.doi.org/10.7554/eLife.13550.001

Complex cis-regulatory landscape of the insulin receptor gene underlies the broad expression of a central signaling regulator

“…6A,C). Interestingly, a recent study of the broadly expressed ptc gene in Drosophila reveals a similar genetic architecture, with large amounts of regulatory DNA devoted to fine-tuning of gene expression via multiple independent elements (Lorberbaum et al, 2016). Our results suggest that the complex regulatory control found for InR might be representative of certain broadly expressed genes that have functions that necessitate complex developmental and physiological inputs, and thus a high degree of regulatory precision.…”

“…These enhancers overlap some of the fragments tested as GAL4 drivers, but there was not a complete agreement between these different methods. The two types of assays relied on distinct basal promoters, which might have biased detection because of enhancerpromoter specificity (Marinićet al, 2013;Zabidi et al, 2015;Lorberbaum et al, 2016).…”

Functional regulatory evolution outside of the minimaleven-skippedstripe 2 enhancer

“…However, in even the earliest studies, it was clear that minimal enhancers are insufficient to define the normal gene expression pattern with complete fidelity [2]. More recently, genomic studies have provided evidence that minimal enhancers are embedded within larger regions containing additional transcription factor binding sites that may be required for normal enhancer function [6,7,8].…”

Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution

“…To test if diverged CNEs significantly overlap regulatory elements active in a particular tissue, we used LOLA and random subsampling as we did for regulatory domains of gene sets (see above). In addition to our ATAC-seq peaks, we obtained a large number of publicly available regulatory datasets 22,33,40,[48][49][50][51][52]86,87,[126][127][128][129][130][131] to get tissue-specific peaks. In short, for each experimental assay, we selected peaks observed in at least two tissue/stage replicates (when available), and obtained tissue-specific peaks by subtracting peaks observed with this assay in other tissues (when available).…”