1
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Hall HN, Parry D, Halachev M, Williamson KA, Donnelly K, Campos Parada J, Bhatia S, Joseph J, Holden S, Prescott TE, Bitoun P, Kirk EP, Newbury-Ecob R, Lachlan K, Bernar J, van Heyningen V, FitzPatrick DR, Meynert A. Short-read whole genome sequencing identifies causative variants in most individuals with previously unexplained aniridia. J Med Genet 2024; 61:250-261. [PMID: 38050128 PMCID: PMC7615962 DOI: 10.1136/jmg-2023-109181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 09/25/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Classic aniridia is a highly penetrant autosomal dominant disorder characterised by congenital absence of the iris, foveal hypoplasia, optic disc anomalies and progressive opacification of the cornea. >90% of cases of classic aniridia are caused by heterozygous, loss-of-function variants affecting the PAX6 locus. METHODS Short-read whole genome sequencing was performed on 51 (39 affected) individuals from 37 different families who had screened negative for mutations in the PAX6 coding region. RESULTS Likely causative mutations were identified in 22 out of 37 (59%) families. In 19 out of 22 families, the causative genomic changes have an interpretable deleterious impact on the PAX6 locus. Of these 19 families, 1 has a novel heterozygous PAX6 frameshift variant missed on previous screens, 4 have single nucleotide variants (SNVs) (one novel) affecting essential splice sites of PAX6 5' non-coding exons and 2 have deep intronic SNV (one novel) resulting in gain of a donor splice site. In 12 out of 19, the causative variants are large-scale structural variants; 5 have partial or whole gene deletions of PAX6, 3 have deletions encompassing critical PAX6 cis-regulatory elements, 2 have balanced inversions with disruptive breakpoints within the PAX6 locus and 2 have complex rearrangements disrupting PAX6. The remaining 3 of 22 families have deletions encompassing FOXC1 (a known cause of atypical aniridia). Seven of the causative variants occurred de novo and one cosegregated with familial aniridia. We were unable to establish inheritance status in the remaining probands. No plausibly causative SNVs were identified in PAX6 cis-regulatory elements. CONCLUSION Whole genome sequencing proves to be an effective diagnostic test in most individuals with previously unexplained aniridia.
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Affiliation(s)
- Hildegard Nikki Hall
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - David Parry
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
- Illumina United Kingdom, Edinburgh, UK
| | - Mihail Halachev
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Kathleen A Williamson
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Kevin Donnelly
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Jose Campos Parada
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Shipra Bhatia
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Jeffrey Joseph
- MRC Human Genetics Unit, The University of Edinburgh, Edinburgh, UK
| | - Simon Holden
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Trine E Prescott
- Department of Medical Genetics, Telemark Hospital, Skien, Norway
| | - Pierre Bitoun
- Consultations de Génétique médicale, Service de Pédiatrie, CHU Paris-Nord, Hôpital Jean Verdier, Bondy, France
| | - Edwin P Kirk
- Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Katherine Lachlan
- University Hospital Southampton, NHS Foundation Trust Wessex Clinical Genetics Service, Southampton, UK
| | - Juan Bernar
- Department of Genetics, Hospital Ruber Internacional, Madrid, Spain
| | - Veronica van Heyningen
- MRC Human Genetics Unit, The University of Edinburgh, Edinburgh, UK
- Institute of Ophthalmology, University College London, London, UK
| | - David R FitzPatrick
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Alison Meynert
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
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2
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Hollingsworth EW, Liu TA, Jacinto SH, Chen CX, Alcantara JA, Kvon EZ. Rapid and Quantitative Functional Interrogation of Human Enhancer Variant Activity in Live Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570890. [PMID: 38105996 PMCID: PMC10723448 DOI: 10.1101/2023.12.10.570890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Functional analysis of non-coding variants associated with human congenital disorders remains challenging due to the lack of efficient in vivo models. Here we introduce dual-enSERT, a robust Cas9-based two-color fluorescent reporter system which enables rapid, quantitative comparison of enhancer allele activities in live mice of any genetic background. We use this new technology to examine and measure the gain- and loss-of-function effects of enhancer variants linked to limb polydactyly, autism, and craniofacial malformation. By combining dual-enSERT with single-cell transcriptomics, we characterize variant enhancer alleles at cellular resolution, thereby implicating candidate molecular pathways in pathogenic enhancer misregulation. We further show that independent, polydactyly-linked enhancer variants lead to ectopic expression in the same cell populations, indicating shared genetic mechanisms underlying non-coding variant pathogenesis. Finally, we streamline dual-enSERT for analysis in F0 animals by placing both reporters on the same transgene separated by a synthetic insulator. Dual-enSERT allows researchers to go from identifying candidate enhancer variants to analysis of comparative enhancer activity in live embryos in under two weeks.
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Affiliation(s)
- Ethan W. Hollingsworth
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
- Medical Scientist Training Program, University of California, Irvine School of Medicine, Irvine, CA 92697, USA
| | - Taryn A. Liu
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Sandra H. Jacinto
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Cindy X. Chen
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Joshua A. Alcantara
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Evgeny Z. Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
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3
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Jimenez Gonzalez A, Baranasic D, Müller F. Zebrafish regulatory genomic resources for disease modelling and regeneration. Dis Model Mech 2023; 16:dmm050280. [PMID: 37529920 PMCID: PMC10417509 DOI: 10.1242/dmm.050280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
In the past decades, the zebrafish has become a disease model with increasing popularity owing to its advantages that include fast development, easy genetic manipulation, simplicity for imaging, and sharing conserved disease-associated genes and pathways with those of human. In parallel, studies of disease mechanisms are increasingly focusing on non-coding mutations, which require genome annotation maps of regulatory elements, such as enhancers and promoters. In line with this, genomic resources for zebrafish research are expanding, producing a variety of genomic data that help in defining regulatory elements and their conservation between zebrafish and humans. Here, we discuss recent developments in generating functional annotation maps for regulatory elements of the zebrafish genome and how this can be applied to human diseases. We highlight community-driven developments, such as DANIO-CODE, in generating a centralised and standardised catalogue of zebrafish genomics data and functional annotations; consider the advantages and limitations of current annotation maps; and offer considerations for interpreting and integrating existing maps with comparative genomics tools. We also discuss the need for developing standardised genomics protocols and bioinformatic pipelines and provide suggestions for the development of analysis and visualisation tools that will integrate various multiomic bulk sequencing data together with fast-expanding data on single-cell methods, such as single-cell assay for transposase-accessible chromatin with sequencing. Such integration tools are essential to exploit the multiomic chromatin characterisation offered by bulk genomics together with the cell-type resolution offered by emerging single-cell methods. Together, these advances will build an expansive toolkit for interrogating the mechanisms of human disease in zebrafish.
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Affiliation(s)
- Ada Jimenez Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Damir Baranasic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London SW7 2AZ, UK
- MRC London Institute of Medical Sciences, London W12 0NN, UK
- Division of Electronics, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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4
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van Heyningen V. A Journey Through Genetics to Biology. Annu Rev Genomics Hum Genet 2022; 23:1-27. [PMID: 35567277 DOI: 10.1146/annurev-genom-010622-095109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although my engagement with human genetics emerged gradually, and sometimes serendipitously, it has held me spellbound for decades. Without my teachers, students, postdocs, colleagues, and collaborators, I would not be writing this review of my scientific adventures. Early gene and disease mapping was a satisfying puzzle-solving exercise, but building biological insight was my main goal. The project trajectory was hugely influenced by the evolutionarily conserved nature of the implicated genes and by the pace of progress in genetic technologies. The rich detail of clinical observations, particularly in eye disease, makes humans an excellent model, especially when complemented by the use of multiple other animal species for experimental validation. The contributions of collaborators and rivals also influenced our approach. We are very fortunate to work in this era of unprecedented progress in genetics and genomics. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Veronica van Heyningen
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom;
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5
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Functional Validation of Osteoporosis Genetic Findings Using Small Fish Models. Genes (Basel) 2022; 13:genes13020279. [PMID: 35205324 PMCID: PMC8872034 DOI: 10.3390/genes13020279] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/11/2022] Open
Abstract
The advancement of human genomics has revolutionized our understanding of the genetic architecture of many skeletal diseases, including osteoporosis. However, interpreting results from human association studies remains a challenge, since index variants often reside in non-coding regions of the genome and do not possess an obvious regulatory function. To bridge the gap between genetic association and causality, a systematic functional investigation is necessary, such as the one offered by animal models. These models enable us to identify causal mechanisms, clarify the underlying biology, and apply interventions. Over the past several decades, small teleost fishes, mostly zebrafish and medaka, have emerged as powerful systems for modeling the genetics of human diseases. Due to their amenability to genetic intervention and the highly conserved genetic and physiological features, fish have become indispensable for skeletal genomic studies. The goal of this review is to summarize the evidence supporting the utility of Zebrafish (Danio rerio) for accelerating our understanding of human skeletal genomics and outlining the remaining gaps in knowledge. We provide an overview of zebrafish skeletal morphophysiology and gene homology, shedding light on the advantages of human skeletal genomic exploration and validation. Knowledge of the biology underlying osteoporosis through animal models will lead to the translation into new, better and more effective therapeutic approaches.
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6
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Shimai K, Veeman M. Quantitative Dissection of the Proximal Ciona brachyury Enhancer. Front Cell Dev Biol 2022; 9:804032. [PMID: 35127721 PMCID: PMC8814421 DOI: 10.3389/fcell.2021.804032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
A major goal in biology is to understand the rules by which cis-regulatory sequences control spatially and temporally precise expression patterns. Here we present a systematic dissection of the proximal enhancer for the notochord-specific transcription factor brachyury in the ascidian chordate Ciona. The study uses a quantitative image-based reporter assay that incorporates a dual-reporter strategy to control for variable electroporation efficiency. We identified and mutated multiple predicted transcription factor binding sites of interest based on statistical matches to the JASPAR binding motif database. Most sites (Zic, Ets, FoxA, RBPJ) were selected based on prior knowledge of cell fate specification in both the primary and secondary notochord. We also mutated predicted Brachyury sites to investigate potential autoregulation as well as Fos/Jun (AP1) sites that had very strong matches to JASPAR. Our goal was to quantitatively define the relative importance of these different sites, to explore the importance of predicted high-affinity versus low-affinity motifs, and to attempt to design mutant enhancers that were specifically expressed in only the primary or secondary notochord lineages. We found that the mutation of all predicted high-affinity sites for Zic, FoxA or Ets led to quantifiably distinct effects. The FoxA construct caused a severe loss of reporter expression whereas the Ets construct had little effect. A strong Ets phenotype was only seen when much lower-scoring binding sites were also mutated. This supports the enhancer suboptimization hypothesis proposed by Farley and Levine but suggests that it may only apply to some but not all transcription factor families. We quantified reporter expression separately in the two notochord lineages with the expectation that Ets mutations and RBPJ mutations would have distinct effects given that primary notochord is induced by Ets-mediated FGF signaling whereas secondary notochord is induced by RBPJ/Su(H)-mediated Notch/Delta signaling. We found, however, that ETS mutations affected primary and secondary notochord expression relatively equally and that RBPJ mutations were only moderately more severe in their effect on secondary versus primary notochord. Our results point to the promise of quantitative reporter assays for understanding cis-regulatory logic but also highlight the challenge of arbitrary statistical thresholds for predicting potentially important sites.
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7
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Rauner M, Foessl I, Formosa MM, Kague E, Prijatelj V, Lopez NA, Banerjee B, Bergen D, Busse B, Calado Â, Douni E, Gabet Y, Giralt NG, Grinberg D, Lovsin NM, Solan XN, Ostanek B, Pavlos NJ, Rivadeneira F, Soldatovic I, van de Peppel J, van der Eerden B, van Hul W, Balcells S, Marc J, Reppe S, Søe K, Karasik D. Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques. Front Endocrinol (Lausanne) 2021; 12:731217. [PMID: 34938269 PMCID: PMC8686830 DOI: 10.3389/fendo.2021.731217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022] Open
Abstract
The availability of large human datasets for genome-wide association studies (GWAS) and the advancement of sequencing technologies have boosted the identification of genetic variants in complex and rare diseases in the skeletal field. Yet, interpreting results from human association studies remains a challenge. To bridge the gap between genetic association and causality, a systematic functional investigation is necessary. Multiple unknowns exist for putative causal genes, including cellular localization of the molecular function. Intermediate traits ("endophenotypes"), e.g. molecular quantitative trait loci (molQTLs), are needed to identify mechanisms of underlying associations. Furthermore, index variants often reside in non-coding regions of the genome, therefore challenging for interpretation. Knowledge of non-coding variance (e.g. ncRNAs), repetitive sequences, and regulatory interactions between enhancers and their target genes is central for understanding causal genes in skeletal conditions. Animal models with deep skeletal phenotyping and cell culture models have already facilitated fine mapping of some association signals, elucidated gene mechanisms, and revealed disease-relevant biology. However, to accelerate research towards bridging the current gap between association and causality in skeletal diseases, alternative in vivo platforms need to be used and developed in parallel with the current -omics and traditional in vivo resources. Therefore, we argue that as a field we need to establish resource-sharing standards to collectively address complex research questions. These standards will promote data integration from various -omics technologies and functional dissection of human complex traits. In this mission statement, we review the current available resources and as a group propose a consensus to facilitate resource sharing using existing and future resources. Such coordination efforts will maximize the acquisition of knowledge from different approaches and thus reduce redundancy and duplication of resources. These measures will help to understand the pathogenesis of osteoporosis and other skeletal diseases towards defining new and more efficient therapeutic targets.
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Affiliation(s)
- Martina Rauner
- Department of Medicine III, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
- University Hospital Carl Gustav Carus, Dresden, Germany
| | - Ines Foessl
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Endocrine Lab Platform, Medical University of Graz, Graz, Austria
| | - Melissa M. Formosa
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Erika Kague
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Vid Prijatelj
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- The Generation R Study, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Nerea Alonso Lopez
- Rheumatology and Bone Disease Unit, CGEM, Institute of Genetics and Cancer (IGC), Edinburgh, United Kingdom
| | - Bodhisattwa Banerjee
- Musculoskeletal Genetics Laboratory, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Dylan Bergen
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Björn Busse
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ângelo Calado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | - Eleni Douni
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
- Institute for Bioinnovation, B.S.R.C. “Alexander Fleming”, Vari, Greece
| | - Yankel Gabet
- Department of Anatomy & Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Natalia García Giralt
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Nika M. Lovsin
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Xavier Nogues Solan
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Barbara Ostanek
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Nathan J. Pavlos
- Bone Biology & Disease Laboratory, School of Biomedical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | | | - Ivan Soldatovic
- Institute of Medical Statistics and Informatic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jeroen van de Peppel
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Bram van der Eerden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Wim van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Janja Marc
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Sjur Reppe
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Kent Søe
- Clinical Cell Biology, Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Israel
- Marcus Research Institute, Hebrew SeniorLife, Boston, MA, United States
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8
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Bhatia S, Kleinjan DJ, Uttley K, Mann A, Dellepiane N, Bickmore WA. Quantitative spatial and temporal assessment of regulatory element activity in zebrafish. eLife 2021; 10:65601. [PMID: 34796872 PMCID: PMC8604437 DOI: 10.7554/elife.65601] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Mutations or genetic variation in noncoding regions of the genome harbouring cis-regulatory elements (CREs), or enhancers, have been widely implicated in human disease and disease risk. However, our ability to assay the impact of these DNA sequence changes on enhancer activity is currently very limited because of the need to assay these elements in an appropriate biological context. Here, we describe a method for simultaneous quantitative assessment of the spatial and temporal activity of wild-type and disease-associated mutant human CRE alleles using live imaging in zebrafish embryonic development. We generated transgenic lines harbouring a dual-CRE dual-reporter cassette in a pre-defined neutral docking site in the zebrafish genome. The activity of each CRE allele is reported via expression of a specific fluorescent reporter, allowing simultaneous visualisation of where and when in development the wild-type allele is active and how this activity is altered by mutation.
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Affiliation(s)
- Shipra Bhatia
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Dirk Jan Kleinjan
- Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Kirsty Uttley
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Anita Mann
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Nefeli Dellepiane
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
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9
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Bengani H, Grozeva D, Moyon L, Bhatia S, Louros SR, Hope J, Jackson A, Prendergast JG, Owen LJ, Naville M, Rainger J, Grimes G, Halachev M, Murphy LC, Spasic-Boskovic O, van Heyningen V, Kind P, Abbott CM, Osterweil E, Raymond FL, Roest Crollius H, FitzPatrick DR. Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability. PLoS One 2021; 16:e0256181. [PMID: 34388204 PMCID: PMC8362966 DOI: 10.1371/journal.pone.0256181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/01/2021] [Indexed: 11/18/2022] Open
Abstract
Identifying causative variants in cis-regulatory elements (CRE) in neurodevelopmental disorders has proven challenging. We have used in vivo functional analyses to categorize rigorously filtered CRE variants in a clinical cohort that is plausibly enriched for causative CRE mutations: 48 unrelated males with a family history consistent with X-linked intellectual disability (XLID) in whom no detectable cause could be identified in the coding regions of the X chromosome (chrX). Targeted sequencing of all chrX CRE identified six rare variants in five affected individuals that altered conserved bases in CRE targeting known XLID genes and segregated appropriately in families. Two of these variants, FMR1CRE and TENM1CRE, showed consistent site- and stage-specific differences of enhancer function in the developing zebrafish brain using dual-color fluorescent reporter assay. Mouse models were created for both variants. In male mice Fmr1CRE induced alterations in neurodevelopmental Fmr1 expression, olfactory behavior and neurophysiological indicators of FMRP function. The absence of another likely causative variant on whole genome sequencing further supported FMR1CRE as the likely basis of the XLID in this family. Tenm1CRE mice showed no phenotypic anomalies. Following the release of gnomAD 2.1, reanalysis showed that TENM1CRE exceeded the maximum plausible population frequency of a XLID causative allele. Assigning causative status to any ultra-rare CRE variant remains problematic and requires disease-relevant in vivo functional data from multiple sources. The sequential and bespoke nature of such analyses renders them time-consuming and challenging to scale for routine clinical use.
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Affiliation(s)
- Hemant Bengani
- MRC Human Genetics Unit, IGMM, University of Edinburgh (UoE), Edinburgh, United Kingdom
| | - Detelina Grozeva
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Institute of Psychological Medicine & Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Lambert Moyon
- Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France
| | - Shipra Bhatia
- MRC Human Genetics Unit, IGMM, University of Edinburgh (UoE), Edinburgh, United Kingdom
| | - Susana R. Louros
- Centre for Discovery Brain Sciences, Patrick Wild Centre, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
| | - Jilly Hope
- Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Adam Jackson
- Centre for Discovery Brain Sciences, Patrick Wild Centre, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Liusaidh J. Owen
- MRC Human Genetics Unit, IGMM, University of Edinburgh (UoE), Edinburgh, United Kingdom
| | - Magali Naville
- Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France
| | - Jacqueline Rainger
- MRC Human Genetics Unit, IGMM, University of Edinburgh (UoE), Edinburgh, United Kingdom
| | - Graeme Grimes
- Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Mihail Halachev
- Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura C. Murphy
- Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Olivera Spasic-Boskovic
- East Midlands and East of England NHS Genomic Laboratory Hub, Molecular Genetics, Adden brooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust Cambridge, Cambridge, United Kingdom
| | | | - Peter Kind
- Centre for Discovery Brain Sciences, Patrick Wild Centre, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
| | - Catherine M. Abbott
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Emily Osterweil
- Centre for Discovery Brain Sciences, Patrick Wild Centre, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
| | - F. Lucy Raymond
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | | | - David R. FitzPatrick
- MRC Human Genetics Unit, IGMM, University of Edinburgh (UoE), Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
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10
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Lampreys, the jawless vertebrates, contain three Pax6 genes with distinct expression in eye, brain and pancreas. Sci Rep 2019; 9:19559. [PMID: 31863055 PMCID: PMC6925180 DOI: 10.1038/s41598-019-56085-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 12/02/2019] [Indexed: 12/22/2022] Open
Abstract
The transcription factor Pax6 is crucial for the development of the central nervous system, eye, olfactory system and pancreas, and is implicated in human disease. While a single Pax6 gene exists in human and chicken, Pax6 occurs as a gene family in other vertebrates, with two members in elephant shark, Xenopus tropicalis and Anolis lizard and three members in teleost fish such as stickleback and medaka. However, the complement of Pax6 genes in jawless vertebrates (cyclostomes), the sister group of jawed vertebrates (gnathostomes), is unknown. Using a combination of BAC sequencing and genome analysis, we discovered three Pax6 genes in lampreys. Unlike the paired-less Pax6 present in some gnathostomes, all three lamprey Pax6 have a highly conserved full-length paired domain. All three Pax6 genes are expressed in the eye and brain, with variable expression in other tissues. Notably, lamprey Pax6α transcripts are found in the pancreas, a vertebrate-specific organ, indicating the involvement of Pax6 in development of the pancreas in the vertebrate ancestor. Multi-species sequence comparisons revealed only a single conserved non-coding element, in the lamprey Pax6β locus, with similarity to the PAX6 neuroretina enhancer. Using a transgenic zebrafish enhancer assay we demonstrate functional conservation of this element over 500 million years of vertebrate evolution.
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11
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Hamada H, Uemoto T, Tanaka Y, Honda Y, Kitajima K, Umeda T, Kawakami A, Shinya M, Kawakami K, Tamura K, Abe G. Pattern of fin rays along the antero-posterior axis based on their connection to distal radials. ZOOLOGICAL LETTERS 2019; 5:30. [PMID: 31548912 PMCID: PMC6751676 DOI: 10.1186/s40851-019-0145-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Teleost paired fins are composed of two endoskeletal domains, proximal and distal radials, and an exoskeletal domain, the fin ray. The zebrafish pectoral fin displays elaborately patterned radials along the anteroposterior (AP) axis. Radials are considered homologous to tetrapod limb skeletons, and their patterning mechanisms in embryonic development are similar to those of limb development. Nevertheless, the pattern along the AP axis in fin rays has not been well described in the zebrafish pectoral fin, although several recent reports have revealed that fin ray development shares some cellular and genetic properties with fin/limb endoskeleton development. Thus, fin ray morphogenesis may involve developmental mechanisms for AP patterning in the fin/limb endoskeleton, and may have a specific pattern along the AP axis. RESULTS We conducted detailed morphological observations on fin rays and their connection to distal radials by comparing intra- and inter-strain zebrafish specimens. Although the number of fin rays varied, pectoral fin rays could be categorized into three domains along the AP axis, according to the connection between the fin rays and distal radials; additionally, the number of fin rays varied in the posterior part of the three domains. This result was confirmed by observation of the morphogenesis process of fin rays and distal radials, which showed altered localization of distal radials in the middle domain. We also evaluated the expression pattern of lhx genes, which have AP patterning activity in limb development, in fin rays and during distal radial development and found these genes to be expressed during morphogenesis in both fin rays and distal radials. CONCLUSION The fin ray and its connection to the endoskeleton are patterned along the AP axis, and the pattern along the AP axis in the fin ray and the radial connection is constructed by the developmental mechanism related to AP patterning in the limb/fin bud. Our results indicate the possibility that the developmental mechanisms of fin rays and their connection are comparable to those of the distal element of the limb skeleton.
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Affiliation(s)
- Hiroki Hamada
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Toshiaki Uemoto
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Yoshitaka Tanaka
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Yuki Honda
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Keiichi Kitajima
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Tetsuya Umeda
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Atsushi Kawakami
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Minori Shinya
- Department of Biology, Keio University, Yokohama, 223-8521 Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540 Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, 411-8540 Japan
| | - Koji Tamura
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Gembu Abe
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
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12
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Mann A, Bhatia S. Zebrafish: A Powerful Model for Understanding the Functional Relevance of Noncoding Region Mutations in Human Genetic Diseases. Biomedicines 2019; 7:E71. [PMID: 31527394 PMCID: PMC6784013 DOI: 10.3390/biomedicines7030071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023] Open
Abstract
Determining aetiology of genetic disorders caused by damaging mutations in protein-coding genes is well established. However, understanding how mutations in the vast stretches of the noncoding genome contribute to genetic abnormalities remains a huge challenge. Cis-regulatory elements (CREs) or enhancers are an important class of noncoding elements. CREs function as the primary determinants of precise spatial and temporal regulation of their target genes during development by serving as docking sites for tissue-specific transcription factors. Although a large number of potential disease-associated CRE mutations are being identified in patients, lack of robust methods for mechanistically linking these mutations to disease phenotype is currently hampering the understanding of their roles in disease aetiology. Here, we have described the various systems available for testing the CRE potential of stretches of noncoding regions harbouring mutations implicated in human disease. We highlight advances in the field leading to the establishment of zebrafish as a powerful system for robust and cost-effective functional assays of CRE activity, enabling rapid identification of causal variants in regulatory regions and the validation of their role in disruption of appropriate gene expression.
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Affiliation(s)
- Anita Mann
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
| | - Shipra Bhatia
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
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13
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van Heyningen V. Genome sequencing-the dawn of a game-changing era. Heredity (Edinb) 2019; 123:58-66. [PMID: 31189904 PMCID: PMC6781137 DOI: 10.1038/s41437-019-0226-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/16/2019] [Indexed: 01/14/2023] Open
Abstract
The development of genome sequencing technologies has revolutionized the biological sciences in ways which could not have been imagined at the time. This article sets out to document the dawning of the age of genomics and to consider the impact of this revolution on biological investigation, our understanding of life, and the relationship between science and society.
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Affiliation(s)
- Veronica van Heyningen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Crewe Road, Edinburgh, EH4 2XU, UK.
- Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK.
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14
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Logjes RJH, Breugem CC, Van Haaften G, Paes EC, Sperber GH, van den Boogaard MJH, Farlie PG. The ontogeny of Robin sequence. Am J Med Genet A 2018; 176:1349-1368. [PMID: 29696787 DOI: 10.1002/ajmg.a.38718] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 12/17/2017] [Accepted: 03/23/2018] [Indexed: 02/06/2023]
Abstract
The triad of micrognathia, glossoptosis, and concomitant airway obstruction defined as "Robin sequence" (RS) is caused by oropharyngeal developmental events constrained by a reduced stomadeal space. This sequence of abnormal embryonic development also results in an anatomical configuration that might predispose the fetus to a cleft palate. RS is heterogeneous and many different etiologies have been described including syndromic, RS-plus, and isolated forms. For an optimal diagnosis, subsequent treatment and prognosis, a thorough understanding of the embryology and pathogenesis is necessary. This manuscript provides an update about our current understanding of the development of the mandible, tongue, and palate and possible mechanisms involved in the development of RS. Additionally, we provide the reader with an up-to-date summary of the different etiologies of this phenotype and link this to the embryologic, developmental, and genetic mechanisms.
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Affiliation(s)
- Robrecht J H Logjes
- Department of Plastic and Reconstructive Surgery, University Medical Center Utrecht, Wilhelmina Children's Hospital Utrecht, Utrecht, The Netherlands
| | - Corstiaan C Breugem
- Department of Plastic and Reconstructive Surgery, University Medical Center Utrecht, Wilhelmina Children's Hospital Utrecht, Utrecht, The Netherlands
| | - Gijs Van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emma C Paes
- Department of Plastic and Reconstructive Surgery, University Medical Center Utrecht, Wilhelmina Children's Hospital Utrecht, Utrecht, The Netherlands
| | - Geoffrey H Sperber
- Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | | | - Peter G Farlie
- Royal Children's Hospital, Murdoch Children's Research Institute, Parkville, Australia
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15
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Benabdallah NS, Gautier P, Hekimoglu-Balkan B, Lettice LA, Bhatia S, Bickmore WA. SBE6: a novel long-range enhancer involved in driving sonic hedgehog expression in neural progenitor cells. Open Biol 2017; 6:rsob.160197. [PMID: 27852806 PMCID: PMC5133441 DOI: 10.1098/rsob.160197] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/20/2016] [Indexed: 12/14/2022] Open
Abstract
The expression of genes with key roles in development is under very tight spatial and temporal control, mediated by enhancers. A classic example of this is the sonic hedgehog gene (Shh), which plays a pivotal role in the proliferation, differentiation and survival of neural progenitor cells both in vivo and in vitro. Shh expression in the brain is tightly controlled by several known enhancers that have been identified through genetic, genomic and functional assays. Using chromatin profiling during the differentiation of embryonic stem cells to neural progenitor cells, here we report the identification of a novel long-range enhancer for Shh—Shh-brain-enhancer-6 (SBE6)—that is located 100 kb upstream of Shh and that is required for the proper induction of Shh expression during this differentiation programme. This element is capable of driving expression in the vertebrate brain. Our study illustrates how a chromatin-focused approach, coupled to in vivo testing, can be used to identify new cell-type specific cis-regulatory elements, and points to yet further complexity in the control of Shh expression during embryonic brain development.
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Affiliation(s)
- Nezha S Benabdallah
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.,Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Betul Hekimoglu-Balkan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Laura A Lettice
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Shipra Bhatia
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
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16
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Machado RG, Eames BF. Using Zebrafish to Test the Genetic Basis of Human Craniofacial Diseases. J Dent Res 2017; 96:1192-1199. [DOI: 10.1177/0022034517722776] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Genome-wide association studies (GWASs) opened an innovative and productive avenue to investigate the molecular basis of human craniofacial disease. However, GWASs identify candidate genes only; they do not prove that any particular one is the functional villain underlying disease or just an unlucky genomic bystander. Genetic manipulation of animal models is the best approach to reveal which genetic loci identified from human GWASs are functionally related to specific diseases. The purpose of this review is to discuss the potential of zebrafish to resolve which candidate genetic loci are mechanistic drivers of craniofacial diseases. Many anatomic, embryonic, and genetic features of craniofacial development are conserved among zebrafish and mammals, making zebrafish a good model of craniofacial diseases. Also, the ability to manipulate gene function in zebrafish was greatly expanded over the past 20 y, enabling systems such as Gateway Tol2 and CRISPR-Cas9 to test gain- and loss-of-function alleles identified from human GWASs in coding and noncoding regions of DNA. With the optimization of genetic editing methods, large numbers of candidate genes can be efficiently interrogated. Finding the functional villains that underlie diseases will permit new treatments and prevention strategies and will increase understanding of how gene pathways operate during normal development.
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Affiliation(s)
- R. Grecco Machado
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, Canada
| | - B. Frank Eames
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, Canada
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17
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Thieme F, Ludwig K. The Role of Noncoding Genetic Variation in Isolated Orofacial Clefts. J Dent Res 2017; 96:1238-1247. [DOI: 10.1177/0022034517720403] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the past decade, medical genetic research has generated multiple discoveries, many of which were obtained via genome-wide association studies (GWASs). A major GWAS finding is that the majority of risk variants for complex traits map to noncoding regions. This has resulted in a paradigm shift in terms of the interpretation of human genomic sequence variation, with more attention now being paid to what was previously termed “junk DNA.” Translation of genetic findings into biologically meaningful results requires 1) large-scale and cell-specific efforts to annotate non-protein–coding regions and 2) the integration of comprehensive genomic data sets. However, this represents an enormous challenge, particularly in the case of human traits that arise during embryonic development, such as orofacial clefts (OFCs). OFC is a multifactorial trait and ranks among the most common of all human congenital malformations. These 2 attributes apply in particular to its isolated forms (nonsyndromic OFC [nsOFC]). Although genetic studies (including GWASs) have yielded novel insights into the genetic architecture of nsOFC, few data are available concerning causality and affected biological pathways. Reasons for this deficiency include the complex genetic architecture at risk loci and the limited availability of functional data sets from human tissues that represent relevant embryonic sites and time points. The present review summarizes current knowledge of the role of noncoding regions in nsOFC etiology. We describe the identification of genetic risk factors for nsOFC and several of the approaches used to identify causal variants at these loci. These strategies include the use of biological and genetic information from public databases, the assessment of the full spectrum of genetic variability within 1 locus, and comprehensive in vitro and in vivo experiments. This review also highlights the role of the emerging research field “functional genomics” and its increasing contribution to our biological understanding of nsOFC.
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Affiliation(s)
- F. Thieme
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - K.U. Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
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18
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Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature 2016; 538:265-269. [DOI: 10.1038/nature19800] [Citation(s) in RCA: 455] [Impact Index Per Article: 56.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 08/23/2016] [Indexed: 01/10/2023]
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19
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Babu Gurramkonda V, Syed AH, Murthy J, V K S Lakkakula B. Association of TFAP2A gene polymorphism with susceptibility to non-syndromic cleft lip with or without palate risk in south Indian population. Meta Gene 2016; 9:181-4. [PMID: 27617216 PMCID: PMC5006125 DOI: 10.1016/j.mgene.2016.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/08/2016] [Accepted: 07/08/2016] [Indexed: 11/25/2022] Open
Abstract
The aetiology of non-syndromic cleft lip with or without cleft palate (NSCL/P) is complex involving multiple interacting genes and environmental factors. The primary objective of the present study was to investigate the role of TFAP2A gene single nucleotide polymorphisms (SNPs) in the pathogenesis of NSCL/P. In this study, 173 unrelated NSCL/P patients and 176 controls without clefts were genotyped with TFAP2A rs1675414 (Exon 1), rs3798691 (Intron 1), and rs303050 (Intron 4) variants by allele-specific amplification using the KASPar SNP genotyping system. The method of multifactor dimensionality reduction (MDR) was used to analyze gene-gene interactions. TFAP2A polymorphisms are not found to be associated with non-syndromic cleft lip with or without cleft palate (NSCL/P) at either the genotype or allele levels. No linkage disequilibrium (LD) was found between TFAP2A variants. MDR analysis did not show a significant effect of the TFAP2A gene polymorphisms on susceptibility to NSCL/P (p > 0.05). These results suggest that the analyzed variations in TFAP2A gene might not be associated with NSCL/P pathogenesis in south Indian population.
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Affiliation(s)
| | - Altaf Hussain Syed
- Department of Plastic Surgery, Sri Ramachandra University, Chennai, India
| | - Jyotsna Murthy
- Department of Plastic Surgery, Sri Ramachandra University, Chennai, India
| | - Bhaskar V K S Lakkakula
- Department of Biomedical Sciences, Sri Ramachandra University, Chennai, India; Sickle Cell Institute Chhattisgarh, Raipur, India
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20
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Ansari M, Rainger J, Hanson IM, Williamson KA, Sharkey F, Harewood L, Sandilands A, Clayton-Smith J, Dollfus H, Bitoun P, Meire F, Fantes J, Franco B, Lorenz B, Taylor DS, Stewart F, Willoughby CE, McEntagart M, Khaw PT, Clericuzio C, Van Maldergem L, Williams D, Newbury-Ecob R, Traboulsi EI, Silva ED, Madlom MM, Goudie DR, Fleck BW, Wieczorek D, Kohlhase J, McTrusty AD, Gardiner C, Yale C, Moore AT, Russell-Eggitt I, Islam L, Lees M, Beales PL, Tuft SJ, Solano JB, Splitt M, Hertz JM, Prescott TE, Shears DJ, Nischal KK, Doco-Fenzy M, Prieur F, Temple IK, Lachlan KL, Damante G, Morrison DA, van Heyningen V, FitzPatrick DR. Genetic Analysis of 'PAX6-Negative' Individuals with Aniridia or Gillespie Syndrome. PLoS One 2016; 11:e0153757. [PMID: 27124303 PMCID: PMC4849793 DOI: 10.1371/journal.pone.0153757] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/04/2016] [Indexed: 12/26/2022] Open
Abstract
We report molecular genetic analysis of 42 affected individuals referred with a diagnosis of aniridia who previously screened as negative for intragenic PAX6 mutations. Of these 42, the diagnoses were 31 individuals with aniridia and 11 individuals referred with a diagnosis of Gillespie syndrome (iris hypoplasia, ataxia and mild to moderate developmental delay). Array-based comparative genomic hybridization identified six whole gene deletions: four encompassing PAX6 and two encompassing FOXC1. Six deletions with plausible cis-regulatory effects were identified: five that were 3' (telomeric) to PAX6 and one within a gene desert 5' (telomeric) to PITX2. Sequence analysis of the FOXC1 and PITX2 coding regions identified two plausibly pathogenic de novo FOXC1 missense mutations (p.Pro79Thr and p.Leu101Pro). No intragenic mutations were detected in PITX2. FISH mapping in an individual with Gillespie-like syndrome with an apparently balanced X;11 reciprocal translocation revealed disruption of a gene at each breakpoint: ARHGAP6 on the X chromosome and PHF21A on chromosome 11. In the other individuals with Gillespie syndrome no mutations were identified in either of these genes, or in HCCS which lies close to the Xp breakpoint. Disruption of PHF21A has previously been implicated in the causation of intellectual disability (but not aniridia). Plausibly causative mutations were identified in 15 out of 42 individuals (12/32 aniridia; 3/11 Gillespie syndrome). Fourteen of these mutations presented in the known aniridia genes; PAX6, FOXC1 and PITX2. The large number of individuals in the cohort with no mutation identified suggests greater locus heterogeneity may exist in both isolated and syndromic aniridia than was previously appreciated.
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Affiliation(s)
- Morad Ansari
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Jacqueline Rainger
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Isabel M. Hanson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Kathleen A. Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Freddie Sharkey
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Louise Harewood
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Angela Sandilands
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Jill Clayton-Smith
- Faculty of Medical and Human Sciences, Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, United Kingdom
| | - Helene Dollfus
- Service de Génétique Médicale, Hôpital de Haute-Pierre, Strasbourg, France
| | - Pierre Bitoun
- Medical Genetics Departments, University Hospital Jean Verdier, Bondy, France
| | - Francoise Meire
- Department of ophthalmopediatrics, Hôpital Universitaire des Enfants Reine Fabiola, Bruxelles, Belgium
| | - Judy Fantes
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Brunella Franco
- Medical Genetics, Department of Medical Translational Sciences, Federico II University, Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University Giessen, Universitaetsklinikum Giessen and Marburg UKGM, Giessen, Germany
| | - David S. Taylor
- Institute of Child Health, University College London, UK and Great Ormond Street Hospital for Children, London, United Kingdom
| | - Fiona Stewart
- Northern Ireland Regional Genetics Service (NIRGS), Belfast City Hospital, Belfast, United Kingdom
| | - Colin E. Willoughby
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Meriel McEntagart
- Medical Genetics Unit, St George's University of London, London, United Kingdom
| | - Peng Tee Khaw
- Moorfields Eye Hospital, London, UK and University College London, Institute of Ophthalmology, London, United Kingdom
| | - Carol Clericuzio
- Department of Pediatric Genetics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | | | - Denise Williams
- Clinical Genetics Unit, Birmingham Women's Hospital, Birmingham, United Kingdom
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, University Hospitals, Bristol, United Kingdom
| | - Elias I. Traboulsi
- Center for Genetic Eye Diseases, Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, OH, United States of America
| | - Eduardo D. Silva
- Department Ophthalmology, University Hospital of Coimbra, Coimbra, Portugal
| | - Mukhlis M. Madlom
- Children's Hospital, Doncaster Royal Infirmary, Doncaster, United Kingdom
| | - David R. Goudie
- Human Genetics Unit, University of Dundee College of Medicine, Dentistry and Nursing, Ninewells Hospital, Dundee, United Kingdom
| | - Brian W. Fleck
- Department of Ophthalmology, Princess Alexandra Eye Pavilion, Chalmers Street, Edinburgh, United Kingdom
| | - Dagmar Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | | | - Alice D. McTrusty
- Department of Life Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Carol Gardiner
- Clinical Genetics, Southern General Hospital, Glasgow, United Kingdom
| | - Christopher Yale
- Department of Paediatrics and Child Health, Ipswich Hospital, Ipswich, United Kingdom
| | - Anthony T. Moore
- Moorfields Eye Hospital, London, UK and University College London, Institute of Ophthalmology, London, United Kingdom
| | - Isabelle Russell-Eggitt
- Institute of Child Health, University College London, UK and Great Ormond Street Hospital for Children, London, United Kingdom
| | - Lily Islam
- Institute of Child Health, University College London, UK and Great Ormond Street Hospital for Children, London, United Kingdom
| | - Melissa Lees
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, London, United Kingdom
| | - Philip L. Beales
- Institute of Child Health, University College London, UK and Great Ormond Street Hospital for Children, London, United Kingdom
| | - Stephen J. Tuft
- Moorfields Eye Hospital, London, UK and University College London, Institute of Ophthalmology, London, United Kingdom
| | - Juan B. Solano
- Ruber International Hospital, Medical Genetics Unit, Mirasierra, Madrid, Spain
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, United Kingdom
| | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Trine E. Prescott
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Deborah J. Shears
- Department of Clinical Genetics, Churchill Hospital, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
| | - Ken K. Nischal
- UPMC Eye Center, Children's Hospital of Pittsburgh of UPMC, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Fabienne Prieur
- CHU de Saint Etienne, Service de génétique médicale, Saint-Etienne, France
| | - I. Karen Temple
- Academic Unit of Genetic Medicine, Division of Human Genetics, University of Southampton, Southampton, United Kingdom
| | - Katherine L. Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Giuseppe Damante
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
| | - Danny A. Morrison
- St. Thomas’ Hospital, Westminster Bridge Road, London, United Kingdom
| | - Veronica van Heyningen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - David R. FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
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21
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Cvekl A, Callaerts P. PAX6: 25th anniversary and more to learn. Exp Eye Res 2016; 156:10-21. [PMID: 27126352 DOI: 10.1016/j.exer.2016.04.017] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 04/12/2016] [Accepted: 04/22/2016] [Indexed: 01/29/2023]
Abstract
The DNA-binding transcription factor PAX6 was cloned 25 years ago by multiple teams pursuing identification of human and mouse eye disease causing genes, cloning vertebrate homologues of pattern-forming regulatory genes identified in Drosophila, or abundant eye-specific transcripts. Since its discovery in 1991, genetic, cellular, molecular and evolutionary studies on Pax6 mushroomed in the mid 1990s leading to the transformative thinking regarding the genetic program orchestrating both early and late stages of eye morphogenesis as well as the origin and evolution of diverse visual systems. Since Pax6 is also expressed outside of the eye, namely in the central nervous system and pancreas, a number of important insights into the development and function of these organs have been amassed. In most recent years, genome-wide technologies utilizing massively parallel DNA sequencing have begun to provide unbiased insights into the regulatory hierarchies of specification, determination and differentiation of ocular cells and neurogenesis in general. This review is focused on major advancements in studies on mammalian eye development driven by studies of Pax6 genes in model organisms and future challenges to harness the technology-driven opportunities to reconstruct, step-by-step, the transition from naïve ectoderm, neuroepithelium and periocular mesenchyme/neural crest cells into the three-dimensional architecture of the eye.
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Affiliation(s)
- Ales Cvekl
- The Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; The Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Patrick Callaerts
- Laboratory of Behavioral and Developmental Genetics, K.U. Leuven, VIB, 3000, Leuven, Belgium.
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22
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Van Otterloo E, Williams T, Artinger KB. The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. Dev Biol 2016; 415:171-187. [PMID: 26808208 DOI: 10.1016/j.ydbio.2016.01.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/16/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022]
Abstract
The craniofacial skeletal structures that comprise the human head develop from multiple tissues that converge to form the bones and cartilage of the face. Because of their complex development and morphogenesis, many human birth defects arise due to disruptions in these cellular populations. Thus, determining how these structures normally develop is vital if we are to gain a deeper understanding of craniofacial birth defects and devise treatment and prevention options. In this review, we will focus on how animal model systems have been used historically and in an ongoing context to enhance our understanding of human craniofacial development. We do this by first highlighting "animal to man" approaches; that is, how animal models are being utilized to understand fundamental mechanisms of craniofacial development. We discuss emerging technologies, including high throughput sequencing and genome editing, and new animal repository resources, and how their application can revolutionize the future of animal models in craniofacial research. Secondly, we highlight "man to animal" approaches, including the current use of animal models to test the function of candidate human disease variants. Specifically, we outline a common workflow deployed after discovery of a potentially disease causing variant based on a select set of recent examples in which human mutations are investigated in vivo using animal models. Collectively, these topics will provide a pipeline for the use of animal models in understanding human craniofacial development and disease for clinical geneticist and basic researchers alike.
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Affiliation(s)
- Eric Van Otterloo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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Benabdallah NS, Bickmore WA. Regulatory Domains and Their Mechanisms. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2015; 80:45-51. [PMID: 26590168 DOI: 10.1101/sqb.2015.80.027268] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The concept of gene regulation is being refined as our understanding of the role of enhancer elements grows. Although described more than 30 years ago, the mechanisms through which these cis-regulating elements operate remain under debate. With the recognition that most of the human genetic variation contributing to common disease risk lies outside of genes and probably in enhancers, unraveling these mechanisms becomes ever more important. Originally, a popular view was to consider regulatory elements as an entry site for the transcription machinery that could scan the intervening chromatin until the cognate core promoter was located. Now, the most prominent model for distal enhancer-promoter interaction involves direct enhancer/promoter contacts with a looping out of intervening chromatin. However, a rising awareness of the importance of chromatin architecture and organization forces us to consider enhancer-promoter communication in light of the polymer folding properties of chromatin. Here, we discuss how three-dimensional chromatin folding, topological domains, and the constrained motion, plasticity, and accessibility of chromatin could offer a structural basis for regulatory domains that greatly enhances the probability of enhancer-promoter and transcription factor-promoter interactions and gene activation.
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Affiliation(s)
- Nezha S Benabdallah
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH42XU, United Kingdom Edinburgh Super Resolution Imaging Consortium, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH42XU, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH42XU, United Kingdom
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