Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain

Jailynn Harke; Jeewon R Lee; Son C Nguyen; Arian Arab; Staci M Rakowiecki; Siewert Hugelier; Christina Paliou; Antonella Rauseo; Rebecca Yunker; Kellen Xu; Yao Yao; Melike Lakadamyali; Guillaume Andrey; Douglas J Epstein; Eric F Joyce

doi:10.1016/j.molcel.2024.10.042

Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain

Mol Cell. 2024 Nov 14:S1097-2765(24)00882-7. doi: 10.1016/j.molcel.2024.10.042. Online ahead of print.

Authors

Affiliations

¹ Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
² Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
³ Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁴ Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁵ Andalusian Center for Developmental Biology (CABD), Spanish National Research Council, Pablo de Olavide University, Andalusian Regional Government, Seville, Spain.
⁶ Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland; Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.
⁷ Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
⁸ Department of Animal and Dairy Science, Regenerative Bioscience Center, University of Georgia, Athens, GA, USA.
⁹ Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Electronic address: epsteind@pennmedicine.upenn.edu.
¹⁰ Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Electronic address: erjoyce@upenn.edu.

PMID: 39579767
DOI: 10.1016/j.molcel.2024.10.042

Abstract

Developmental gene regulation requires input from enhancers spread over large genomic distances. Our understanding of long-range enhancer-promoter (E-P) communication, characterized as loops, remains incomplete without addressing the role of intervening chromatin. Here, we examine the topology of the entire Sonic hedgehog (Shh) regulatory domain in individual alleles from the mouse embryonic forebrain. Through sequential Oligopaint labeling and super-resolution microscopy, we find that the Shh locus maintains a compact structure that adopts several diverse configurations independent of Shh expression. The most frequent configuration contained distal E-P contacts at the expense of those more proximal to Shh, consistent with an interconnected loop. Genetic perturbations demonstrate that this long-range E-P communication operates by Shh-expression-independent and dependent mechanisms, involving CTCF binding sites and active enhancers, respectively. We propose a model whereby gene regulatory elements secure long-range E-P interactions amid an inherent architectural framework to coordinate spatiotemporal patterns of gene expression.

Keywords: 3D genome organization; CTCF; E-P; Shh; allelic configurations; developmental gene regulation; enhancer activity; enhancer-promoter communication; sequential DNA-FISH; super-resolution microscopy.