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Amano T. Gene regulatory landscape of the sonic hedgehog locus in embryonic development. Dev Growth Differ 2020; 62:334-342. [PMID: 32343848 DOI: 10.1111/dgd.12668] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/31/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022]
Abstract
The organs of vertebrate species display a wide variety of morphology. A remaining challenge in evolutionary developmental biology is to elucidate how vertebrate lineages acquire distinct morphological features. Developmental programs are driven by spatiotemporal regulation of gene expression controlled by hundreds of thousands of cis-regulatory elements. Changes in the regulatory elements caused by the introduction of genetic variants can confer regulatory innovation that may underlie morphological novelties. Recent advances in sequencing technology have revealed a number of potential regulatory variants that can alter gene expression patterns. However, a limited number of studies demonstrate causal dependence between genetic and morphological changes. Regulation of Shh expression is a good model to understand how multiple regulatory elements organize tissue-specific gene expression patterns. This model also provides insights into how evolution of molecular traits, such as gene regulatory networks, lead to phenotypic novelty.
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Affiliation(s)
- Takanori Amano
- Next Generation Human Disease Model Team, RIKEN BioResource Research Center, Tsukuba, Japan
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A novel ZRS variant causes preaxial polydactyly type I by increased sonic hedgehog expression in the developing limb bud. Genet Med 2019; 22:189-198. [PMID: 31395945 PMCID: PMC6944640 DOI: 10.1038/s41436-019-0626-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 07/22/2019] [Indexed: 02/06/2023] Open
Abstract
Purpose Preaxial polydactyly (PPD) is a common congenital hand malformation classified into four subtypes (PPD I–IV). Variants in the zone of polarizing activity regulatory sequence (ZRS) within intron 5 of the LMBR1 gene are linked to most PPD types. However, the genes responsible for PPD I and the underlying mechanisms are unknown. Methods A rare large four-generation family with isolated PPD I was subjected to genome-wide genotyping and sequence analysis. In vitro and in vivo functional studies were performed in Caco-2 cells, 293T cells, and a knockin transgenic mouse model. Results A novel g.101779T>A (reference sequence: NG_009240.2; position 446 of the ZRS) variant segregates with all PPD I–affected individuals. The knockin mouse with this ZRS variant exhibited PPD I phenotype accompanying ectopic and excess expression of Shh. We confirmed that HnRNP K can bind the ZRS and SHH promoters. The ZRS mutant enhanced the binding affinity for HnRNP K and upregulated SHH expression. Conclusion Our results identify the first PPD I disease-causing variant. The variant leading to PPD I may be associated with enhancing SHH expression mediated by HnRNP K. This study adds to the ZRS-associated syndromes classification system for PPD and clarifies the underlying molecular mechanisms.
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Paliou C, Guckelberger P, Schöpflin R, Heinrich V, Esposito A, Chiariello AM, Bianco S, Annunziatella C, Helmuth J, Haas S, Jerković I, Brieske N, Wittler L, Timmermann B, Nicodemi M, Vingron M, Mundlos S, Andrey G. Preformed chromatin topology assists transcriptional robustness of Shh during limb development. Proc Natl Acad Sci U S A 2019; 116:12390-12399. [PMID: 31147463 PMCID: PMC6589666 DOI: 10.1073/pnas.1900672116] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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 the Shh gene by its unique limb enhancer, the ZRS, in vivo during mouse development. Abrogating the constitutive transcription covering the ZRS region led to a shift within the Shh-ZRS contacts and a moderate reduction in Shh transcription. Deletion of the CTCF binding sites around the ZRS resulted in the loss of the Shh-ZRS preformed interaction and a 50% decrease in Shh expression 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 hypomorphic ZRS allele, resulting in severe Shh loss of function and digit agenesis. Our results indicate that the preformed chromatin structure of the Shh locus is sustained by multiple components and acts to reinforce enhancer-promoter communication for robust transcription.
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Affiliation(s)
- Christina Paliou
- Research Group Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Philine Guckelberger
- Research Group Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Robert Schöpflin
- Research Group Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Verena Heinrich
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II, 80126 Naples, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
- Berlin Institute of Health (BIH), Max Delbrück Center-Berlin, 13125 Berlin, Germany
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II, 80126 Naples, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II, 80126 Naples, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Carlo Annunziatella
- Dipartimento di Fisica, Università di Napoli Federico II, 80126 Naples, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Johannes Helmuth
- Otto-Warburg-Laboratory: Epigenomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Stefan Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ivana Jerković
- Research Group Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Norbert Brieske
- Research Group Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, 80126 Naples, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
- Berlin Institute of Health (BIH), Max Delbrück Center-Berlin, 13125 Berlin, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Stefan Mundlos
- Research Group Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Guillaume Andrey
- Research Group Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
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