Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder

Hannah K Long; Marco Osterwalder; Ian C Welsh; Karissa Hansen; James O J Davies; Yiran E Liu; Mervenaz Koska; Alexander T Adams; Robert Aho; Neha Arora; Kazuya Ikeda; Ruth M Williams; Tatjana Sauka-Spengler; Matthew H Porteus; Tim Mohun; Diane E Dickel; Tomek Swigut; Jim R Hughes; Douglas R Higgs; Axel Visel; Licia Selleri; Joanna Wysocka

doi:10.1016/j.stem.2020.09.001

Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder

Cell Stem Cell. 2020 Nov 5;27(5):765-783.e14. doi: 10.1016/j.stem.2020.09.001. Epub 2020 Sep 28.

Authors

Hannah K Long¹, Marco Osterwalder², Ian C Welsh³, Karissa Hansen³, James O J Davies⁴, Yiran E Liu⁵, Mervenaz Koska⁶, Alexander T Adams⁷, Robert Aho³, Neha Arora⁸, Kazuya Ikeda⁹, Ruth M Williams¹⁰, Tatjana Sauka-Spengler¹⁰, Matthew H Porteus⁹, Tim Mohun¹¹, Diane E Dickel², Tomek Swigut⁸, Jim R Hughes⁴, Douglas R Higgs¹², Axel Visel¹³, Licia Selleri³, Joanna Wysocka¹⁴

Affiliations

¹ Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
² Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
³ Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
⁴ MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
⁵ Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁶ Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁷ Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.
⁸ Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁹ Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
¹⁰ MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
¹¹ The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
¹² MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
¹³ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA.
¹⁴ Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: wysocka@stanford.edu.

Abstract

Non-coding mutations at the far end of a large gene desert surrounding the SOX9 gene result in a human craniofacial disorder called Pierre Robin sequence (PRS). Leveraging a human stem cell differentiation model, we identify two clusters of enhancers within the PRS-associated region that regulate SOX9 expression during a restricted window of facial progenitor development at distances up to 1.45 Mb. Enhancers within the 1.45 Mb cluster exhibit highly synergistic activity that is dependent on the Coordinator motif. Using mouse models, we demonstrate that PRS phenotypic specificity arises from the convergence of two mechanisms: confinement of Sox9 dosage perturbation to developing facial structures through context-specific enhancer activity and heightened sensitivity of the lower jaw to Sox9 expression reduction. Overall, we characterize the longest-range human enhancers involved in congenital malformations, directly demonstrate that PRS is an enhanceropathy, and illustrate how small changes in gene expression can lead to morphological variation.

Keywords: Pierre Robin sequence; SOX9; craniofacial; enhancer; enhanceropathy; gene dosage; long-range regulation; neural crest; non-coding mutation; transcription.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Cell Differentiation
Humans
Mutation / genetics
Neural Crest*
Pierre Robin Syndrome*
Regulatory Sequences, Nucleic Acid
SOX9 Transcription Factor / genetics

Substances

SOX9 Transcription Factor

Abstract

Publication types

MeSH terms

Substances

Grants and funding