Preformed chromatin topology assists transcriptional robustness ofShhduring limb development

• DOI: 10.1073/pnas.1900672116
• Publication Date: 2019-05-31T00:45:16Z
• Authors: Christina Paliou; Philine Guckelberger; Robert Schöpflin; Verena Heinrich; Andrea Esposito; Andrea M. Chiariello; Simona Bianco; Carlo Annunziatella; Johannes Helmuth; Stefan Haas; Ivana Jerković; Norbert Brieske; Lars Wittler; Bernd Timmermann; Mario Nicodemi; Martin Vingron; Stefan Mundlos; Guillaume Andrey
• Keywords: CCCTC-Binding Factor; Transcription, Genetic; Chromosomal Proteins, Non-Histone; Polymer modelling; Down-Regulation; statistical physics; Cell Cycle Proteins; Development; Limb; Mice; 03 medical and health sciences; Genetics; Animals; Hedgehog Proteins; Promoter Regions, Genetic; Cohesins; 0303 health sciences; Binding Sites; Membrane Proteins; Extremities; Polymer modelling; statistical physics; 3D genome; Development; Gene regulation; Genetics; Limb; 3D genome; Chromatin; Gene regulation; Enhancer Elements, Genetic

Long-range gene regulation involves physical proximity between enhancers and promoters to generate precise patterns of gene expression in space and time. However, in some cases, proximity coincides with gene activation, whereas, in others, preformed topologies already exist before activation. In this study, we investigate the preformed configuration underlying the regulation of theShhgene by its unique limb enhancer, theZRS, in vivo during mouse development. Abrogating the constitutive transcription covering theZRSregion led to a shift within theShh–ZRScontacts and a moderate reduction inShhtranscription. Deletion of the CTCF binding sites around theZRSresulted in the loss of theShh–ZRSpreformed interaction and a 50% decrease inShhexpression but no phenotype, suggesting an additional, CTCF-independent mechanism of promoter–enhancer communication. This residual activity, however, was diminished by combining the loss of CTCF binding with a hypomorphicZRSallele, resulting in severeShhloss of function and digit agenesis. Our results indicate that the preformed chromatin structure of theShhlocus is sustained by multiple components and acts to reinforce enhancer–promoter communication for robust transcription.