Multi-enhancer transcriptional hubs confer phenotypic robustness

Abstract

We previously showed in Drosophila melanogaster embryos that low-affinity Ultrabithorax (Ubx)-responsive shavenbaby (svb) enhancers drive expression using localized transcriptional environments and that active svb enhancers on different chromosomes tended to colocalize (Tsai et al., 2017). Here, we test the hypothesis that these multi-enhancer ‘hubs’ improve phenotypic resilience to stress by buffering against decreases in transcription factor concentrations and transcriptional output. 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.

Decoding the Notch signal

“…In agreement with this model, several TFs (Bicoid [Mir et al, 2017[Mir et al, , 2018, Dorsal [Yamada et al, 2019], Zelda [Dufourt et al, 2018;Mir et al, 2018] and Ultrabithorax [Tsai, Alves, & Crocker, 2019;Tsai et al, 2017]) are present in foci or "hubs" in the nucleus. interact with nascent sites of transcription, suggesting a "hit and run" mechanism for initiating transcription (Mir et al, 2018), rather than a model where TFs become integrated with stable PolII/Med clusters.…”

“…This "bursty" transcription has been formalized as a two state model of a promoter's activity, which cycles between ON and OFF states with stochastic rate constants (Larson, Singer, & Zenklusen, 2009;Peccoud & Ycart, 1995 The formation of PolII clusters or aggregates is thought to be driven by weak interactions between intrinsically disordered regions/low complexity domains (LCD) in PolII and other proteins (Boehning et al, 2018;Cho et al, 2018;Lu et al, 2018). Similarly, many TFs In agreement with this model, several TFs (Bicoid [Mir et al, 2017[Mir et al, , 2018, Dorsal [Yamada et al, 2019], Zelda [Dufourt et al, 2018;Mir et al, 2018] and Ultrabithorax [Tsai, Alves, & Crocker, 2019;Tsai et al, 2017]) are present in foci or "hubs" in the nucleus. Similarly, many TFs In agreement with this model, several TFs (Bicoid [Mir et al, 2017[Mir et al, , 2018, Dorsal [Yamada et al, 2019], Zelda [Dufourt et al, 2018;Mir et al, 2018] and Ultrabithorax [Tsai, Alves, & Crocker, 2019;Tsai et al, 2017]) are present in foci or "hubs" in the nucleus.…”

Precision of tissue patterning is controlled by dynamical properties of gene regulatory networks

“…How is noise buffered in developing tissues to ensure that developmental signals generate precise and reproducible patterns of gene expression? For individual genes, the activity of redundant regulatory elements (so-called shadow enhancers), the three-dimensional architecture of the genome, the presence of multiple alleles, and the effect of RNA processing, have all been proposed to buffer fluctuations and increase the robustness of gene expression ( Perry et al, 2010 ; Frankel et al, 2010 ; Lagha et al, 2012 ; Little et al, 2013 ; Battich et al, 2015 ; Cannavò et al, 2016 ; Dickel et al, 2018 ; Osterwalder et al, 2018 ; Paliou et al, 2019 ; Tsai et al, 2019 ). At the level of the tissue, mechanisms that regulate the shape, steepness or variance of gradients have been explored and their effect on the precision of gene expression detailed ( Bollenbach et al, 2008 ; Sokolowski et al, 2012 ; Tkačik et al, 2015 ; Zagorski et al, 2017 ; Lucas et al, 2018 ).…”

Transcriptional Enhancers inDrosophila

“…Significantly, while such mutations provide the most physiologically relevant information, there is a strong possibility of false-negative results because of enhancer redundancy. For instance, mutations of the complex enhancers regulating shaven-baby cause phenotypic changes only when assayed in specific genetic backgrounds, or in heat-stressed conditions (Tsai et al 2019). Also, genomic perturbations may impact gene expression in unexpected ways.…”

“…In the Drosophila embryo, such membraneless compartments may potentiate the recruitment of primary patterning proteins Bcd and Dl by the Zld pioneer factor (Mir et al 2018;Yamada et al 2019). These compartments may underlie local subnuclear concentrations of TFs that appear to attract or at least activate enhancers containing TF binding sites of low or high affinity (Tsai et al 2017(Tsai et al , 2019.…”