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Abu-Shamma R. Enhancing Our Understanding of Cell Types, Differentiation, and Disease Through Enhancers: An Interview with César Daniel Meléndez-Ramírez, MS. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2023; 96:569-572. [PMID: 38161574 PMCID: PMC10751870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Affiliation(s)
- Reem Abu-Shamma
- Biological and Biomedical Sciences Department, Yale University, New Haven, CT, USA
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Kaucka M. Cis-regulatory landscapes in the evolution and development of the mammalian skull. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220079. [PMID: 37183897 PMCID: PMC10184250 DOI: 10.1098/rstb.2022.0079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Extensive morphological variation found in mammals reflects the wide spectrum of their ecological adaptations. The highest morphological diversity is present in the craniofacial region, where geometry is mainly dictated by the bony skull. Mammalian craniofacial development represents complex multistep processes governed by numerous conserved genes that require precise spatio-temporal control. A central question in contemporary evolutionary biology is how a defined set of conserved genes can orchestrate formation of fundamentally different structures, and therefore how morphological variability arises. In principle, differential gene expression patterns during development are the source of morphological variation. With the emergence of multicellular organisms, precise regulation of gene expression in time and space is attributed to cis-regulatory elements. These elements contribute to higher-order chromatin structure and together with trans-acting factors control transcriptional landscapes that underlie intricate morphogenetic processes. Consequently, divergence in cis-regulation is believed to rewire existing gene regulatory networks and form the core of morphological evolution. This review outlines the fundamental principles of the genetic code and genomic regulation interplay during development. Recent work that deepened our comprehension of cis-regulatory element origin, divergence and function is presented here to illustrate the state-of-the-art research that uncovered the principles of morphological novelty. This article is part of the theme issue 'The mammalian skull: development, structure and function'.
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Affiliation(s)
- Marketa Kaucka
- Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
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Song S, Du B, Chung-Davidson YW, Cui W, Li Y, Chen H, Huang R, Li W, Li F, Wang C, Ren J. Disruption of T-box transcription factor eomesa results in abnormal development of median fins in Oujiang color common carp Cyprinus carpio. PLoS One 2023; 18:e0281297. [PMID: 36862620 PMCID: PMC9980737 DOI: 10.1371/journal.pone.0281297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 01/19/2023] [Indexed: 03/03/2023] Open
Abstract
Median fins are thought to be ancestors of paired fins which in turn give rise to limbs in tetrapods. However, the developmental mechanisms of median fins remain largely unknown. Nonsense mutation of the T-box transcription factor eomesa in zebrafish results in a phenotype without dorsal fin. Compared to zebrafish, the common carp undergo an additional round of whole genome duplication, acquiring an extra copy of protein-coding genes. To verify the function of eomesa genes in common carp, we established a biallelic gene editing technology in this tetraploidy fish through simultaneous disruption of two homologous genes, eomesa1 and eomesa2. We targeted four sites located upstream or within the sequences encoding the T-box domain. Sanger sequencing data indicated the average knockout efficiency was around 40% at T1-T3 sites and 10% at T4 site in embryos at 24 hours post fertilization. The individual editing efficiency was high to about 80% at T1-T3 sites and low to 13.3% at T4 site in larvae at 7 days post fertilization. Among 145 mosaic F0 examined at four months old, three individuals (Mutant 1-3) showed varying degrees of maldevelopment in the dorsal fin and loss of anal fin. Genotyping showed the genomes of all three mutants were disrupted at T3 sites. The null mutation rates on the eomesa1 and eomesa2 loci were 0% and 60% in Mutant 1, 66.7% and 100% in Mutant 2, and 90% and 77.8% in Mutant 3, respectively. In conclusion, we demonstrated a role of eomesa in the formation and development of median fins in Oujiang color common carp and established an method that simultaneously disrupt two homologous genes with one gRNA, which would be useful in genome editing in other polyploidy fishes.
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Affiliation(s)
- Shiying Song
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Bobo Du
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Yu-Wen Chung-Davidson
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States of America
| | - Wenyao Cui
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Yaru Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Honglin Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Rong Huang
- Guangdong Aquarium Association, Guangzhou, China
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States of America
| | - Fei Li
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Chenghui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Jianfeng Ren
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
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Ellingford JM, Ahn JW, Bagnall RD, Baralle D, Barton S, Campbell C, Downes K, Ellard S, Duff-Farrier C, FitzPatrick DR, Greally JM, Ingles J, Krishnan N, Lord J, Martin HC, Newman WG, O'Donnell-Luria A, Ramsden SC, Rehm HL, Richardson E, Singer-Berk M, Taylor JC, Williams M, Wood JC, Wright CF, Harrison SM, Whiffin N. Recommendations for clinical interpretation of variants found in non-coding regions of the genome. Genome Med 2022; 14:73. [PMID: 35850704 PMCID: PMC9295495 DOI: 10.1186/s13073-022-01073-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/16/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts. METHODS We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups. RESULTS We discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for the interpretation of these variants. CONCLUSIONS These recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms.
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Affiliation(s)
- Jamie M Ellingford
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, M13 9PT, UK.
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK.
- Genomics England, London, UK.
| | - Joo Wook Ahn
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Richard D Bagnall
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, Australia
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Stephanie Barton
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Chris Campbell
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Kate Downes
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
- South West Genomic Laboratory Hub, Exeter Genomic Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Celia Duff-Farrier
- South West NHS Genomic Laboratory Hub, Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John M Greally
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | - Jodie Ingles
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Neesha Krishnan
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hilary C Martin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - William G Newman
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, M13 9PT, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ebony Richardson
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Maggie Williams
- South West NHS Genomic Laboratory Hub, Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Jordan C Wood
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Steven M Harrison
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ambry Genetics, Aliso Viejo, CA, USA
| | - Nicola Whiffin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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Abstract
Enhancers control the establishment of spatiotemporal gene expression patterns throughout development. Over the past decade, the development of new technologies has improved our capacity to link enhancers with their target genes based on their colocalization within the same topological domains. However, the mechanisms that regulate how enhancers specifically activate some genes but not others within a given domain remain unclear. In this Review, we discuss recent insights into the factors controlling enhancer specificity, including the genetic composition of enhancers and promoters, the linear and 3D distance between enhancers and their target genes, and cell-type specific chromatin landscapes. We also discuss how elucidating the molecular principles of enhancer specificity might help us to better understand and predict the pathological consequences of human genetic, epigenetic and structural variants.
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Affiliation(s)
- Tomás Pachano
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Albert Einstein 22, 39011 Santander, Spain
| | - Endika Haro
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Albert Einstein 22, 39011 Santander, Spain
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Albert Einstein 22, 39011 Santander, Spain
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Lo M, Sharir A, Paul MD, Torosyan H, Agnew C, Li A, Neben C, Marangoni P, Xu L, Raleigh DR, Jura N, Klein OD. CNPY4 inhibits the Hedgehog pathway by modulating membrane sterol lipids. Nat Commun 2022; 13:2407. [PMID: 35504891 PMCID: PMC9065090 DOI: 10.1038/s41467-022-30186-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/20/2022] [Indexed: 11/09/2022] Open
Abstract
The Hedgehog (HH) pathway is critical for development and adult tissue homeostasis. Aberrant HH signaling can lead to congenital malformations and diseases including cancer. Although cholesterol and several oxysterol lipids have been shown to play crucial roles in HH activation, the molecular mechanisms governing their regulation remain unresolved. Here, we identify Canopy4 (CNPY4), a Saposin-like protein, as a regulator of the HH pathway that modulates levels of membrane sterol lipids. Cnpy4-/- embryos exhibit multiple defects consistent with HH signaling perturbations, most notably changes in digit number. Knockdown of Cnpy4 hyperactivates the HH pathway in vitro and elevates membrane levels of accessible sterol lipids, such as cholesterol, an endogenous ligand involved in HH activation. Our data demonstrate that CNPY4 is a negative regulator that fine-tunes HH signal transduction, revealing a previously undescribed facet of HH pathway regulation that operates through control of membrane composition.
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Affiliation(s)
- Megan Lo
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Amnon Sharir
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, CA, USA
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, Hebrew University, Ein Kerem, Jerusalem, Israel
| | - Michael D Paul
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Hayarpi Torosyan
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Christopher Agnew
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Amy Li
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Cynthia Neben
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Pauline Marangoni
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Ophir D Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, CA, USA.
- Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, CA, USA.
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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7
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Green DJ, Lenassi E, Manning CS, McGaughey D, Sharma V, Black GC, Ellingford JM, Sergouniotis PI. North Carolina Macular Dystrophy: Phenotypic Variability and Computational Analysis of Disease-Associated Noncoding Variants. Invest Ophthalmol Vis Sci 2021; 62:16. [PMID: 34125159 PMCID: PMC8212441 DOI: 10.1167/iovs.62.7.16] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Purpose North Carolina macular dystrophy (NCMD) is an autosomal dominant, congenital disorder affecting the central retina. Here, we report clinical and genetic findings in three families segregating NCMD and use epigenomic datasets from human tissues to gain insights into the effect of NCMD-implicated variants. Methods Clinical assessment and genetic testing were performed. Publicly available transcriptomic and epigenomic datasets were analyzed and the activity-by-contact method for scoring enhancer elements and linking them to target genes was used. Results A previously described, heterozygous, noncoding variant upstream of the PRDM13 gene was detected in all six affected study participants (chr6:100,040,987G>C [GRCh37/hg19]). Interfamilial and intrafamilial variability were observed; the visual acuity ranged from 0.0 to 1.6 LogMAR and fundoscopic findings ranged from visually insignificant, confluent, drusen-like macular deposits to coloboma-like macular lesions. Variable degrees of peripheral retinal spots (which were easily detected on widefield retinal imaging) were observed in all study subjects. Notably, a 6-year-old patient developed choroidal neovascularization and required treatment with intravitreal bevacizumab injections. Computational analysis of the five single nucleotide variants that have been implicated in NCMD revealed that these noncoding changes lie within two putative enhancer elements; these elements are predicted to interact with PRDM13 in the developing human retina. PRDM13 was found to be expressed in the fetal retina, with greatest expression in the amacrine precursor cell population. Conclusions We provide further evidence supporting the role of PRDM13 dysregulation in the pathogenesis of NCMD and highlight the usefulness of widefield retinal imaging in individuals suspected to have this condition.
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Affiliation(s)
- David J Green
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Eva Lenassi
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Cerys S Manning
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David McGaughey
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Vinod Sharma
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Graeme C Black
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Jamie M Ellingford
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Panagiotis I Sergouniotis
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Ushiki A, Zhang Y, Xiong C, Zhao J, Georgakopoulos-Soares I, Kane L, Jamieson K, Bamshad MJ, Nickerson DA, Shen Y, Lettice LA, Silveira-Lucas EL, Petit F, Ahituv N. Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia. Nat Commun 2021; 12:2282. [PMID: 33863876 PMCID: PMC8052326 DOI: 10.1038/s41467-021-22470-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/12/2021] [Indexed: 12/18/2022] Open
Abstract
Acheiropodia, congenital limb truncation, is associated with homozygous deletions in the LMBR1 gene around ZRS, an enhancer regulating SHH during limb development. How these deletions lead to this phenotype is unknown. Using whole-genome sequencing, we fine-mapped the acheiropodia-associated region to 12 kb and show that it does not function as an enhancer. CTCF and RAD21 ChIP-seq together with 4C-seq and DNA FISH identify three CTCF sites within the acheiropodia-deleted region that mediate the interaction between the ZRS and the SHH promoter. This interaction is substituted with other CTCF sites centromeric to the ZRS in the disease state. Mouse knockouts of the orthologous 12 kb sequence have no apparent abnormalities, showcasing the challenges in modelling CTCF alterations in animal models due to inherent motif differences between species. Our results show that alterations in CTCF motifs can lead to a Mendelian condition due to altered enhancer-promoter interactions.
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Affiliation(s)
- Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yichi Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Chenling Xiong
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Lauren Kane
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Kirsty Jamieson
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute, Seattle, WA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute, Seattle, WA, USA
| | - Yin Shen
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Laura A Lettice
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Florence Petit
- CHU Lille, University of Lille, EA7364 RADEME, Lille, France
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
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9
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Yin Z, Lin J, Yan R, Liu R, Liu M, Zhou B, Zhou W, An C, Chen Y, Hu Y, Fan C, Zhao K, Wu B, Zou X, Zhang J, El‐Hashash AH, Chen X, Ouyang H. Atlas of Musculoskeletal Stem Cells with the Soft and Hard Tissue Differentiation Architecture. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000938. [PMID: 33304744 PMCID: PMC7710003 DOI: 10.1002/advs.202000938] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 08/26/2020] [Indexed: 05/05/2023]
Abstract
Although being of utmost importance for human health and mobility, stem cell identity and hierarchical organization of musculoskeletal progenitors remain largely unexplored. Here, cells from E10.5, E12.5, and E15.5 murine limbs are analyzed by high throughput single-cell RNA sequencing to illustrate the cellular architecture during limb development. Single-cell transcriptional profiling demonstrates the identity and differentiation architecture of musculoskeletal stem cells (MSSC), soft and hard tissue progenitors through expression pattern of musculoskeletal markers (scleraxis [Scx], Hoxd13, Sox9, and Col1a1). This is confirmed by genetic in vivo lineage tracing. Moreover, single-cell analyses of Scx knockout mice tissues illustrates that Scx regulates MSSC self-renewal and proliferation potential. A high-throughput and low-cost multi-tissues RNA sequencing strategy further provides evidence that musculoskeletal system tissues, including muscle, bone, meniscus, and cartilage, are all abnormally developed in Scx knockout mice. These results establish the presence of an indispensable limb Scx+Hoxd13+ MSSC population and their differentiation into soft tissue progenitors (Scx+Col1a1+) and hard tissue progenitors (Scx+Sox9+). Collectively, this study paves the way for systematically decoding the complex molecular mechanisms and cellular programs of musculoskeletal tissues morphogenesis in limb development and regeneration.
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Affiliation(s)
- Zi Yin
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhou310058China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- China Orthopedic Regenerative Medicine (CORMed)Hangzhou310058China
| | - Junxin Lin
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Ruojin Yan
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Richun Liu
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Mengfei Liu
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Bo Zhou
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Wenyan Zhou
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
- Zhejiang University‐University of Edinburgh Institute & School of Basic MedicineZhejiang University School of MedicineHangzhou310058China
| | - Chengrui An
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Yangwu Chen
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Yejun Hu
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Chunmei Fan
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhou310058China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
| | - Kun Zhao
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Bingbing Wu
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Xiaohui Zou
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Department of Gynecologythe First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou310058China
| | - Jin Zhang
- The First Affiliated Hospital and Center for Stem Cell and Regenerative MedicineDepartment of Basic Medical SciencesSchool of MedicineZhejiang UniversityHangzhou310058China
| | - Ahmed H. El‐Hashash
- Zhejiang University‐University of Edinburgh Institute & School of Basic MedicineZhejiang University School of MedicineHangzhou310058China
- Edinburgh Medical SchoolUniversity of EdinburghEdinburghEH16 4SBUK
| | - Xiao Chen
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- China Orthopedic Regenerative Medicine (CORMed)Hangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
- Department of Sports MedicineSchool of MedicineZhejiang UniversityHangzhou310058China
| | - Hongwei Ouyang
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- China Orthopedic Regenerative Medicine (CORMed)Hangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
- Zhejiang University‐University of Edinburgh Institute & School of Basic MedicineZhejiang University School of MedicineHangzhou310058China
- Department of Sports MedicineSchool of MedicineZhejiang UniversityHangzhou310058China
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10
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Abstract
Over a thousand diseases are caused by mutations that alter gene expression levels. The potential of nuclease-deficient zinc fingers, TALEs or CRISPR fusion systems to treat these diseases by modulating gene expression has recently emerged. These systems can be applied to modify the activity of gene-regulatory elements - promoters, enhancers, silencers and insulators, subsequently changing their target gene expression levels to achieve therapeutic benefits - an approach termed cis-regulation therapy (CRT). Here, we review emerging CRT technologies and assess their therapeutic potential for treating a wide range of diseases caused by abnormal gene dosage. The challenges facing the translation of CRT into the clinic are discussed.
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11
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Differences in postembryonic dorsal fin development resulted in phenotypic divergence in two goldfish strains, Red Cap Oranda and Ranchu. AQUACULTURE AND FISHERIES 2020. [DOI: 10.1016/j.aaf.2020.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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12
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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: 14] [Impact Index Per Article: 3.5] [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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13
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Kvon EZ, Zhu Y, Kelman G, Novak CS, Plajzer-Frick I, Kato M, Garvin TH, Pham Q, Harrington AN, Hunter RD, Godoy J, Meky EM, Akiyama JA, Afzal V, Tran S, Escande F, Gilbert-Dussardier B, Jean-Marçais N, Hudaiberdiev S, Ovcharenko I, Dobbs MB, Gurnett CA, Manouvrier-Hanu S, Petit F, Visel A, Dickel DE, Pennacchio LA. Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants. Cell 2020; 180:1262-1271.e15. [PMID: 32169219 PMCID: PMC7179509 DOI: 10.1016/j.cell.2020.02.031] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/13/2020] [Accepted: 02/12/2020] [Indexed: 12/17/2022]
Abstract
Establishing causal links between non-coding variants and human phenotypes is an increasing challenge. Here, we introduce a high-throughput mouse reporter assay for assessing the pathogenic potential of human enhancer variants in vivo and examine nearly a thousand variants in an enhancer repeatedly linked to polydactyly. We show that 71% of all rare non-coding variants previously proposed as causal lead to reporter gene expression in a pattern consistent with their pathogenic role. Variants observed to alter enhancer activity were further confirmed to cause polydactyly in knockin mice. We also used combinatorial and single-nucleotide mutagenesis to evaluate the in vivo impact of mutations affecting all positions of the enhancer and identified additional functional substitutions, including potentially pathogenic variants hitherto not observed in humans. Our results uncover the functional consequences of hundreds of mutations in a phenotype-associated enhancer and establish a widely applicable strategy for systematic in vivo evaluation of human enhancer variants.
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Affiliation(s)
- Evgeny Z Kvon
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yiwen Zhu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Guy Kelman
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Catherine S Novak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tyler H Garvin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Quan Pham
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anne N Harrington
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Riana D Hunter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Janeth Godoy
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eman M Meky
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Veena Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stella Tran
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | | | - Sanjarbek Hudaiberdiev
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew B Dobbs
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christina A Gurnett
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Florence Petit
- CHU Lille, University of Lille, EA7364, F-59000, Lille, France
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; School of Natural Sciences, University of California, Merced, CA 95343, USA.
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA.
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14
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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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15
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Nishizaki SS, Ng N, Dong S, Porter RS, Morterud C, Williams C, Asman C, Switzenberg JA, Boyle AP. Predicting the effects of SNPs on transcription factor binding affinity. Bioinformatics 2019; 36:364-372. [PMID: 31373606 PMCID: PMC7999143 DOI: 10.1093/bioinformatics/btz612] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/15/2019] [Accepted: 08/01/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION Genome-wide association studies have revealed that 88% of disease-associated single-nucleotide polymorphisms (SNPs) reside in noncoding regions. However, noncoding SNPs remain understudied, partly because they are challenging to prioritize for experimental validation. To address this deficiency, we developed the SNP effect matrix pipeline (SEMpl). RESULTS SEMpl estimates transcription factor-binding affinity by observing differences in chromatin immunoprecipitation followed by deep sequencing signal intensity for SNPs within functional transcription factor-binding sites (TFBSs) genome-wide. By cataloging the effects of every possible mutation within the TFBS motif, SEMpl can predict the consequences of SNPs to transcription factor binding. This knowledge can be used to identify potential disease-causing regulatory loci. AVAILABILITY AND IMPLEMENTATION SEMpl is available from https://github.com/Boyle-Lab/SEM_CPP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sierra S Nishizaki
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natalie Ng
- Department of Human Genetics, Stanford University, Stanford, CA 94305, USA
| | - Shengcheng Dong
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert S Porter
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Cody Morterud
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Colten Williams
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Courtney Asman
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jessica A Switzenberg
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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16
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Holt-Oram syndrome: clinical and molecular description of 78 patients with TBX5 variants. Eur J Hum Genet 2018; 27:360-368. [PMID: 30552424 DOI: 10.1038/s41431-018-0303-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/12/2018] [Accepted: 10/25/2018] [Indexed: 12/24/2022] Open
Abstract
Holt-Oram syndrome (HOS) is an autosomal dominant condition characterised by the association of congenital heart defect (CHD), with or without rhythm disturbances and radial defects, due to TBX5 variants. The diagnosis is challenged by the variability of expression and the large phenotypic overlap with other conditions, like Okihiro syndrome, TAR syndrome or Fanconi disease. We retrospectively reviewed 212 patients referred for suspicion of HOS between 2002 and 2014, who underwent TBX5 screening. A TBX5 variant has been identified in 78 patients, representing the largest molecular series ever described. In the cohort, 61 met the previously described diagnostic criteria and 17 have been considered with an uncertain HOS diagnosis. A CHD was present in 91% of the patients with a TBX5 variant, atrial septal defects being the most common (61.5%). The genotype-phenotype study highlights the importance of some critical features in HOS: the septal characteristic of the CHD, the bilateral and asymmetric characteristics of the radial defect and the presence of shoulder or elbow mobility defect. Besides, 21 patients presented with an overlapping condition. Among them, 13 had a typical HOS presentation. We discuss the strategies that could be adopted to improve the molecular delineation of the remaining typical patients.
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17
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Potuijt JWP, Baas M, Sukenik-Halevy R, Douben H, Nguyen P, Venter DJ, Gallagher R, Swagemakers SM, Hovius SER, van Nieuwenhoven CA, Galjaard RJH, van der Spek PJ, Ahituv N, de Klein A. A point mutation in the pre-ZRS disrupts sonic hedgehog expression in the limb bud and results in triphalangeal thumb-polysyndactyly syndrome. Genet Med 2018. [PMID: 29543231 DOI: 10.1038/gim.2018.18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE The zone of polarizing activity regulatory sequence (ZRS) is an enhancer that regulates sonic hedgehog during embryonic limb development. Recently, mutations in a noncoding evolutionary conserved sequence 500 bp upstream of the ZRS, termed the pre-ZRS (pZRS), have been associated with polydactyly in dogs and humans. Here, we report the first case of triphalangeal thumb-polysyndactyly syndrome (TPT-PS) to be associated with mutations in this region and show via mouse enhancer assays how this mutation leads to ectopic expression throughout the developing limb bud. METHODS We used linkage analysis, whole-exome sequencing, Sanger sequencing, fluorescence in situ hybridization, multiplex ligation-dependent probe amplification, single-nucleotide polymorphism array, and a mouse transgenic enhancer assay. RESULTS Ten members of a TPT-PS family were included in this study. The mutation was linked to chromosome 7q36 (LOD score 3.0). No aberrations in the ZRS could be identified. A point mutation in the pZRS (chr7:156585476G>C; GRCh37/hg19) was detected in all affected family members. Functional characterization using a mouse transgenic enhancer essay showed extended ectopic expression dispersed throughout the entire limb bud (E11.5). CONCLUSION Our work describes the first mutation in the pZRS to be associated with TPT-PS and provides functional evidence that this mutation leads to ectopic expression of this enhancer within the developing limb.
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Affiliation(s)
- Jacob W P Potuijt
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Martijn Baas
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rivka Sukenik-Halevy
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California-San Francisco, San Francisco, California, USA.,Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Hannie Douben
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Picard Nguyen
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Deon J Venter
- Department of Pathology, Mater Health Services, South Brisbane, Queensland, Australia.,Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, Sydney, Australia.,School of Medicine, University of Wollongong, Wollongong, New South Wales, Australia
| | - Renée Gallagher
- Department of Pathology, Mater Health Services, South Brisbane, Queensland, Australia
| | - Sigrid M Swagemakers
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Steven E R Hovius
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Christianne A van Nieuwenhoven
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Robert-Jan H Galjaard
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter J van der Spek
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California-San Francisco, San Francisco, California, USA
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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18
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Zone of Polarizing Activity Regulatory Sequence Mutations/Duplications with Preaxial Polydactyly and Longitudinal Preaxial Ray Deficiency in the Phenotype: A Review of Human Cases, Animal Models, and Insights Regarding the Pathogenesis. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1573871. [PMID: 29651423 PMCID: PMC5832050 DOI: 10.1155/2018/1573871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/19/2017] [Accepted: 01/16/2018] [Indexed: 02/06/2023]
Abstract
Clinicians and scientists interested in developmental biology have viewed preaxial polydactyly (PPD) and longitudinal preaxial ray deficiency (LPAD) as two different entities. Point mutations and duplications in the zone of polarizing activity regulatory sequence (ZRS) are associated with anterior ectopic expression of Sonic Hedgehog (SHH) in the limb bud and usually result in a PPD phenotype. However, some of these mutations/duplications also have LPAD in the phenotype. This unusual PPD-LPAD association in ZRS mutations/duplications has not been specifically reviewed in the literature. The author reviews this unusual entity and gives insights regarding its pathogenesis.
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19
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Collinson JM, Lindström NO, Neves C, Wallace K, Meharg C, Charles RH, Ross ZK, Fraser AM, Mbogo I, Oras K, Nakamoto M, Barker S, Duce S, Miedzybrodzka Z, Vargesson N. The developmental and genetic basis of 'clubfoot' in the peroneal muscular atrophy mutant mouse. Development 2018; 145:145/3/dev160093. [PMID: 29439133 DOI: 10.1242/dev.160093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/28/2017] [Indexed: 12/19/2022]
Abstract
Genetic factors underlying the human limb abnormality congenital talipes equinovarus ('clubfoot') remain incompletely understood. The spontaneous autosomal recessive mouse 'peroneal muscular atrophy' mutant (PMA) is a faithful morphological model of human clubfoot. In PMA mice, the dorsal (peroneal) branches of the sciatic nerves are absent. In this study, the primary developmental defect was identified as a reduced growth of sciatic nerve lateral motor column (LMC) neurons leading to failure to project to dorsal (peroneal) lower limb muscle blocks. The pma mutation was mapped and a candidate gene encoding LIM-domain kinase 1 (Limk1) identified, which is upregulated in mutant lateral LMC motor neurons. Genetic and molecular analyses showed that the mutation acts in the EphA4-Limk1-Cfl1/cofilin-actin pathway to modulate growth cone extension/collapse. In the chicken, both experimental upregulation of Limk1 by electroporation and pharmacological inhibition of actin turnover led to defects in hindlimb spinal motor neuron growth and pathfinding, and mimicked the clubfoot phenotype. The data support a neuromuscular aetiology for clubfoot and provide a mechanistic framework to understand clubfoot in humans.
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Affiliation(s)
- J Martin Collinson
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Nils O Lindström
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Carlos Neves
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Karen Wallace
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Caroline Meharg
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Rebecca H Charles
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Zoe K Ross
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Amy M Fraser
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Ivan Mbogo
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Kadri Oras
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Masaru Nakamoto
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Simon Barker
- Royal Aberdeen Children's Hospital, Foresterhill, Aberdeen AB25 2ZN, UK
| | - Suzanne Duce
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Zosia Miedzybrodzka
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Neil Vargesson
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
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20
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Abstract
An enhancer named MFCS1 regulates Sonic hedgehog (Shh) expression in the posterior mesenchyme of limb buds. Several mutations in MFCS1 induce ectopic Shh expression in the anterior limb bud, and these result in preaxial polydactyly (PPD). However, the molecular basis of ectopic Shh expression remains elusive, although some mutations are known to disrupt the negative regulation of Shh expression in the anterior limb bud. Here, we analyzed the molecular mechanism of ectopic Shh expression in PPD including in a mouse mutation-hemimelic extra toes (Hx)-and in other MFCS1 mutations in different species. First, we generated transgenic mouse lines with a LacZ reporter cassette flanked with tandem repeats of 40 bp MFCS1 fragments harboring a mutation. The transgenic mouse line with the Hx-type fragment showed reporter expression exclusively in the anterior, but not in the posterior margins of limb buds. In contrast, no specific LacZ expression was observed in lines carrying the MFCS1 fragment with other mutations. Yeast one-hybrid assays revealed that the msh-like homeodomain protein, MSX1, bound specifically to the Hx sequence of MFCS1. Thus, PPD caused by mutations in MFCS1 has two major types of molecular etiology: loss of a cis-motif for negative regulation of Shh, and acquisition of a new cis-motif binding to a preexisting transcription factor, as represented by the Hx mutation.
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21
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Starita LM, Ahituv N, Dunham MJ, Kitzman JO, Roth FP, Seelig G, Shendure J, Fowler DM. Variant Interpretation: Functional Assays to the Rescue. Am J Hum Genet 2017; 101:315-325. [PMID: 28886340 PMCID: PMC5590843 DOI: 10.1016/j.ajhg.2017.07.014] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Classical genetic approaches for interpreting variants, such as case-control or co-segregation studies, require finding many individuals with each variant. Because the overwhelming majority of variants are present in only a few living humans, this strategy has clear limits. Fully realizing the clinical potential of genetics requires that we accurately infer pathogenicity even for rare or private variation. Many computational approaches to predicting variant effects have been developed, but they can identify only a small fraction of pathogenic variants with the high confidence that is required in the clinic. Experimentally measuring a variant's functional consequences can provide clearer guidance, but individual assays performed only after the discovery of the variant are both time and resource intensive. Here, we discuss how multiplex assays of variant effect (MAVEs) can be used to measure the functional consequences of all possible variants in disease-relevant loci for a variety of molecular and cellular phenotypes. The resulting large-scale functional data can be combined with machine learning and clinical knowledge for the development of "lookup tables" of accurate pathogenicity predictions. A coordinated effort to produce, analyze, and disseminate large-scale functional data generated by multiplex assays could be essential to addressing the variant-interpretation crisis.
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Affiliation(s)
- Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Bioinformatics & Computational Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Frederick P Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada; Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA; Department of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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22
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Fuentes-Pardo AP, Ruzzante DE. Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations. Mol Ecol 2017; 26:5369-5406. [PMID: 28746784 DOI: 10.1111/mec.14264] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 12/14/2022]
Abstract
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.
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23
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Abstract
Gene expression changes, the driving forces for cellular diversity in multicellular organisms, are regulated by a diverse set of gene regulatory elements that direct transcription in specific cells. Mutations in these elements, ranging from chromosomal aberrations to single-nucleotide polymorphisms, are a major cause of human disease. However, we currently have a very limited understanding of how regulatory element genotypes lead to specific phenotypes. In this review, we discuss the various methods of regulatory element identification, the different types of mutations they harbor, and their impact on human disease. We highlight how these variations can affect transcription of multiple genes in gene regulatory networks. In addition, we describe how novel technologies, such as massively parallel reporter assays and CRISPR/Cas9 genome editing, are beginning to provide a better understanding of the functional roles that these elements have and how their alteration can lead to specific phenotypes.
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Affiliation(s)
- Sumantra Chatterjee
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences and Institute for Human Genetics, University of California, San Francisco, California 94158;
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24
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Abstract
The limb is a commonly used model system for developmental biology. Given the need for precise control of complex signalling pathways to achieve proper patterning, the limb is also becoming a model system for gene regulation studies. Recent developments in genomic technologies have enabled the genome-wide identification of regulatory elements that control limb development, yielding insights into the determination of limb morphology and forelimb versus hindlimb identity. The modulation of regulatory interactions - for example, through the modification of regulatory sequences or chromatin architecture - can lead to morphological evolution, acquired regeneration capacity or limb malformations in diverse species, including humans.
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Affiliation(s)
- Florence Petit
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, California 94158, USA.,University of Lille, CHU Lille, EA 7364-RADEME, F-59000 Lille, France
| | - Karen E Sears
- School of Integrative Biology, Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, California 94158, USA.,Institute for Human Genetics, University of California San Francisco, California 94158, USA
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25
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Kvon EZ, Kamneva OK, Melo US, Barozzi I, Osterwalder M, Mannion BJ, Tissières V, Pickle CS, Plajzer-Frick I, Lee EA, Kato M, Garvin TH, Akiyama JA, Afzal V, Lopez-Rios J, Rubin EM, Dickel DE, Pennacchio LA, Visel A. Progressive Loss of Function in a Limb Enhancer during Snake Evolution. Cell 2016; 167:633-642.e11. [PMID: 27768887 DOI: 10.1016/j.cell.2016.09.028] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 08/07/2016] [Accepted: 09/15/2016] [Indexed: 01/08/2023]
Abstract
The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP.
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Affiliation(s)
- Evgeny Z Kvon
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Olga K Kamneva
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Uirá S Melo
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Iros Barozzi
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marco Osterwalder
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brandon J Mannion
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Catherine S Pickle
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Elizabeth A Lee
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Momoe Kato
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tyler H Garvin
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer A Akiyama
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Veena Afzal
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Javier Lopez-Rios
- Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Edward M Rubin
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Diane E Dickel
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Len A Pennacchio
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
| | - Axel Visel
- MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95343, USA.
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26
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Wang B, Diao Y, Liu Q, An H, Ma R, Jiang G, Lai N, Li Z, Zhu X, Zhao L, Guo Q, Zhang Z, Sun R, Li X. An increased duplication of ZRS region that caused more than one supernumerary digits preaxial polydactyly in a large Chinese family. Sci Rep 2016; 6:38500. [PMID: 27922091 PMCID: PMC5138840 DOI: 10.1038/srep38500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/10/2016] [Indexed: 01/30/2023] Open
Abstract
Preaxial polydactyly (PPD) is inherited in an autosomal dominant fashion and characterized by the presence of one or more supernumerary digits on the thumb side. It had been identified that point mutation or genomic duplications of the long-range limb-specific cis-regulator - zone of polarizing activity regulatory sequence (ZRS) cause PPD or other limb deformities such as syndactyly type IV (SD4) and Triphalangeal thumb-polysyndactyly syndrome (TPTPS). Most previously reported cases involved with no more than one extra finger; however, the role of the point mutation or genomic duplications of ZRS in the case of more than one redundant finger polydactyly remains unclear. In this article, we reported a family case of more than one redundant finger polydactyly on the thumb side for bilateral hands with a pedigree chart of the family. Results of quantitative PCR (qPCR) and sequence analysis suggested that the relative copy number (RCN) of ZRS but not point mutation (including insertion and deletion) was involved in all affected individuals.
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Affiliation(s)
- Bin Wang
- Department of peripheral vascular disease, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, 42 Wenhua xi Road, Jinan 250011, Shandong, China
| | - Yutao Diao
- Key Laboratory for Rare &Uncommon diseases of Shandong province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Jinan 250062, Shandong, China
| | - Qiji Liu
- Department of medical genetics, Shandong University, School of Medicine, Jinan 250012, Shandong, China
| | - Hongqiang An
- Department of Orthopedic Surgery, People's Hospital of Xintai, Xintai 271200, Shandong, China
| | - Ruiping Ma
- Shandong Provincial Qianfoshan Hospital, 16766 Jingshi Road, Jinan 250014, Shandong, China
| | - Guosheng Jiang
- Key Laboratory for Rare &Uncommon diseases of Shandong province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Jinan 250062, Shandong, China
| | - Nannan Lai
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Ziwei Li
- Key Laboratory for Rare &Uncommon diseases of Shandong province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Jinan 250062, Shandong, China
| | - Xiaoxiao Zhu
- Key Laboratory for Rare &Uncommon diseases of Shandong province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Jinan 250062, Shandong, China
| | - Lin Zhao
- Key Laboratory for Rare &Uncommon diseases of Shandong province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Jinan 250062, Shandong, China
| | - Qiang Guo
- Key Laboratory for Rare &Uncommon diseases of Shandong province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Jinan 250062, Shandong, China
| | - Zhen Zhang
- Key Laboratory for Rare &Uncommon diseases of Shandong province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Jinan 250062, Shandong, China
| | - Rong Sun
- Shandong Academy of Chinese Medicine, Yanzi Shanxi Road, Jinan 250014, Shandong, China
| | - Xia Li
- Key Laboratory for Rare &Uncommon diseases of Shandong province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Jinan 250062, Shandong, China
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27
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Wu PF, Guo S, Fan XF, Fan LL, Jin JY, Tang JY, Xiang R. A Novel ZRS Mutation in a Chinese Patient with Preaxial Polydactyly and Triphalangeal Thumb. Cytogenet Genome Res 2016; 149:171-175. [PMID: 27592358 DOI: 10.1159/000448820] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2016] [Indexed: 11/19/2022] Open
Abstract
Preaxial polydactyly (PPD; OMIM 603596), which is characterized as having supernumerary fingers, is an unusual congenital hand abnormality. Triphalangeal thumb (TPT; OMIM 190600) is identified by an extra phalangeal bone and is often found in association with PPD. When in combination, the disease is referred to as PPD type II (PPD II; OMIM 174500). Previous studies have demonstrated that variations in the zone of polarizing activity regulatory sequence (ZRS; chr7:156,583,796-156,584,569; hg19) region are associated with PPD II. In this study, our patient was diagnosed with PPD II, having bilateral thumb duplication and unilateral TPT (on the right hand). Further investigation of possible causative genes identified a de novo heterozygous ZRS mutation (ZRS 428T>A). This novel mutation was neither found in 200 normal controls nor reported in online databases. Moreover, the bioinformatics program Genomic Evolutionary Rate Profiling (GERP) revealed this site (ZRS428) to be evolutionarily highly conserved, and the 428T>A point mutation was predicted to be deleterious by MutationTaster. In conclusion, the affected individual shows bilateral thumb duplication, but unilateral TPT making this case special. Thus, our findings not only further support the important role of ZRS in limb morphogenesis and expand the spectrum of ZRS mutations, but also emphasize the significance of genetic diagnosis and counseling of families with digit number and identity alterations as well.
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Affiliation(s)
- Pan-Feng Wu
- Department of Orthopaedics, Xiangya Hospital, Changsha, PR China
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28
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Ali S, Amina B, Anwar S, Minhas R, Parveen N, Nawaz U, Azam SS, Abbasi AA. Genomic features of human limb specific enhancers. Genomics 2016; 108:143-150. [PMID: 27580967 DOI: 10.1016/j.ygeno.2016.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/08/2016] [Accepted: 08/27/2016] [Indexed: 12/18/2022]
Abstract
To elucidate important cellular and molecular interactions that regulate patterning and skeletal development, vertebrate limbs served as a model organ. A growing body of evidence from detailed studies on a subset of limb regulators like the HOXD cluster or SHH, reveals the importance of enhancers in limb related developmental and disease processes. Exploiting the recent genome-wide availability of functionally confirmed enhancer dataset, this study establishes regulatory interactions for dozens of human limb developmental genes. From these data, it appears that the long-range regulatory interactions are fairly common during limb development. This observation highlights the significance of chromosomal breaks/translocations in human limb deformities. Transcriptional factor (TF) analysis predicts that the differentiation of early nascent limb-bud into future territories entail distinct TF interaction networks. Conclusively, an important motivation for annotating the human limb specific regulatory networks is to pave way for the systematic exploration of their role in disease and evolution.
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Affiliation(s)
- Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Bibi Amina
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Saneela Anwar
- National Center for Bioinformatics, Computational Biology Lab, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Rashid Minhas
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Nazia Parveen
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Uzma Nawaz
- Department of Statistics, The Women University, Multan 60000, Pakistan.
| | - Syed Sikandar Azam
- National Center for Bioinformatics, Computational Biology Lab, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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29
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Lu Q, Powles RL, Wang Q, He BJ, Zhao H. Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies. PLoS Genet 2016; 12:e1005947. [PMID: 27058395 PMCID: PMC4825932 DOI: 10.1371/journal.pgen.1005947] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/01/2016] [Indexed: 12/20/2022] Open
Abstract
Extensive efforts have been made to understand genomic function through both experimental and computational approaches, yet proper annotation still remains challenging, especially in non-coding regions. In this manuscript, we introduce GenoSkyline, an unsupervised learning framework to predict tissue-specific functional regions through integrating high-throughput epigenetic annotations. GenoSkyline successfully identified a variety of non-coding regulatory machinery including enhancers, regulatory miRNA, and hypomethylated transposable elements in extensive case studies. Integrative analysis of GenoSkyline annotations and results from genome-wide association studies (GWAS) led to novel biological insights on the etiologies of a number of human complex traits. We also explored using tissue-specific functional annotations to prioritize GWAS signals and predict relevant tissue types for each risk locus. Brain and blood-specific annotations led to better prioritization performance for schizophrenia than standard GWAS p-values and non-tissue-specific annotations. As for coronary artery disease, heart-specific functional regions was highly enriched of GWAS signals, but previously identified risk loci were found to be most functional in other tissues, suggesting a substantial proportion of still undetected heart-related loci. In summary, GenoSkyline annotations can guide genetic studies at multiple resolutions and provide valuable insights in understanding complex diseases. GenoSkyline is available at http://genocanyon.med.yale.edu/GenoSkyline.
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Affiliation(s)
- Qiongshi Lu
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Ryan Lee Powles
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Qian Wang
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Beixin Julie He
- Division of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
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30
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Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N. Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus. PLoS Genet 2016; 12:e1005738. [PMID: 27019019 PMCID: PMC4809552 DOI: 10.1371/journal.pgen.1005738] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/23/2015] [Indexed: 02/06/2023] Open
Abstract
The molecular events leading to the development of the bat wing remain largely unknown, and are thought to be caused, in part, by changes in gene expression during limb development. These expression changes could be instigated by variations in gene regulatory enhancers. Here, we used a comparative genomics approach to identify regions that evolved rapidly in the bat ancestor, but are highly conserved in other vertebrates. We discovered 166 bat accelerated regions (BARs) that overlap H3K27ac and p300 ChIP-seq peaks in developing mouse limbs. Using a mouse enhancer assay, we show that five Myotis lucifugus BARs drive gene expression in the developing mouse limb, with the majority showing differential enhancer activity compared to the mouse orthologous BAR sequences. These include BAR116, which is located telomeric to the HoxD cluster and had robust forelimb expression for the M. lucifugus sequence and no activity for the mouse sequence at embryonic day 12.5. Developing limb expression analysis of Hoxd10-Hoxd13 in Miniopterus natalensis bats showed a high-forelimb weak-hindlimb expression for Hoxd10-Hoxd11, similar to the expression trend observed for M. lucifugus BAR116 in mice, suggesting that it could be involved in the regulation of the bat HoxD complex. Combined, our results highlight novel regulatory regions that could be instrumental for the morphological differences leading to the development of the bat wing.
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Affiliation(s)
- Betty M. Booker
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Tara Friedrich
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Gladstone Institutes, San Francisco, California, United States of America
| | - Mandy K. Mason
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Julia E. VanderMeer
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Key Laboratory of Advanced Control and Optimization for Chemical Processes of the Ministry of Education, East China University of Science and Technology, Shanghai, China
| | - Walter L. Eckalbar
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Malcolm Logan
- Division of Developmental Biology, MRC-National Institute for Medical Research, Mill Hill, London, United Kingdom
- Randall Division of Cell and Molecular Biophysics, King’s College London, Guys Campus, London, United Kingdom
| | - Nicola Illing
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Katherine S. Pollard
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Gladstone Institutes, San Francisco, California, United States of America
- Division of Biostatistics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (KSP); (NA)
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (KSP); (NA)
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31
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Abstract
Physicians who specialize in pediatric orthopedics and hand surgery frequently encounter congenital hand abnormalities, despite their relative rarity. The treating physician should be aware of the associated syndromes and malformations that may, in some cases, be fatal if not recognized and treated appropriately. Although these congenital disorders have a wide variability, their treatment principles are similar in that the physician should promote functional use and cosmesis for the hand. This article discusses syndactyly, preaxial polydactyly and post-axial polydactyly, and the hypoplastic thumb.
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Affiliation(s)
- Kevin J Little
- Division of Pediatric Orthopaedics, Department of Orthopaedic Surgery, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, 3333 Burnet Avenue, ML 2017, Cincinnati, OH 45229, USA.
| | - Roger Cornwall
- Division of Pediatric Orthopaedics, Department of Orthopaedic Surgery, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, 3333 Burnet Avenue, ML 2017, Cincinnati, OH 45229, USA
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32
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Matharu N, Ahituv N. Minor Loops in Major Folds: Enhancer-Promoter Looping, Chromatin Restructuring, and Their Association with Transcriptional Regulation and Disease. PLoS Genet 2015; 11:e1005640. [PMID: 26632825 PMCID: PMC4669122 DOI: 10.1371/journal.pgen.1005640] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The organization and folding of chromatin within the nucleus can determine the outcome of gene expression. Recent technological advancements have enabled us to study chromatin interactions in a genome-wide manner at high resolution. These studies have increased our understanding of the hierarchy and dynamics of chromatin domains that facilitate cognate enhancer–promoter looping, defining the transcriptional program of different cell types. In this review, we focus on vertebrate chromatin long-range interactions as they relate to transcriptional regulation. In addition, we describe how the alteration of boundaries that mark discrete regions in the genome with high interaction frequencies within them, called topological associated domains (TADs), could lead to various phenotypes, including human diseases, which we term as “TADopathies.”
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Affiliation(s)
- Navneet Matharu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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33
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Yousaf A, Sohail Raza M, Ali Abbasi A. The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape. Genome Biol Evol 2015; 7:2333-43. [PMID: 26253316 PMCID: PMC4558863 DOI: 10.1093/gbe/evv146] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Enhancers lie at the heart of transcriptional and developmental gene regulation. Therefore, changes in enhancer sequences usually disrupt the target gene expression and result in disease phenotypes. Despite the well-established role of enhancers in development and disease, evolutionary sequence studies are lacking. The current study attempts to unravel the puzzle of bony vertebrates’ conserved noncoding elements (CNE) enhancer evolution. Bayesian phylogenetics of enhancer sequences spotlights promising interordinal relationships among placental mammals, proposing a closer relationship between humans and laurasiatherians while placing rodents at the basal position. Clock-based estimates of enhancer evolution provided a dynamic picture of interspecific rate changes across the bony vertebrate lineage. Moreover, coelacanth in the study augmented our appreciation of the vertebrate cis-regulatory evolution during water–land transition. Intriguingly, we observed a pronounced upsurge in enhancer evolution in land-dwelling vertebrates. These novel findings triggered us to further investigate the evolutionary trend of coding as well as CNE nonenhancer repertoires, to highlight the relative evolutionary dynamics of diverse genomic landscapes. Surprisingly, the evolutionary rates of enhancer sequences were clearly at odds with those of the coding and the CNE nonenhancer sequences during vertebrate adaptation to land, with land vertebrates exhibiting significantly reduced rates of coding sequence evolution in comparison to their fast evolving regulatory landscape. The observed variation in tetrapod cis-regulatory elements caused the fine-tuning of associated gene regulatory networks. Therefore, the increased evolutionary rate of tetrapods’ enhancer sequences might be responsible for the variation in developmental regulatory circuits during the process of vertebrate adaptation to land.
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Affiliation(s)
- Aisha Yousaf
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Sohail Raza
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data. Sci Rep 2015; 5:10576. [PMID: 26015273 PMCID: PMC4444969 DOI: 10.1038/srep10576] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/20/2015] [Indexed: 12/16/2022] Open
Abstract
Identifying functional regions in the human genome is a major goal in human genetics. Great efforts have been made to functionally annotate the human genome either through computational predictions, such as genomic conservation, or high-throughput experiments, such as the ENCODE project. These efforts have resulted in a rich collection of functional annotation data of diverse types that need to be jointly analyzed for integrated interpretation and annotation. Here we present GenoCanyon, a whole-genome annotation method that performs unsupervised statistical learning using 22 computational and experimental annotations thereby inferring the functional potential of each position in the human genome. With GenoCanyon, we are able to predict many of the known functional regions. The ability of predicting functional regions as well as its generalizable statistical framework makes GenoCanyon a unique and powerful tool for whole-genome annotation. The GenoCanyon web server is available at http://genocanyon.med.yale.edu
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Mathelier A, Lefebvre C, Zhang AW, Arenillas DJ, Ding J, Wasserman WW, Shah SP. Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas. Genome Biol 2015; 16:84. [PMID: 25903198 PMCID: PMC4467049 DOI: 10.1186/s13059-015-0648-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/07/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND With the rapid increase of whole-genome sequencing of human cancers, an important opportunity to analyze and characterize somatic mutations lying within cis-regulatory regions has emerged. A focus on protein-coding regions to identify nonsense or missense mutations disruptive to protein structure and/or function has led to important insights; however, the impact on gene expression of mutations lying within cis-regulatory regions remains under-explored. We analyzed somatic mutations from 84 matched tumor-normal whole genomes from B-cell lymphomas with accompanying gene expression measurements to elucidate the extent to which these cancers are disrupted by cis-regulatory mutations. RESULTS We characterize mutations overlapping a high quality set of well-annotated transcription factor binding sites (TFBSs), covering a similar portion of the genome as protein-coding exons. Our results indicate that cis-regulatory mutations overlapping predicted TFBSs are enriched in promoter regions of genes involved in apoptosis or growth/proliferation. By integrating gene expression data with mutation data, our computational approach culminates with identification of cis-regulatory mutations most likely to participate in dysregulation of the gene expression program. The impact can be measured along with protein-coding mutations to highlight key mutations disrupting gene expression and pathways in cancer. CONCLUSIONS Our study yields specific genes with disrupted expression triggered by genomic mutations in either the coding or the regulatory space. It implies that mutated regulatory components of the genome contribute substantially to cancer pathways. Our analyses demonstrate that identifying genomically altered cis-regulatory elements coupled with analysis of gene expression data will augment biological interpretation of mutational landscapes of cancers.
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Affiliation(s)
- Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, V5Z 4H4, Vancouver, BC, Canada.
| | - Calvin Lefebvre
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, V5Z 1L3, BC, Canada. .,Bioinformatics Graduate Program, University of British Columbia, Vancouver, V5Z 1L3, BC, Canada.
| | - Allen W Zhang
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, V5Z 4H4, Vancouver, BC, Canada. .,Bioinformatics Graduate Program, University of British Columbia, Vancouver, V5Z 1L3, BC, Canada.
| | - David J Arenillas
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, V5Z 4H4, Vancouver, BC, Canada.
| | - Jiarui Ding
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, V5Z 1L3, BC, Canada. .,Department of Computer Science, University of British Columbia, Vancouver, V6T 1Z4, BC, Canada.
| | - Wyeth W Wasserman
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, V5Z 4H4, Vancouver, BC, Canada.
| | - Sohrab P Shah
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, V5Z 1L3, BC, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, G227-2211, BC, Canada.
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The disruption of a novel limb cis-regulatory element of SHH is associated with autosomal dominant preaxial polydactyly-hypertrichosis. Eur J Hum Genet 2015; 24:37-43. [PMID: 25782671 DOI: 10.1038/ejhg.2015.53] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 02/12/2015] [Accepted: 02/19/2015] [Indexed: 12/16/2022] Open
Abstract
The expression gradient of the morphogen Sonic Hedgehog (SHH) is crucial in establishing the number and the identity of the digits during anteroposterior patterning of the limb. Its anterior ectopic expression is responsible for preaxial polydactyly (PPD). Most of these malformations are due to the gain-of-function of the Zone of Polarizing Activity Regulatory Sequence, the only limb-specific enhancer of SHH known to date. We report a family affected with a novel condition associating PPD and hypertrichosis of the upper back, following an autosomal dominant mode of inheritance. This phenotype is consistent with deregulation of SHH expression during limb and follicle development. In affected members, we identified a 2 kb deletion located ~240 kb upstream from the SHH promoter. The deleted sequence is capable of repressing the transcriptional activity of the SHH promoter in vitro, consistent with a silencer activity. We hypothesize that the deletion of this silencer could be responsible for SHH deregulation during development, leading to a PPD-hypertrichosis phenotype.
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Ruan W, Guo M, Cai L, Hu H, Li C, Liu Y, Wu Z, Mao C, Yi K, Wu P, Mo X. Genetic manipulation of a high-affinity PHR1 target cis-element to improve phosphorous uptake in Oryza sativa L. PLANT MOLECULAR BIOLOGY 2015; 87:429-40. [PMID: 25657119 DOI: 10.1007/s11103-015-0289-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 01/23/2015] [Indexed: 05/08/2023]
Abstract
Phosphorus (P) is an essential macronutrient for crop development and production. Phosphate starvation response 1 (PHR1) acts as the central regulator for Pi-signaling and Pi-homeostasis in plants by binding to the cis-element PHR1 binding sequence (P1BS; GNATATNC). However, how phosphate starvation-induced gene expression is regulated remains obscure. In this work, we investigated the DNA binding affinity of the PHR1 ortholog OsPHR2 to its downstream target genes in Oryza sativa (rice). We confirmed that a combination of P1BS and P1BS-like motifs are essential for stable binding by OsPHR2. Furthermore, we report that variations in P1BS motif bases affected the binding affinity of OsPHR2 and that the highest affinity motif was GaATATtC (designated the A-T-type P1BS). We also found that a combination of two A-T-type P1BS elements in tandem, namely HA-P1BS, was very efficient for binding of OsPHR2. Using the cis-regulator HA-P1BS, we modified the promoters of Transporter Traffic Facilitator 1 (PHF1), a key factor controlling endoplasmic reticulum-exit of phosphate transporters to the plasma membrane, for efficient uptake of phosphorous in an energetically neutral way. Transgenic plants with the modified promoters showed significantly enhanced tolerance to low phosphate stress in both solution and soil conditions, which provides a new strategy for crop improvement to enhance tolerance of nutrient deficiency.
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Affiliation(s)
- Wenyuan Ruan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China,
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Vanlerberghe C, Faivre L, Petit F, Fruchart O, Jourdain AS, Clavier F, Gay S, Manouvrier-Hanu S, Escande F. Intrafamilial variability of ZRS-associated syndrome: characterization of a mosaic ZRS mutation by pyrosequencing. Clin Genet 2015; 88:479-83. [PMID: 25382487 DOI: 10.1111/cge.12534] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/29/2014] [Accepted: 11/03/2014] [Indexed: 12/13/2022]
Abstract
During limb development, the spatio-temporal expression of sonic hedgehog (SHH) is driven by the Zone of polarizing activity Regulatory Sequence (ZRS), located 1 megabase upstream from SHH. Gain-of-function mutations of this enhancer, which cause ectopic expression of SHH, are known to be responsible for congenital limb malformations with variable expressivity, ranging from preaxial polydactyly or triphalangeal thumbs to polysyndactyly, which may also be associated with mesomelic deficiency. In this report, we describe a patient affected with mirror-image polydactyly of the four extremities and bilateral tibial deficiency. The proband's father had isolated preaxial polydactyly type II (PPD2). Using Sanger sequencing, a ZRS point mutation (NC_000007.14, g.156584153A>G, UCSC, Build hg.19) was only identified in the patient. However, pyrosequencing analysis enabled the detection of a 10% somatic mosaic in the blood and saliva from the father. To our knowledge, this is the first description of a ZRS mosaic mutation. This report highlights the complexity of genotype-phenotype correlation in ZRS-associated syndromes and the importance of detecting somatic mosaicism for accurate genetic counselling.
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Affiliation(s)
- C Vanlerberghe
- Institut de Biochimie et Génétique Moléculaire, Centre de Biologie Pathologie, CHRU, Lille, France.,Clinique de Génétique médicale, Hôpital Jeanne de Flandre, CHRU, Lille, France.,RADEME Research Team for Rare Metabolic and Developmental Diseases, Université Lille 2, Lille, France
| | - L Faivre
- Service de Génétique clinique, Hôpital d'enfants, Dijon, France
| | - F Petit
- Clinique de Génétique médicale, Hôpital Jeanne de Flandre, CHRU, Lille, France.,RADEME Research Team for Rare Metabolic and Developmental Diseases, Université Lille 2, Lille, France.,Faculté de Médecine, Université Lille II, Lille, France
| | - O Fruchart
- Institut de Biochimie et Génétique Moléculaire, Centre de Biologie Pathologie, CHRU, Lille, France.,RADEME Research Team for Rare Metabolic and Developmental Diseases, Université Lille 2, Lille, France
| | - A-S Jourdain
- Institut de Biochimie et Génétique Moléculaire, Centre de Biologie Pathologie, CHRU, Lille, France.,RADEME Research Team for Rare Metabolic and Developmental Diseases, Université Lille 2, Lille, France
| | - F Clavier
- Centre de référence national maladies rares des malformations des membres et de l'arthrogrypose chez l'enfant Saint Maurice, Hôpital Saint Maurice, Saint Maurice, France
| | - S Gay
- Service de pédiatrie, Centre Hospitalier William Morey, Chalon sur Saône, France
| | - S Manouvrier-Hanu
- Clinique de Génétique médicale, Hôpital Jeanne de Flandre, CHRU, Lille, France.,RADEME Research Team for Rare Metabolic and Developmental Diseases, Université Lille 2, Lille, France.,Faculté de Médecine, Université Lille II, Lille, France
| | - F Escande
- Institut de Biochimie et Génétique Moléculaire, Centre de Biologie Pathologie, CHRU, Lille, France.,RADEME Research Team for Rare Metabolic and Developmental Diseases, Université Lille 2, Lille, France
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VanderMeer JE, Smith RP, Jones SL, Ahituv N. Genome-wide identification of signaling center enhancers in the developing limb. Development 2014; 141:4194-8. [PMID: 25273087 PMCID: PMC4302890 DOI: 10.1242/dev.110965] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The limb is widely used as a model developmental system and changes to gene expression patterns in its signaling centers, notably the zone of polarizing activity (ZPA) and the apical ectodermal ridge (AER), are known to cause limb malformations and evolutionary differences in limb morphology. Although several genes that define these limb signaling centers have been described, the identification of regulatory elements that are active within these centers has been limited. By dissecting mouse E11.5 limbs that fluorescently mark the ZPA or AER, followed by fluorescence-activated cell sorting and low-cell H3K27ac ChIP-seq, we identified thousands of specific signaling-center enhancers. Our ChIP-seq datasets show strong correlation with ZPA- and AER-expressed genes, previously characterized functional ZPA and AER enhancers and enrichment for relevant biological terms related to limb development and malformation for the neighboring genes. Using transgenic assays, we show that several of these sequences function as ZPA and AER enhancers. Our results identify novel ZPA and AER enhancers that could be important regulators of genes involved in the establishment of these specialized regions and the patterning of tetrapod limbs.
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Affiliation(s)
- Julia E VanderMeer
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Robin P Smith
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Stacy L Jones
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
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40
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VanderMeer JE, Lozano R, Sun M, Xue Y, Daentl D, Jabs EW, Wilcox WR, Ahituv N. A novel ZRS mutation leads to preaxial polydactyly type 2 in a heterozygous form and Werner mesomelic syndrome in a homozygous form. Hum Mutat 2014; 35:945-8. [PMID: 24777739 DOI: 10.1002/humu.22581] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Point mutations in the zone of polarizing activity regulatory sequence (ZRS) are known to cause human limb malformations. Although most mutations cause preaxial polydactyly (PPD), triphalangeal thumb (TPT) or both, a mutation in position 404 of the ZRS causes more severe Werner mesomelic syndrome (WMS) for which malformations include the distal arm or leg bones in addition to the hands and/or feet. Of more than 15 reported families with ZRS mutations, only one homozygous individual has been reported, with no change in phenotype compared with heterozygotes. Here, we describe a novel point mutation in the ZRS, 402C>T (AC007097.4:g.105548C>T), that is transmitted through two Mexican families with one homozygous individual. The homozygous phenotype for this mutation, WMS, is more severe than the numerous heterozygous individuals genotyped from both families who have TPT and PPD. A mouse transgenic enhancer assay shows that this mutation causes an expansion of the enhancer's expression domain in the developing mouse limb, confirming its pathogenicity. Combined, our results identify a novel ZRS mutation in the Mexican population, 402C>T, and suggest that a dosage effect exists for this ZRS mutation.
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Affiliation(s)
- Julia E VanderMeer
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California; Institute for Human Genetics, University of California San Francisco, San Francisco, California
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41
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Ekblom AG, Laurell T, Arner M. Epidemiology of congenital upper limb anomalies in Stockholm, Sweden, 1997 to 2007: application of the Oberg, Manske, and Tonkin classification. J Hand Surg Am 2014; 39:237-48. [PMID: 24480684 DOI: 10.1016/j.jhsa.2013.11.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 11/03/2013] [Accepted: 11/04/2013] [Indexed: 02/02/2023]
Abstract
PURPOSE To investigate the epidemiology of congenital upper limb anomalies (CULA) based on the newly proposed Oberg, Manske, and Tonkin (OMT) classification, to compare this classification with the International Federation of Societies for Surgery of the Hand (IFSSH) classification, and to provide incidence rates of the different CULA. METHODS In this study, the same 562 individuals with a CULA who were analyzed in a previous epidemiologic study based on the IFSSH classification were reclassified according to the OMT classification. All children identified with CULA and born in Stockholm County between January 1, 1997 and December 31, 2007 were included in the study. During the period there were 261,914 live births in Stockholm County, and the population of Stockholm County was 1,949,516 inhabitants at the end of the period. From medical records and available radiographs, all cases were analyzed regarding type of CULA, sex, affected side, associated nonhand anomalies, and occurrence among relatives. Individuals with right and left side anomalies belonging to different OMT subgroups were counted as 2 anomalies; thus, the material consisted of 577 CULA in 562 children. RESULTS It was possible to organize all CULA into the OMT classification. The largest main category was malformations (429 cases), followed by deformations (124 cases), dysplasias (10 cases), and syndromes (14 cases). We present the relation between the IFSSH and OMT classifications, elucidate difficulties within the OMT classification, and propose additions to the classification. CONCLUSIONS This study confirms that the OMT classification is useful and accurate, but also points out difficulties. With further refinements, we regard the OMT classification as a needed and appropriate replacement for the IFSSH classification. TYPE OF STUDY/LEVEL OF EVIDENCE Diagnostic III.
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Affiliation(s)
- Anna Gerber Ekblom
- Section of Hand Surgery, Department of Clinical Science and Education; and the Department of Hand Surgery, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden.
| | - Tobias Laurell
- Section of Hand Surgery, Department of Clinical Science and Education; and the Department of Hand Surgery, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
| | - Marianne Arner
- Section of Hand Surgery, Department of Clinical Science and Education; and the Department of Hand Surgery, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
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42
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Dai L, Guo H, Meng H, Zhang K, Hu H, Yao H, Bai Y. Confirmation of genetic homogeneity of syndactyly type IV and triphalangeal thumb-polysyndactyly syndrome in a Chinese family and review of the literature. Eur J Pediatr 2013; 172:1467-73. [PMID: 23793141 DOI: 10.1007/s00431-013-2071-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/09/2013] [Indexed: 12/11/2022]
Abstract
UNLABELLED Syndactyly type IV (SD4) is inherited in an autosomal dominant fashion and characterized by complete cutaneous syndactyly of all fingers accompanied with polydactyly. Triphalangeal thumb-polysyndactyly syndrome (TPTPS) consists of a triphalangeal thumb, polydactyly, and syndactyly and is transmitted in an autosomal dominant manner with variable expression. Genomic duplications of the long-range limb-specific cis-regulator (ZRS) cause SD4 and TPTPS. Here, we report two individuals from a Chinese family with syndactyly. One individual had overlapping clinical symptoms of TPTPS and SD4, while the other had a typical SD4 with postaxial polydactyly of the toe. Results of quantitative PCR suggested that the duplication of ZRS involved all affected individuals, and array comparative genomic hybridization detected its size as 115.3 kb. CONCLUSION This work confirms the genetic homogeneity of SD4 and TPTPS. Our result expands the spectrum of ZRS duplications. TPTPS and SD4 should be considered as a continuum of phenotypes.
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Affiliation(s)
- Limeng Dai
- Department of Medical Genetics, College of Basic Medical Science, Third Military Medical University, Chongqing, 400038, China
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Coutton C, Poreau B, Devillard F, Durand C, Odent S, Rozel C, Vieville G, Amblard F, Jouk PS, Satre V. Currarino Syndrome and HPE Microform Associated with a 2.7-Mb Deletion in 7q36.3 Excluding SHH Gene. Mol Syndromol 2013; 5:25-31. [PMID: 24550762 DOI: 10.1159/000355391] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2013] [Indexed: 01/28/2023] Open
Abstract
Holoprosencephaly (HPE) is the most common forebrain defect in humans. It results from incomplete midline cleavage of the prosencephalon and can be caused by environmental and genetic factors. HPE is usually described as a continuum of brain malformations from the most severe alobar HPE to the middle interhemispheric fusion variant or syntelencephaly. A microform of HPE is limited to craniofacial features such as congenital nasal pyriform aperture stenosis and single central maxillary incisor, without brain malformation. Among the heterogeneous causes of HPE, point mutations and deletions in the SHH gene at 7q36 have been identified as well as extremely rare chromosomal rearrangements in the long-range enhancers of this gene. Here, we report a boy with an HPE microform associated with a Currarino syndrome. Array CGH detected a de novo 2.7-Mb deletion in the 7q36.3 region including the MNX1 gene, usually responsible for the Currarino triad but excluding SHH, which is just outside the deletion. This new case provides further evidence of the importance of the SHH long-range enhancers in the HPE spectrum.
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Affiliation(s)
- C Coutton
- Laboratoire de Génétique Chromosomique, Grenoble, France ; AGIM CNRS FRE3405, Equipe 'Andrologie, Génétique et Cancer', Université Joseph Fourier, Grenoble, France
| | - B Poreau
- Service de Génétique Clinique, Département de Génétique et Procréation, Grenoble, France
| | - F Devillard
- Laboratoire de Génétique Chromosomique, Grenoble, France
| | - C Durand
- Service de Radiopédiatrie, Hôpital Couple Enfant, CHU Grenoble, Grenoble, France
| | - S Odent
- Service de Génétique Clinique, Rennes, France
| | - C Rozel
- Service de Radiologie et Imagerie Médicale, Hôpital Sud, Rennes, France
| | - G Vieville
- Laboratoire de Génétique Chromosomique, Grenoble, France
| | - F Amblard
- Laboratoire de Génétique Chromosomique, Grenoble, France
| | - P-S Jouk
- Service de Génétique Clinique, Département de Génétique et Procréation, Grenoble, France
| | - V Satre
- Laboratoire de Génétique Chromosomique, Grenoble, France ; AGIM CNRS FRE3405, Equipe 'Andrologie, Génétique et Cancer', Université Joseph Fourier, Grenoble, France
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Su MY, Steiner LA, Bogardus H, Mishra T, Schulz VP, Hardison RC, Gallagher PG. Identification of biologically relevant enhancers in human erythroid cells. J Biol Chem 2013; 288:8433-8444. [PMID: 23341446 DOI: 10.1074/jbc.m112.413260] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Identification of cell type-specific enhancers is important for understanding the regulation of programs controlling cellular development and differentiation. Enhancers are typically marked by the co-transcriptional activator protein p300 or by groups of cell-expressed transcription factors. We hypothesized that a unique set of enhancers regulates gene expression in human erythroid cells, a highly specialized cell type evolved to provide adequate amounts of oxygen throughout the body. Using chromatin immunoprecipitation followed by massively parallel sequencing, genome-wide maps of candidate enhancers were constructed for p300 and four transcription factors, GATA1, NF-E2, KLF1, and SCL, using primary human erythroid cells. These data were combined with gene expression analyses, and candidate enhancers were identified. Consistent with their predicted function as candidate enhancers, there was statistically significant enrichment of p300 and combinations of co-localizing erythroid transcription factors within 1-50 kb of the transcriptional start site (TSS) of genes highly expressed in erythroid cells. Candidate enhancers were also enriched near genes with known erythroid cell function or phenotype. Candidate enhancers exhibited moderate conservation with mouse and minimal conservation with nonplacental vertebrates. Candidate enhancers were mapped to a set of erythroid-associated, biologically relevant, SNPs from the genome-wide association studies (GWAS) catalogue of NHGRI, National Institutes of Health. Fourteen candidate enhancers, representing 10 genetic loci, mapped to sites associated with biologically relevant erythroid traits. Fragments from these loci directed statistically significant expression in reporter gene assays. Identification of enhancers in human erythroid cells will allow a better understanding of erythroid cell development, differentiation, structure, and function and provide insights into inherited and acquired hematologic disease.
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Affiliation(s)
- Mack Y Su
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Laurie A Steiner
- Department of Pediatrics, University of Rochester, Rochester, New York 14642
| | - Hannah Bogardus
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Tejaswini Mishra
- Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Vincent P Schulz
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Patrick G Gallagher
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520; Departments of Pathology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06520.
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Selmer KK, Bryne E, Rødningen OK, Fannemel M. A de novo 163 kb interstitial 1q44 microdeletion in a boy with thin corpus callosum, psychomotor delay and seizures. Eur J Med Genet 2012; 55:715-8. [DOI: 10.1016/j.ejmg.2012.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 08/11/2012] [Indexed: 10/28/2022]
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Birnbaum RY, Everman DB, Murphy KK, Gurrieri F, Schwartz CE, Ahituv N. Functional characterization of tissue-specific enhancers in the DLX5/6 locus. Hum Mol Genet 2012; 21:4930-8. [PMID: 22914741 DOI: 10.1093/hmg/dds336] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Disruption of distaless homeobox 5 and 6 (Dlx5/6) in mice results in brain, craniofacial, genital, ear and limb defects. In humans, chromosomal aberrations in the DLX5/6 region, some of which do not encompass DLX5/6, are associated with split hand/foot malformation 1 (SHFM1) as well as intellectual disability, craniofacial anomalies and hearing loss, suggesting that the disruption of DLX5/6 regulatory elements could lead to these abnormalities. Here, we characterized enhancers in the DLX5/6 locus whose tissue-specific expression and genomic location along with previously characterized enhancers correlate with phenotypes observed in individuals with chromosomal abnormalities. By analyzing chromosomal aberrations at 7q21, we refined the minimal SHFM1 critical region and used comparative genomics to select 26 evolutionary conserved non-coding sequences in this critical region for zebrafish enhancer assays. Eight of these sequences were shown to function as brain, olfactory bulb, branchial arch, otic vesicle and fin enhancers, recapitulating dlx5a/6a expression. Using a mouse enhancer assay, several of these zebrafish enhancers showed comparable expression patterns in the branchial arch, otic vesicle, forebrain and/or limb at embryonic day 11.5. Examination of the coordinates of various chromosomal rearrangements in conjunction with the genomic location of these tissue-specific enhancers showed a correlation with the observed clinical abnormalities. Our findings suggest that chromosomal abnormalities that disrupt the function of these tissue-specific enhancers could be the cause of SHFM1 and its associated phenotypes. In addition, they highlight specific enhancers in which mutations could lead to non-syndromic hearing loss, craniofacial defects or limb malformations.
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Affiliation(s)
- Ramon Y Birnbaum
- Department of Bioengineering and Therapeutic Sciences and 2Institute for Human Genetics, University of California-San Francisco, CA, USA
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Al-Qattan MM, Al Abdulkareem I, Al Haidan Y, Al Balwi M. A novel mutation in the SHH long-range regulator (ZRS) is associated with preaxial polydactyly, triphalangeal thumb, and severe radial ray deficiency. Am J Med Genet A 2012; 158A:2610-5. [PMID: 22903933 DOI: 10.1002/ajmg.a.35584] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 07/02/2012] [Indexed: 12/12/2022]
Abstract
Sonic Hedgehog (SHH) within the posteriorly located zone of polarizing activity is the main controller of the antero-posterior axis of limb development. The ZRS (zone of polarizing activity regulatory sequence) is a long-range limb-specific SHH enhancer. Several point mutations in the ZRS have been described in humans. These mutations cause enhanced SHH activity and ectopic anterior expression of SHH and a variable phenotype of preaxial polydactyly and triphalangeal thumb. Absent thumb or radius has not been reported with ZRS mutations. Here, we report on a family with a variable phenotype of preaxial polydactyly as well as absent thumb and radius, with kidney and cardiac defects. The family was screened for SALL1, SALL4, and TBX5 mutations, but all were normal. Finally, they were screened for ZRS mutations, which showed a novel point mutation within the ZRS, NG_009240.1: g.106954C>T (traditional nomenclature: ZRS619C>T) in the five affected members. This mutation was not previously reported in any public domain database, and was not found in our healthy and ethnically matched control individuals or unaffected family members. We hypothesize that interactions of SHH and SALL1 explain the overlapping features of the family described here and patients with Townes-Brocks syndrome.
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Zuniga A, Laurent F, Lopez-Rios J, Klasen C, Matt N, Zeller R. Conserved cis-regulatory regions in a large genomic landscape control SHH and BMP-regulated Gremlin1 expression in mouse limb buds. BMC DEVELOPMENTAL BIOLOGY 2012; 12:23. [PMID: 22888807 PMCID: PMC3541112 DOI: 10.1186/1471-213x-12-23] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/12/2012] [Indexed: 02/07/2023]
Abstract
Background Mouse limb bud is a prime model to study the regulatory interactions that control vertebrate organogenesis. Major aspects of limb bud development are controlled by feedback loops that define a self-regulatory signalling system. The SHH/GREM1/AER-FGF feedback loop forms the core of this signalling system that operates between the posterior mesenchymal organiser and the ectodermal signalling centre. The BMP antagonist Gremlin1 (GREM1) is a critical node in this system, whose dynamic expression is controlled by BMP, SHH, and FGF signalling and key to normal progression of limb bud development. Previous analysis identified a distant cis-regulatory landscape within the neighbouring Formin1 (Fmn1) locus that is required for Grem1 expression, reminiscent of the genomic landscapes controlling HoxD and Shh expression in limb buds. Results Three highly conserved regions (HMCO1-3) were identified within the previously defined critical genomic region and tested for their ability to regulate Grem1 expression in mouse limb buds. Using a combination of BAC and conventional transgenic approaches, a 9 kb region located ~70 kb downstream of the Grem1 transcription unit was identified. This region, termed Grem1 Regulatory Sequence 1 (GRS1), is able to recapitulate major aspects of Grem1 expression, as it drives expression of a LacZ reporter into the posterior and, to a lesser extent, in the distal-anterior mesenchyme. Crossing the GRS1 transgene into embryos with alterations in the SHH and BMP pathways established that GRS1 depends on SHH and is modulated by BMP signalling, i.e. integrates inputs from these pathways. Chromatin immunoprecipitation revealed interaction of endogenous GLI3 proteins with the core cis-regulatory elements in the GRS1 region. As GLI3 is a mediator of SHH signal transduction, these results indicated that SHH directly controls Grem1 expression through the GRS1 region. Finally, all cis-regulatory regions within the Grem1 genomic landscape locate to the DNAse I hypersensitive sites identified in this genomic region by the ENCODE consortium. Conclusions This study establishes that distant cis-regulatory regions scattered through a larger genomic landscape control the highly dynamic expression of Grem1, which is key to normal progression of mouse limb bud development.
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Affiliation(s)
- Aimée Zuniga
- Developmental Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058, Basel, Switzerland.
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VanderMeer JE, Afzal M, Alyas S, Haque S, Ahituv N, Malik S. A novel ZRS mutation in a Balochi tribal family with triphalangeal thumb, pre-axial polydactyly, post-axial polydactyly, and syndactyly. Am J Med Genet A 2012; 158A:2031-5. [PMID: 22786669 DOI: 10.1002/ajmg.a.35473] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/18/2012] [Indexed: 12/19/2022]
Abstract
Limb malformations are one of the most common types of human congenital malformations. Mutations in the ZRS enhancer of Sonic Hedgehog are thought to be responsible for pre-axial polydactyly in multiple independent families. Here, we describe a large Balochi tribal family from Southern Punjab, Pakistan, with a variable set of limb malformations and a novel ZRS mutation. The family has a limb phenotype characterized by triphalangeal thumb, pre-axial polydactyly, and post-axial polydactyly. There is also a high degree of phenotypic heterogeneity with less common clinical findings in the affected family members that include osseous syndactyly of forth-fifth fingers, clinodactyly, hypoplasia of mesoaxial fingers, and bifid halluces. The presentation in most of the affected patients was bilateral and symmetrical. A heterozygous C>A mutation at position 287 of the ZRS enhancer (chr7:156,584,283; hg19) was detected in all affected subjects and is absent from four unaffected family members, 42 unrelated samples, and multiple databases of human variation. Combined, these results identify a novel ZRS287 C>A mutation which leads to a variable spectrum of limb phenotypes.
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Affiliation(s)
- Julia E VanderMeer
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94143, USA
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Lu W, Bacino CA, Richards BS, Alvarez C, VanderMeer JE, Vella M, Ahituv N, Sikka N, Dietz FR, Blanton SH, Hecht JT. Studies of TBX4 and chromosome 17q23.1q23.2: an uncommon cause of nonsyndromic clubfoot. Am J Med Genet A 2012; 158A:1620-7. [PMID: 22678995 DOI: 10.1002/ajmg.a.35418] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 03/21/2012] [Indexed: 01/28/2023]
Abstract
Clubfoot is a common birth defect characterized by inward posturing and rigid downward displacement of one or both feet. The etiology of syndromic forms of clubfoot is varied and the causes of isolated clubfoot are not well understood. A microduplication of 2.2 Mb on chromosome 17q23.1q23.2 which includes T-box 4 (TBX4), a hindlimb-specific gene, and 16 other genes was recently identified in 3 of 66 families reported as nonsyndromic clubfoot, but additional non-foot malformations place them in the syndromic clubfoot category. Our study assesses whether variation in or around TBX4 contributes to nonsyndromic clubfoot. To determine whether this microduplication was a common cause of nonsyndromic clubfoot, 605 probands (from 148 multiplex and 457 simplex families) with nonsyndromic clubfoot were evaluated by copy number and oligonucleotide array CGH testing modalities. Only one multiplex family (0.68%) that had 16 with clubfoot and 9 with other foot anomalies, had a 350 kb microduplication, which included the complete duplication of TBX4 and NACA2 and partial duplication of BRIP1. The microduplication was transmitted in an autosomal dominant pattern and all with the microduplication had a range of phenotypes from short wide feet and toes to bilateral clubfoot. Minimal evidence was found for an association between TBX4 and clubfoot and no pathogenic sequence variants were identified in the two known TBX4 hindlimb enhancer elements. Altogether, these results demonstrate that variation in and around the TBX4 gene and the 17q23.1q23.2 microduplication are not a frequent cause of this common orthopedic birth defect and narrows the 17q23.1q23.2 nonsyndromic clubfoot-associated region.
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Affiliation(s)
- W Lu
- Department of Pediatrics, University of Texas Medical School at Houston, Houston, Texas 77030, USA
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