Enhancer Poising Enables Pathogenic Gene Activation by Noncoding Variants [RNA-seq]

Single nucleotide variants within enhancers—non-coding DNA elements that regulate transcription—often lead to aberrant gene activation and contribute to a wide range of genetic disorders (Claussnitzer et al. 2015; Doan et al. 2016; Turner et al. 2017; Yanchus et al. 2022; Lettice et al. 2008). The mechanism by which ectopic gene activation occurs through these gain-of-function enhancer mutations remains poorly understood. Using the ZRS, a benchmark disease-associated enhancer of Sonic hedgehog (Shh), as a model, we demonstrate that poised (i.e., accessible but inactive) chromatin sensitizes Shh to aberrant activation in anterior limb bud, leading to polydactyly. In the anterior limb cells of wild-type mice, Shh is inactive, but the ZRS is accessible and marked by enhancer-associated histone modifications. We demonstrate that this poising signature explains how over 20 independent rare variants within the ZRS cause Shh misexpression in the same anterior limb bud cell population, resulting in similar limb malformations, despite affecting binding sites for different activators and repressors. Disabling pioneer transcription factor binding to the ZRS suppresses its poised state in anterior cells, prevents aberrant activation of the ZRS by rare variants, and fully rescues limb malformations in variant knock-in mice. A thorough examination of other disease-associated enhancers with pathogenic gain-of-function variants revealed that they are all poised in tissues with ectopic activity. We use this poising signature to predict and validate in vivo ectopic forebrain activity of previously uncharacterized autism-associated non-coding variants. Our findings suggest that spatial enhancer poising, likely a byproduct of development, leads to susceptibility to non-coding mutations offering a potential mechanistic explanation for the burden of disease-associated non-coding variants. Overall design: Purified populations of anterior (mCherry+) and central (mCherry-) hindlimb cells were obtained from H11^hZRS404G>A-mCherry transgenic reporter mice at embryonic day 11.5. Each tissue domain was dissected, dissociated into single cells, and then fluorescently sorted. Sorted cells were snap-frozen before being processed for total RNA extraction. cDNA libraries were generated and sequencing was performed by Novogene at a median depth of 25M reads.