Multi-enhancer transcriptional hubs confer phenotypic robustness

Abstract

We had previously shown in Drosophila melanogaster embryos that low-affinity Ultrabithorax (Ubx)-responsive shavenbaby (svb) enhancers drive robust expression using localized transcriptional environments and that active svb enhancers tended to colocalize, even when placed on different chromosomes (Tsai et al., 2017). Here, we test the hypothesis that these multi-enhancer “hubs” improve robustness by increasing transcription factor retention near transcription sites. Deleting a redundant enhancer from the svb locus led to reduced trichome numbers in embryos raised at elevated temperatures. Using high-resolution fluorescence microscopy, we observed lower Ubx concentration and transcriptional output in this deletion allele. Transcription sites of the full svb cis-regulatory region inserted into a different chromosome colocalized with the svb locus, increasing Ubx concentration, the transcriptional output of svb, and partially rescuing the phenotype. Thus, multiple enhancers could reinforce a local transcriptional hub to buffer against environmental stresses and genetic perturbations, providing a mechanism for phenotypical robustness. Impact statement Multiple enhancers in physical proximity can reinforce shared transcriptional “hubs” to retain transcription factors, providing a buffer during environmental stresses and genetic perturbations to preserve phenotypic robustness.