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Feng Y, Xie N, Inoue F, Fan S, Saskin J, Zhang C, Zhang F, Hansen MEB, Nyambo T, Mpoloka SW, Mokone GG, Fokunang C, Belay G, Njamnshi AK, Marks MS, Oancea E, Ahituv N, Tishkoff SA. Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans. Nat Genet 2024; 56:258-272. [PMID: 38200130 PMCID: PMC11005318 DOI: 10.1038/s41588-023-01626-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/28/2023] [Indexed: 01/12/2024]
Abstract
Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles. We combine Hi-C, genome editing and melanin assays to identify regulatory elements for MFSD12, HMG20B, OCA2, MITF, LEF1, TRPS1, BLOC1S6 and CYB561A3 that impact melanin levels in vitro and modulate human skin color. We found that independent mutations in an OCA2 enhancer contribute to the evolution of human skin color diversity and detect signals of local adaptation at enhancers of MITF, LEF1 and TRPS1, which may contribute to the light skin color of Khoesan-speaking populations from Southern Africa. Additionally, we identified CYB561A3 as a novel pigmentation regulator that impacts genes involved in oxidative phosphorylation and melanogenesis. These results provide insights into the mechanisms underlying human skin color diversity and adaptive evolution.
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Affiliation(s)
- Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ning Xie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fumitaka Inoue
- 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
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Shaohua Fan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Human Phenome Institute, School of Life Science, Fudan University, Shanghai, China
| | - Joshua Saskin
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Chao Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fang Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Nyambo
- Department of Biochemistry and Molecular Biology, Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alfred K Njamnshi
- Brain Research Africa Initiative (BRAIN); Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Department of Neurology, Central Hospital Yaoundé, Yaoundé, Cameroon
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Elena Oancea
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - 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
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Global Genomics and Health Equity, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Beyer T, Martins T, Srikaran JJ, Seda M, Peskett E, Klose F, Junger K, Beales PL, Ueffing M, Boldt K, Jenkins D. Affinity Purification of Intraflagellar Transport (IFT) Proteins in Mice Using Endogenous Streptavidin/FLAG Tags. Methods Mol Biol 2024; 2725:199-212. [PMID: 37856026 DOI: 10.1007/978-1-0716-3507-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Biological complexity is achieved through elaborate interactions between relatively few individual components. Affinity purification (AP) has allowed these networks of protein-protein interactions that regulate key biological processes to be interrogated systematically. In order to perform these studies at the required scale, easily transfectable immortalized cell lines have typically been used. Gene-editing now affords the systematic creation of isogenic mouse models carrying endogenous tags for affinity proteomics. This may allow protein-protein interactions to be characterized in the appropriate tissue for a particular biological process or disease phenotype under physiological conditions, and for interaction landscapes to be compared across tissues. Here we demonstrate application to intraflagellar transport (IFT) proteins, which are WD40-domain-containing proteins that are essential for the formation and function of all types of cilia. We describe a method to generate mice with an endogenous C-terminal streptavidin/FLAG tag, using Ift80 as an example, and demonstrate the successful implementation of AP in this model. This method can easily be adapted for N- and C-terminal tagging of many other proteins in vivo.
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Affiliation(s)
- Tina Beyer
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Tiago Martins
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Marian Seda
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Emma Peskett
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Franziska Klose
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Katrin Junger
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Philip L Beales
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Marius Ueffing
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Karsten Boldt
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Dagan Jenkins
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK.
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3
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Guardia A, Fernández A, Seruggia D, Chotard V, Sánchez-Castillo C, Kutsyr O, Sánchez-Sáez X, Zurita E, Cantero M, Rebsam A, Cuenca N, Montoliu L. A Slc38a8 Mouse Model of FHONDA Syndrome Faithfully Recapitulates the Visual Deficits of Albinism Without Pigmentation Defects. Invest Ophthalmol Vis Sci 2023; 64:32. [PMID: 37862028 PMCID: PMC10599165 DOI: 10.1167/iovs.64.13.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023] Open
Abstract
Purpose We aimed to generate and phenotype a mouse model of foveal hypoplasia, optic nerve decussation defects, and anterior segment dysgenesis (FHONDA), a rare disease associated with mutations in Slc38a8 that causes severe visual alterations similar to albinism without affecting pigmentation. Methods The FHONDA mouse model was generated with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology using an RNA guide targeting the Scl38a8 murine locus. The resulting mice were backcrossed to C57BL/6J. Melanin content was measured using spectrophotometry. Retinal cell architecture was analyzed through light and electron microscopy. Retinal projections to the brain were evaluated with anterograde labelling in embryos and adults. Visual function was assessed by electroretinography (ERG) and the optomotor test (OT). Results From numerous Slc38a8 mouse mutant alleles generated, we selected one that encodes a truncated protein (p.196Pro*, equivalent to p.199Pro* in the human protein) closely resembling a mutant allele described in patients (p.200Gln*). Slc38a8 mutant mice exhibit wild-type eye and coat pigmentation with comparable melanin content. Subcellular abnormalities were observed in retinal pigment epithelium cells of Slc38a8 mutant mice. Anterograde labeling experiments of retinal projections in embryos and adults showed a reduction of ipsilateral fibers. Functional visual analyses revealed a decreased ERG response in scotopic conditions and a reduction of visual acuity in mutant mice measured by OT. Conclusions Slc38a8 mutant mice recapitulate the phenotype of patients with FHONDA concerning their normal pigmentation and their abnormal visual system, in the latter being a hallmark of all types of albinism. These mice will be helpful in better understanding the pathophysiology of this genetic condition.
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Affiliation(s)
- Ana Guardia
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain
| | - Almudena Fernández
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain
| | - Davide Seruggia
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain
| | - Virginie Chotard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Carla Sánchez-Castillo
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Oksana Kutsyr
- Department of Optics, Pharmacology and Anatomy, University of Alicante, Alicante, Spain
| | - Xavier Sánchez-Sáez
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Esther Zurita
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain
| | - Marta Cantero
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain
| | - Alexandra Rebsam
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Nicolás Cuenca
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Lluís Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain
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Huang L, Han F, Huang Y, Liu J, Liao X, Cao Z, Li W. Sphk1 deficiency induces apoptosis and developmental defects and premature death in zebrafish. FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:737-750. [PMID: 37464180 DOI: 10.1007/s10695-023-01215-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/24/2023] [Indexed: 07/20/2023]
Abstract
The sphk1 gene plays a crucial role in cell growth and signal transduction. However, the developmental functions of the sphk1 gene during early vertebrate zebrafish embryo remain not completely understood. In this study, we constructed zebrafish sphk1 mutants through CRISPR/Cas9 to investigate its role in zebrafish embryonic development. Knockout of the sphk1 gene was found to cause abnormal development in zebrafish embryos, such as darkening and atrophy of the head, trunk deformities, pericardial edema, retarded yolk sac development, reduced heart rate, and premature death. The acetylcholinesterase activity was significantly increased after the knockout of sphk1, and some of the neurodevelopmental genes and neurotransmission system-related genes were expressed abnormally. The deletion of sphk1 led to abnormal expression of immune genes, as well as a significant decrease in the number of hematopoietic stem cells and neutrophils. The mRNA levels of cardiac development-related genes were significantly decreased. In addition, cell apoptosis increases in the sphk1 mutants, and the proliferation of head cells decreases. Therefore, our study has shown that the sphk1 is a key gene for zebrafish embryonic survival and regulation of organ development. It deepened our understanding of its physiological function. Our study lays the foundation for investigating the mechanism of the sphk1 gene in early zebrafish embryonic development.
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Affiliation(s)
- Ling Huang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Fang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Ying Huang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Jieping Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Xinjun Liao
- Jiangxi Engineering Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases, Jiangxi Key Laboratory of Developmental Biology of Organs, College of Life Sciences, Jinggangshan University, Ji'an, China
| | - Zigang Cao
- Jiangxi Engineering Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases, Jiangxi Key Laboratory of Developmental Biology of Organs, College of Life Sciences, Jinggangshan University, Ji'an, China.
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China.
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5
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Alonso-Lerma B, Jabalera Y, Samperio S, Morin M, Fernandez A, Hille LT, Silverstein RA, Quesada-Ganuza A, Reifs A, Fernández-Peñalver S, Benitez Y, Soletto L, Gavira JA, Diaz A, Vranken W, Sanchez-Mejias A, Güell M, Mojica FJM, Kleinstiver BP, Moreno-Pelayo MA, Montoliu L, Perez-Jimenez R. Evolution of CRISPR-associated endonucleases as inferred from resurrected proteins. Nat Microbiol 2023; 8:77-90. [PMID: 36593295 DOI: 10.1038/s41564-022-01265-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/07/2022] [Indexed: 01/03/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas9 is an effector protein that targets invading DNA and plays a major role in the prokaryotic adaptive immune system. Although Streptococcus pyogenes CRISPR-Cas9 has been widely studied and repurposed for applications including genome editing, its origin and evolution are poorly understood. Here, we investigate the evolution of Cas9 from resurrected ancient nucleases (anCas) in extinct firmicutes species that last lived 2.6 billion years before the present. We demonstrate that these ancient forms were much more flexible in their guide RNA and protospacer-adjacent motif requirements compared with modern-day Cas9 enzymes. Furthermore, anCas portrays a gradual palaeoenzymatic adaptation from nickase to double-strand break activity, exhibits high levels of activity with both single-stranded DNA and single-stranded RNA targets and is capable of editing activity in human cells. Prediction and characterization of anCas with a resurrected protein approach uncovers an evolutionary trajectory leading to functionally flexible ancient enzymes.
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Affiliation(s)
| | | | | | - Matias Morin
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Centro de Investigaciones Biomédicas en Red de Enfermedades Raras, Madrid, Spain
| | - Almudena Fernandez
- Department of Molecular and Cellular Biology, National Centre for Biotechnology and Centre for Biomedical Network Research on Rare Diseases, Madrid, Spain
| | - Logan T Hille
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,PhD Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA
| | - Rachel A Silverstein
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,PhD Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA
| | | | | | - Sergio Fernández-Peñalver
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Centro de Investigaciones Biomédicas en Red de Enfermedades Raras, Madrid, Spain
| | - Yolanda Benitez
- Department of Molecular and Cellular Biology, National Centre for Biotechnology and Centre for Biomedical Network Research on Rare Diseases, Madrid, Spain.,INGEMM, Hospital Universitario La Paz, Madrid, Spain
| | - Lucia Soletto
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Centro de Investigaciones Biomédicas en Red de Enfermedades Raras, Madrid, Spain
| | - Jose A Gavira
- Laboratorio de Estudios Cristalográficos, IACT, Armilla, Spain
| | - Adrian Diaz
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Centre, VIB, Brussels, Belgium
| | | | - Marc Güell
- Integra Therapeutics S.L., Barcelona, Spain.,Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francisco J M Mojica
- Dpto. Fisiología, Genética y Microbiología and Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Universidad de Alicante, Alicante, Spain
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Miguel A Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Centro de Investigaciones Biomédicas en Red de Enfermedades Raras, Madrid, Spain
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology and Centre for Biomedical Network Research on Rare Diseases, Madrid, Spain
| | - Raul Perez-Jimenez
- CIC nanoGUNE BRTA, San Sebastian, Spain. .,Ikerbasque Foundation for Science, Bilbao, Spain.
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6
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Montoliu L. Transgenesis and Genome Engineering: A Historical Review. Methods Mol Biol 2023; 2631:1-32. [PMID: 36995662 DOI: 10.1007/978-1-0716-2990-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Our ability to modify DNA molecules and to introduce them into mammalian cells or embryos almost appears in parallel, starting from the 1970s of the last century. Genetic engineering techniques rapidly developed between 1970 and 1980. In contrast, robust procedures to microinject or introduce DNA constructs into individuals did not take off until 1980 and evolved during the following two decades. For some years, it was only possible to add transgenes, de novo, of different formats, including artificial chromosomes, in a variety of vertebrate species or to introduce specific mutations essentially in mice, thanks to the gene-targeting methods by homologous recombination approaches using mouse embryonic stem (ES) cells. Eventually, genome-editing tools brought the possibility to add or inactivate DNA sequences, at specific sites, at will, irrespective of the animal species involved. Together with a variety of additional techniques, this chapter will summarize the milestones in the transgenesis and genome engineering fields from the 1970s to date.
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Affiliation(s)
- Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC) and Center for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain.
- National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.
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7
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Ferre-Fernández JJ, Muheisen S, Thompson S, Semina EV. CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements. Hum Genomics 2022; 16:49. [PMID: 36284357 PMCID: PMC9597995 DOI: 10.1186/s40246-022-00423-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
FOXC1 encodes a forkhead-domain transcription factor associated with several ocular disorders. Correct FOXC1 dosage is critical to normal development, yet the mechanisms controlling its expression remain unknown. Together with FOXQ1 and FOXF2, FOXC1 is part of a cluster of FOX genes conserved in vertebrates. CRISPR-Cas9-mediated dissection of genomic sequences surrounding two zebrafish orthologs of FOXC1 was performed. This included five zebrafish-human conserved regions, three downstream of foxc1a and two remotely upstream of foxf2a/foxc1a or foxf2b/foxc1b clusters, as well as two intergenic regions between foxc1a/b and foxf2a/b lacking sequence conservation but positionally corresponding to the area encompassing a previously reported glaucoma-associated SNP in humans. Removal of downstream sequences altered foxc1a expression; moreover, zebrafish carrying deletions of two or three downstream elements demonstrated abnormal phenotypes including enlargement of the anterior chamber of the eye reminiscent of human congenital glaucoma. Deletions of distant upstream conserved elements influenced the expression of foxf2a/b or foxq1a/b but not foxc1a/b within each cluster. Removal of either intergenic sequence reduced foxc1a or foxc1b expression during late development, suggesting a role in transcriptional regulation despite the lack of conservation at the nucleotide level. Further studies of the identified regions in human patients may explain additional individuals with developmental ocular disorders.
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Affiliation(s)
- Jesús-José Ferre-Fernández
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Sanaa Muheisen
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Samuel Thompson
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA.
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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8
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Mukherjee P, Roy S, Ghosh D, Nandi SK. Role of animal models in biomedical research: a review. Lab Anim Res 2022; 38:18. [PMID: 35778730 PMCID: PMC9247923 DOI: 10.1186/s42826-022-00128-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
The animal model deals with the species other than the human, as it can imitate the disease progression, its’ diagnosis as well as a treatment similar to human. Discovery of a drug and/or component, equipment, their toxicological studies, dose, side effects are in vivo studied for future use in humans considering its’ ethical issues. Here lies the importance of the animal model for its enormous use in biomedical research. Animal models have many facets that mimic various disease conditions in humans like systemic autoimmune diseases, rheumatoid arthritis, epilepsy, Alzheimer’s disease, cardiovascular diseases, Atherosclerosis, diabetes, etc., and many more. Besides, the model has tremendous importance in drug development, development of medical devices, tissue engineering, wound healing, and bone and cartilage regeneration studies, as a model in vascular surgeries as well as the model for vertebral disc regeneration surgery. Though, all the models have some advantages as well as challenges, but, present review has emphasized the importance of various small and large animal models in pharmaceutical drug development, transgenic animal models, models for medical device developments, studies for various human diseases, bone and cartilage regeneration model, diabetic and burn wound model as well as surgical models like vascular surgeries and surgeries for intervertebral disc degeneration considering all the ethical issues of that specific animal model. Despite, the process of using the animal model has facilitated researchers to carry out the researches that would have been impossible to accomplish in human considering the ethical prohibitions.
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Affiliation(s)
- P Mukherjee
- Department of Veterinary Clinical Complex, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, India
| | - S Roy
- Department of Veterinary Clinical Complex, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, India
| | - D Ghosh
- Department of Veterinary Surgery and Radiology, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - S K Nandi
- Department of Veterinary Surgery and Radiology, West Bengal University of Animal and Fishery Sciences, Kolkata, India.
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9
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López-Márquez A, Morín M, Fernández-Peñalver S, Badosa C, Hernández-Delgado A, Natera-de Benito D, Ortez C, Nascimento A, Grinberg D, Balcells S, Roldán M, Moreno-Pelayo MÁ, Jiménez-Mallebrera C. CRISPR/Cas9-Mediated Allele-Specific Disruption of a Dominant COL6A1 Pathogenic Variant Improves Collagen VI Network in Patient Fibroblasts. Int J Mol Sci 2022; 23:ijms23084410. [PMID: 35457228 PMCID: PMC9025481 DOI: 10.3390/ijms23084410] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 02/04/2023] Open
Abstract
Collagen VI-related disorders are the second most common congenital muscular dystrophies for which no treatments are presently available. They are mostly caused by dominant-negative pathogenic variants in the genes encoding α chains of collagen VI, a heteromeric network forming collagen; for example, the c.877G>A; p.Gly293Arg COL6A1 variant, which alters the proper association of the tetramers to form microfibrils. We tested the potential of CRISPR/Cas9-based genome editing to silence or correct (using a donor template) a mutant allele in the dermal fibroblasts of four individuals bearing the c.877G>A pathogenic variant. Evaluation of gene-edited cells by next-generation sequencing revealed that correction of the mutant allele by homologous-directed repair occurred at a frequency lower than 1%. However, the presence of frameshift variants and others that provoked the silencing of the mutant allele were found in >40% of reads, with no effects on the wild-type allele. This was confirmed by droplet digital PCR with allele-specific probes, which revealed a reduction in the expression of the mutant allele. Finally, immunofluorescence analyses revealed a recovery in the collagen VI extracellular matrix. In summary, we demonstrate that CRISPR/Cas9 gene-edition can specifically reverse the pathogenic effects of a dominant negative variant in COL6A1.
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Affiliation(s)
- Arístides López-Márquez
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain; (C.B.); (A.H.-D.); (D.N.-d.B.); (C.O.); (A.N.); (C.J.-M.)
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.M.); (D.G.); (S.B.); (M.Á.M.-P.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
- Correspondence:
| | - Matías Morín
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.M.); (D.G.); (S.B.); (M.Á.M.-P.)
- Servicio de Genética, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, Ctra. de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain;
| | - Sergio Fernández-Peñalver
- Servicio de Genética, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, Ctra. de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain;
| | - Carmen Badosa
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain; (C.B.); (A.H.-D.); (D.N.-d.B.); (C.O.); (A.N.); (C.J.-M.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
| | - Alejandro Hernández-Delgado
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain; (C.B.); (A.H.-D.); (D.N.-d.B.); (C.O.); (A.N.); (C.J.-M.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
| | - Daniel Natera-de Benito
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain; (C.B.); (A.H.-D.); (D.N.-d.B.); (C.O.); (A.N.); (C.J.-M.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
| | - Carlos Ortez
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain; (C.B.); (A.H.-D.); (D.N.-d.B.); (C.O.); (A.N.); (C.J.-M.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
| | - Andrés Nascimento
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain; (C.B.); (A.H.-D.); (D.N.-d.B.); (C.O.); (A.N.); (C.J.-M.)
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.M.); (D.G.); (S.B.); (M.Á.M.-P.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
| | - Daniel Grinberg
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.M.); (D.G.); (S.B.); (M.Á.M.-P.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
- Departamento de Genética, Microbiología y Estadística, Facultad de Biología, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Susanna Balcells
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.M.); (D.G.); (S.B.); (M.Á.M.-P.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
- Departamento de Genética, Microbiología y Estadística, Facultad de Biología, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Mónica Roldán
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
- Unidad de Microscopia Confocal e Imagen Celular, Servicio de Medicina Genética y Molecular, Institut Pediàtric de Malalties Rares (IPER), Hospital Sant Joan de Déu, Passeig Sant Joan de Deu, 2, 08950 Esplugues de Llobregat, Spain
| | - Miguel Ángel Moreno-Pelayo
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.M.); (D.G.); (S.B.); (M.Á.M.-P.)
- Servicio de Genética, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, Ctra. de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain;
| | - Cecilia Jiménez-Mallebrera
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain; (C.B.); (A.H.-D.); (D.N.-d.B.); (C.O.); (A.N.); (C.J.-M.)
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.M.); (D.G.); (S.B.); (M.Á.M.-P.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
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10
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Montoliu L. Historical DNA Manipulation Overview. Methods Mol Biol 2022; 2495:3-28. [PMID: 35696025 DOI: 10.1007/978-1-0716-2301-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The history of DNA manipulation for the creation of genetically modified animals began in the 1970s, using viruses as the first DNA molecules microinjected into mouse embryos at different preimplantation stages. Subsequently, simple DNA plasmids were used to microinject into the pronuclei of fertilized mouse oocytes and that method became the reference for many years. The isolation of embryonic stem cells together with advances in genetics allowed the generation of gene-specific knockout mice, later on improved with conditional mutations. Cloning procedures expanded the gene inactivation to livestock and other non-model mammalian species. Lentiviruses, artificial chromosomes, and intracytoplasmic sperm injections expanded the toolbox for DNA manipulation. The last chapter of this short but intense history belongs to programmable nucleases, particularly CRISPR-Cas systems, triggering the development of genomic-editing techniques, the current revolution we are living in.
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Affiliation(s)
- Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC) and Center for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain.
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11
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Singh H, Seruggia D, Madha S, Saxena M, Nagaraja AK, Wu Z, Zhou J, Huebner AJ, Maglieri A, Wezenbeek J, Hochedlinger K, Orkin SH, Bass AJ, Hornick JL, Shivdasani RA. Transcription factor-mediated intestinal metaplasia and the role of a shadow enhancer. Genes Dev 2021; 36:38-52. [PMID: 34969824 PMCID: PMC8763054 DOI: 10.1101/gad.348983.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022]
Abstract
Here, Singh et al. show extensive but selective recruitment of intestinal enhancers by CDX2 in gastric cells and that HNF4A-mediated ectopic CDX2 expression in the stomach occurs through a conserved shadow cis-element. These findings identify mechanisms for TF-driven intestinal metaplasia and a likely pathogenic TF hierarchy. Barrett's esophagus (BE) and gastric intestinal metaplasia are related premalignant conditions in which areas of human stomach epithelium express mixed gastric and intestinal features. Intestinal transcription factors (TFs) are expressed in both conditions, with unclear causal roles and cis-regulatory mechanisms. Ectopic CDX2 reprogrammed isogenic mouse stomach organoid lines to a hybrid stomach–intestinal state transcriptionally similar to clinical metaplasia; squamous esophageal organoids resisted this CDX2-mediated effect. Reprogramming was associated with induced activity at thousands of previously inaccessible intestine-restricted enhancers, where CDX2 occupied DNA directly. HNF4A, a TF recently implicated in BE pathogenesis, induced weaker intestinalization by binding a novel shadow Cdx2 enhancer and hence activating Cdx2 expression. CRISPR/Cas9-mediated germline deletion of that cis-element demonstrated its requirement in Cdx2 induction and in the resulting activation of intestinal genes in stomach cells. dCas9-conjugated KRAB repression mapped this activity to the shadow enhancer's HNF4A binding site. Altogether, we show extensive but selective recruitment of intestinal enhancers by CDX2 in gastric cells and that HNF4A-mediated ectopic CDX2 expression in the stomach occurs through a conserved shadow cis-element. These findings identify mechanisms for TF-driven intestinal metaplasia and a likely pathogenic TF hierarchy.
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Affiliation(s)
- Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Davide Seruggia
- Division of Hematology Oncology, Boston Children's Hospital, Boston, Massachusetts 02215, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Shariq Madha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Madhurima Saxena
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ankur K Nagaraja
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zhong Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Jin Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Aaron J Huebner
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
| | - Adrianna Maglieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Juliette Wezenbeek
- Hubretch Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Utrecht 3584 CT, Netherlands
| | - Konrad Hochedlinger
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Stuart H Orkin
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Hematology Oncology, Boston Children's Hospital, Boston, Massachusetts 02215, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02215, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jason L Hornick
- Departments of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
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12
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Fernández A, Hayashi M, Garrido G, Montero A, Guardia A, Suzuki T, Montoliu L. Genetics of non-syndromic and syndromic oculocutaneous albinism in human and mouse. Pigment Cell Melanoma Res 2021; 34:786-799. [PMID: 33960688 DOI: 10.1111/pcmr.12982] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/12/2023]
Abstract
Oculocutaneous albinism (OCA) is the most frequent presentation of albinism, a heterogeneous rare genetic condition generally associated with variable alterations in pigmentation and with a profound visual impairment. There are non-syndromic and syndromic types of OCA, depending on whether the gene product affected impairs essentially the function of melanosomes or, in addition, that of other lysosome-related organelles (LROs), respectively. Syndromic OCA can be more severe and associated with additional systemic consequences, beyond pigmentation and vision alterations. In addition to OCA, albinism can also be presented without obvious skin and hair pigmentation alterations, in ocular albinism (OA), and a related genetic condition known as foveal hypoplasia, optic nerve decussation defects, and anterior segment dysgenesis (FHONDA). In this review, we will focus only in the genetics of skin pigmentation in OCA, both in human and mouse, updating our current knowledge on this subject.
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Affiliation(s)
- Almudena Fernández
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.,CIBERER-ISCIII, Madrid, Spain
| | - Masahiro Hayashi
- Department of Dermatology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Gema Garrido
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.,CIBERER-ISCIII, Madrid, Spain
| | - Andrea Montero
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.,CIBERER-ISCIII, Madrid, Spain
| | - Ana Guardia
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.,CIBERER-ISCIII, Madrid, Spain
| | - Tamio Suzuki
- Department of Dermatology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.,CIBERER-ISCIII, Madrid, Spain
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13
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Wu Q, Shou J. Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering. J Mol Cell Biol 2021; 12:828-856. [PMID: 33125070 PMCID: PMC7883824 DOI: 10.1093/jmcb/mjaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes. CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries. Recent studies revealed, however, that the CRISPR genome-editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise 1D gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.
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Affiliation(s)
- Qiang Wu
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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14
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Murillo-Cuesta S, Artuch R, Asensio F, de la Villa P, Dierssen M, Enríquez JA, Fillat C, Fourcade S, Ibáñez B, Montoliu L, Oliver E, Pujol A, Salido E, Vallejo M, Varela-Nieto I. The Value of Mouse Models of Rare Diseases: A Spanish Experience. Front Genet 2020; 11:583932. [PMID: 33173540 PMCID: PMC7591746 DOI: 10.3389/fgene.2020.583932] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/14/2020] [Indexed: 11/13/2022] Open
Abstract
Animal models are invaluable for biomedical research, especially in the context of rare diseases, which have a very low prevalence and are often complex. Concretely mouse models provide key information on rare disease mechanisms and therapeutic strategies that cannot be obtained by using only alternative methods, and greatly contribute to accelerate the development of new therapeutic options for rare diseases. Despite this, the use of experimental animals remains controversial. The combination of respectful management, ethical laws and transparency regarding animal experimentation contributes to improve society’s opinion about biomedical research and positively impacts on research quality, which eventually also benefits patients. Here we present examples of current advances in preclinical research in rare diseases using mouse models, together with our perspective on future directions and challenges.
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Affiliation(s)
- Silvia Murillo-Cuesta
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain.,Instituto de Investigaciones Biomédicas Alberto Sols (IIBM), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid, Madrid, Spain.,Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Rafael Artuch
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain.,Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain
| | - Fernando Asensio
- Gregorio Marañón Institute for Health Research (IISGM), Madrid, Spain
| | - Pedro de la Villa
- Faculty of Medicine, University of Alcalá (UAH), Alcalá de Henares, Spain
| | - Mara Dierssen
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain.,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jose Antonio Enríquez
- Spanish National Center for Cardiovascular Research (CNIC), Institute of Health Carlos III, Madrid, Spain.,Biomedical Research Networking Center on Frailty and Healthy Ageing (CIBERFES), Institute of Health Carlos III, Madrid, Spain
| | - Cristina Fillat
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Stéphane Fourcade
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain.,Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Borja Ibáñez
- Spanish National Center for Cardiovascular Research (CNIC), Institute of Health Carlos III, Madrid, Spain.,Biomedical Research Networking Center on Cardiovascular Diseases (CIBERCV), Institute of Health Carlos III, Madrid, Spain.,Cardiology Department, Fundación Jiménez Díaz University Hospital Health Research Institute (IIS-FJD), Madrid, Spain
| | - Lluis Montoliu
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain.,National Center for Biotechnology (CNB), Spanish National Research Council, Madrid, Spain
| | - Eduardo Oliver
- Spanish National Center for Cardiovascular Research (CNIC), Institute of Health Carlos III, Madrid, Spain.,Biomedical Research Networking Center on Cardiovascular Diseases (CIBERCV), Institute of Health Carlos III, Madrid, Spain
| | - Aurora Pujol
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain.,Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eduardo Salido
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain.,Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas (ITB), La Laguna, Spain
| | - Mario Vallejo
- Instituto de Investigaciones Biomédicas Alberto Sols (IIBM), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid, Madrid, Spain.,Biomedical Research Networking Center on Diabetes and Metabolic Diseases (CIBERDEM), Institute of Health Carlos III, Madrid, Spain
| | - Isabel Varela-Nieto
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain.,Instituto de Investigaciones Biomédicas Alberto Sols (IIBM), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid, Madrid, Spain.,Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
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15
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Seruggia D, Josa S, Fernández A, Montoliu L. The structure and function of the mouse tyrosinase locus. Pigment Cell Melanoma Res 2020; 34:212-221. [DOI: 10.1111/pcmr.12942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/06/2020] [Accepted: 10/14/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Davide Seruggia
- Department of Molecular and Cellular Biology National Centre for Biotechnology (CNB‐CSIC) Madrid Madrid Spain
- CIBERER‐ISCIII Madrid Spain
- Division of Hematology/Oncology Boston Children's HospitalHarvard Medical School Boston MA USA
| | - Santiago Josa
- Department of Molecular and Cellular Biology National Centre for Biotechnology (CNB‐CSIC) Madrid Madrid Spain
- CIBERER‐ISCIII Madrid Spain
| | - Almudena Fernández
- Department of Molecular and Cellular Biology National Centre for Biotechnology (CNB‐CSIC) Madrid Madrid Spain
- CIBERER‐ISCIII Madrid Spain
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology National Centre for Biotechnology (CNB‐CSIC) Madrid Madrid Spain
- CIBERER‐ISCIII Madrid Spain
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16
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Sethi S, Vorontsov IE, Kulakovskiy IV, Greenaway S, Williams J, Makeev VJ, Brown SDM, Simon MM, Mallon AM. A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease. BMC Genomics 2020; 21:754. [PMID: 33138777 PMCID: PMC7607678 DOI: 10.1186/s12864-020-07109-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 09/29/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Efforts to elucidate the function of enhancers in vivo are underway but their vast numbers alongside differing enhancer architectures make it difficult to determine their impact on gene activity. By systematically annotating multiple mouse tissues with super- and typical-enhancers, we have explored their relationship with gene function and phenotype. RESULTS Though super-enhancers drive high total- and tissue-specific expression of their associated genes, we find that typical-enhancers also contribute heavily to the tissue-specific expression landscape on account of their large numbers in the genome. Unexpectedly, we demonstrate that both enhancer types are preferentially associated with relevant 'tissue-type' phenotypes and exhibit no difference in phenotype effect size or pleiotropy. Modelling regulatory data alongside molecular data, we built a predictive model to infer gene-phenotype associations and use this model to predict potentially novel disease-associated genes. CONCLUSION Overall our findings reveal that differing enhancer architectures have a similar impact on mammalian phenotypes whilst harbouring differing cellular and expression effects. Together, our results systematically characterise enhancers with predicted phenotypic traits endorsing the role for both types of enhancers in human disease and disorders.
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Affiliation(s)
- Siddharth Sethi
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Ilya E Vorontsov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, 119991, Russia
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino, Moscow Region, 142290, Russia
| | - Ivan V Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, 119991, Russia
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino, Moscow Region, 142290, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia
| | - Simon Greenaway
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - John Williams
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
- Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2TH, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, 119991, Russia
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino, Moscow Region, 142290, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700, Russia
| | - Steve D M Brown
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Michelle M Simon
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK.
| | - Ann-Marie Mallon
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK.
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17
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Seruggia D, Fernández A, Cantero M, Fernández-Miñán A, Gomez-Skarmeta JL, Pelczar P, Montoliu L. Boundary sequences flanking the mouse tyrosinase locus ensure faithful pattern of gene expression. Sci Rep 2020; 10:15494. [PMID: 32968154 PMCID: PMC7511308 DOI: 10.1038/s41598-020-72543-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/02/2020] [Indexed: 12/28/2022] Open
Abstract
Control of gene expression is dictated by cell-type specific regulatory sequences that physically organize the structure of chromatin, including promoters, enhancers and insulators. While promoters and enhancers convey cell-type specific activating signals, insulators prevent the cross-talk of regulatory elements within adjacent loci and safeguard the specificity of action of promoters and enhancers towards their targets in a tissue specific manner. Using the mouse tyrosinase (Tyr) locus as an experimental model, a gene whose mutations are associated with albinism, we described the chromatin structure in cells at two distinct transcriptional states. Guided by chromatin structure, through the use of Chromosome Conformation Capture (3C), we identified sequences at the 5' and 3' boundaries of this mammalian gene that function as enhancers and insulators. By CRISPR/Cas9-mediated chromosomal deletion, we dissected the functions of these two regulatory elements in vivo in the mouse, at the endogenous chromosomal context, and proved their mechanistic role as genomic insulators, shielding the Tyr locus from the expression patterns of adjacent genes.
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Affiliation(s)
- Davide Seruggia
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Campus de Cantoblanco, Darwin 3, 28049, Madrid, Spain
- CIBERER-ISCIII, Madrid, Spain
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Almudena Fernández
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Campus de Cantoblanco, Darwin 3, 28049, Madrid, Spain
- CIBERER-ISCIII, Madrid, Spain
| | - Marta Cantero
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Campus de Cantoblanco, Darwin 3, 28049, Madrid, Spain
- CIBERER-ISCIII, Madrid, Spain
| | - Ana Fernández-Miñán
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - José Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Pawel Pelczar
- Center for Transgenic Models, University of Basel, Basel, Switzerland
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Campus de Cantoblanco, Darwin 3, 28049, Madrid, Spain.
- CIBERER-ISCIII, Madrid, Spain.
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18
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García‐Poyatos C, Cogliati S, Calvo E, Hernansanz‐Agustín P, Lagarrigue S, Magni R, Botos M, Langa X, Amati F, Vázquez J, Mercader N, Enríquez JA. Scaf1 promotes respiratory supercomplexes and metabolic efficiency in zebrafish. EMBO Rep 2020; 21:e50287. [PMID: 32496654 PMCID: PMC7332985 DOI: 10.15252/embr.202050287] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/13/2020] [Accepted: 04/28/2020] [Indexed: 01/01/2023] Open
Abstract
The oxidative phosphorylation (OXPHOS) system is a dynamic system in which the respiratory complexes coexist with super-assembled quaternary structures called supercomplexes (SCs). The physiological role of SCs is still disputed. Here, we used zebrafish to study the relevance of respiratory SCs. We combined immunodetection analysis and deep data-independent proteomics to characterize these structures and found similar SCs to those described in mice, as well as novel SCs including III2 + IV2 , I + IV, and I + III2 + IV2 . To study the physiological role of SCs, we generated two null allele zebrafish lines for supercomplex assembly factor 1 (scaf1). scaf1-/- fish displayed altered OXPHOS activity due to the disrupted interaction of complexes III and IV. scaf1-/- fish were smaller in size and showed abnormal fat deposition and decreased female fertility. These physiological phenotypes were rescued by doubling the food supply, which correlated with improved bioenergetics and alterations in the metabolic gene expression program. These results reveal that SC assembly by Scaf1 modulates OXPHOS efficiency and allows the optimization of metabolic resources.
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Affiliation(s)
- Carolina García‐Poyatos
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
- Institute of AnatomyUniversity of BernBernSwitzerland
| | - Sara Cogliati
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
- Instituto de Nutrición y Tecnología de los Alimentos (INYTA)Universidad de GranadaGranadaSpain
| | - Enrique Calvo
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
| | | | - Sylviane Lagarrigue
- Aging and Muscle Metabolism LaboratoryDepartment of Biomedical SciencesUniversity of LausanneLausanneSwitzerland
| | - Ricardo Magni
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
| | - Marius Botos
- Institute of AnatomyUniversity of BernBernSwitzerland
| | - Xavier Langa
- Institute of AnatomyUniversity of BernBernSwitzerland
| | - Francesca Amati
- Aging and Muscle Metabolism LaboratoryDepartment of Biomedical SciencesUniversity of LausanneLausanneSwitzerland
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
- CIBERCVMadridSpain
| | - Nadia Mercader
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
| | - José Antonio Enríquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
- CIBERFESMadridSpain
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19
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Application of CRISPR Tools for Variant Interpretation and Disease Modeling in Inherited Retinal Dystrophies. Genes (Basel) 2020; 11:genes11050473. [PMID: 32349249 PMCID: PMC7290804 DOI: 10.3390/genes11050473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/23/2020] [Accepted: 04/23/2020] [Indexed: 12/27/2022] Open
Abstract
Inherited retinal dystrophies are an assorted group of rare diseases that collectively account for the major cause of visual impairment of genetic origin worldwide. Besides clinically, these vision loss disorders present a high genetic and allelic heterogeneity. To date, over 250 genes have been associated to retinal dystrophies with reported causative variants of every nature (nonsense, missense, frameshift, splice-site, large rearrangements, and so forth). Except for a fistful of mutations, most of them are private and affect one or few families, making it a challenge to ratify the newly identified candidate genes or the pathogenicity of dubious variants in disease-associated loci. A recurrent option involves altering the gene in in vitro or in vivo systems to contrast the resulting phenotype and molecular imprint. To validate specific mutations, the process must rely on simulating the precise genetic change, which, until recently, proved to be a difficult endeavor. The rise of the CRISPR/Cas9 technology and its adaptation for genetic engineering now offers a resourceful suite of tools to alleviate the process of functional studies. Here we review the implementation of these RNA-programmable Cas9 nucleases in culture-based and animal models to elucidate the role of novel genes and variants in retinal dystrophies.
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20
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Fernández A, Morín M, Muñoz‐Santos D, Josa S, Montero A, Rubio‐Fernández M, Cantero M, Fernández J, del Hierro MJ, Castrillo M, Moreno‐Pelayo MÁ, Montoliu L. Simple Protocol for Generating and Genotyping Genome‐Edited Mice With CRISPR‐Cas9 Reagents. ACTA ACUST UNITED AC 2020; 10:e69. [DOI: 10.1002/cpmo.69] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Almudena Fernández
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | - Matías Morín
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
- Servicio de Genética, Ramón y Cajal University HospitalIRYCIS Madrid Spain
| | - Diego Muñoz‐Santos
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | - Santiago Josa
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | - Andrea Montero
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | - Marcos Rubio‐Fernández
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | - Marta Cantero
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | - Julia Fernández
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | | | | | - Miguel Ángel Moreno‐Pelayo
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
- Servicio de Genética, Ramón y Cajal University HospitalIRYCIS Madrid Spain
| | - Lluís Montoliu
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
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21
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Torres-Perez R, Garcia-Martin JA, Montoliu L, Oliveros JC, Pazos F. WeReview: CRISPR Tools-Live Repository of Computational Tools for Assisting CRISPR/Cas Experiments. Bioengineering (Basel) 2019; 6:E63. [PMID: 31349743 PMCID: PMC6783853 DOI: 10.3390/bioengineering6030063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 12/23/2022] Open
Abstract
Computational tools are essential in the process of designing a CRISPR/Cas experiment for the targeted modification of an organism's genome. Among other functionalities, these tools facilitate the design of a guide-RNA (gRNA) for a given nuclease that maximizes its binding to the intended genomic site, while avoiding binding to undesired sites with similar sequences in the genome of the organism of interest (off-targets). Due to the popularity of this methodology and the rapid pace at which it evolves and changes, new computational tools show up constantly. This rapid turnover, together with the intrinsic high death-rate of bioinformatics tools, mean that many of the published tools become unavailable at some point. Consequently, the traditional ways to inform the community about the landscape of available tools, i.e., reviews in the scientific literature, are not adequate for this fast-moving field. To overcome these limitations, we have developed "WeReview: CRISPR Tools," a live, on-line, user-updatable repository of computational tools to assist researchers in designing CRISPR/Cas experiments. In its web site users can find an updated comprehensive list of tools and search for those fulfilling their specific needs, as well as proposing modifications to the data associated with the tools or the incorporation of new ones.
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Affiliation(s)
- Rafael Torres-Perez
- National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain
| | | | - Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain
- Rare Diseases Networking Biomedical Research Centre (CIBERER-ISCIII), 28049 Madrid, Spain
| | - Juan C Oliveros
- National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain.
| | - Florencio Pazos
- National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain.
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22
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Sher F, Hossain M, Seruggia D, Schoonenberg VAC, Yao Q, Cifani P, Dassama LMK, Cole MA, Ren C, Vinjamur DS, Macias-Trevino C, Luk K, McGuckin C, Schupp PG, Canver MC, Kurita R, Nakamura Y, Fujiwara Y, Wolfe SA, Pinello L, Maeda T, Kentsis A, Orkin SH, Bauer DE. Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis. Nat Genet 2019; 51:1149-1159. [PMID: 31253978 PMCID: PMC6650275 DOI: 10.1038/s41588-019-0453-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 05/21/2019] [Indexed: 12/26/2022]
Abstract
Developmental silencing of fetal globins serves as both a paradigm of spatiotemporal gene regulation and an opportunity for therapeutic intervention of β-hemoglobinopathy. The nucleosome remodeling and deacetylase (NuRD) chromatin complex participates in γ-globin repression. We used pooled CRISPR screening to disrupt NuRD protein coding sequences comprehensively in human adult erythroid precursors. Essential for fetal hemoglobin (HbF) control is a non-redundant subcomplex of NuRD protein family paralogs, whose composition we corroborated by affinity chromatography and proximity labeling mass spectrometry proteomics. Mapping top functional guide RNAs identified key protein interfaces where in-frame alleles resulted in loss-of-function due to destabilization or altered function of subunits. We ascertained mutations of CHD4 that dissociate its requirement for cell fitness from HbF repression in both primary human erythroid precursors and transgenic mice. Finally we demonstrated that sequestering CHD4 from NuRD phenocopied these mutations. These results indicate a generalizable approach to discover protein complex features amenable to rational biochemical targeting.
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Affiliation(s)
- Falak Sher
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
- Center for Translational & Computational Neuroimmunology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, Columbia University, New York, NY, USA
| | - Mir Hossain
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Davide Seruggia
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Vivien A C Schoonenberg
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
- Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Qiuming Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
- Molecular Pathology Unit & Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura M K Dassama
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Mitchel A Cole
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Chunyan Ren
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Divya S Vinjamur
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Claudio Macias-Trevino
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Connor McGuckin
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Patrick G Schupp
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yuko Fujiwara
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit & Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Takahiro Maeda
- Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA.
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23
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Tadić V, Josipović G, Zoldoš V, Vojta A. CRISPR/Cas9-based epigenome editing: An overview of dCas9-based tools with special emphasis on off-target activity. Methods 2019; 164-165:109-119. [PMID: 31071448 DOI: 10.1016/j.ymeth.2019.05.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/29/2019] [Accepted: 05/02/2019] [Indexed: 02/06/2023] Open
Abstract
Molecular tools for gene regulation and epigenome editing consist of two main parts: the targeting moiety binding a specific genomic locus and the effector domain performing the editing or regulatory function. The advent of CRISPR-Cas9 technology enabled easy and flexible targeting of almost any locus by co-expression of a small sgRNA molecule, which is complementary to the target sequence and forms a complex with Cas9, directing it to that particular target. Here, we review strategies for recruitment of effector domains, used in gene regulation and epigenome editing, to the dCas9 DNA-targeting protein. To date, the most important CRISPR-Cas9 applications in gene regulation are CRISPR activation or interference, while epigenome editing focuses on targeted changes in DNA methylation and histone modifications. Several strategies for signal amplification by recruitment of multiple effector domains deserve special focus. While some approaches rely on altering the sgRNA molecule and extending it with aptamers for effector domain recruitment, others use modifications to the Cas9 protein by direct fusions with effector domains or by addition of an epitope tag, which also has the ability to bind multiple effector domains. A major barrier to the widespread use of CRISPR-Cas9 technology for therapeutic purposes is its off-target effect. We review efforts to enhance CRISPR-Cas9 specificity by selection of Cas9 orthologs from various bacterial species and their further refinement by introduction of beneficial mutations. The molecular tools available today enable a researcher to choose the best balance of targeting flexibility, activity amplification, delivery method and specificity.
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Affiliation(s)
- Vanja Tadić
- University of Zagreb, Faculty of Science, Department of Biology, Division of Molecular Biology, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Goran Josipović
- University of Zagreb, Faculty of Science, Department of Biology, Division of Molecular Biology, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Vlatka Zoldoš
- University of Zagreb, Faculty of Science, Department of Biology, Division of Molecular Biology, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Aleksandar Vojta
- University of Zagreb, Faculty of Science, Department of Biology, Division of Molecular Biology, Horvatovac 102a, HR-10000 Zagreb, Croatia.
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24
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Miano JM, Long X, Lyu Q. CRISPR links to long noncoding RNA function in mice: A practical approach. Vascul Pharmacol 2019; 114:1-12. [PMID: 30822570 PMCID: PMC6435418 DOI: 10.1016/j.vph.2019.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/29/2022]
Abstract
Next generation sequencing has uncovered a trove of short noncoding RNAs (e.g., microRNAs) and long noncoding RNAs (lncRNAs) that act as molecular rheostats in the control of diverse homeostatic processes. Meanwhile, the tsunamic emergence of clustered regularly interspaced short palindromic repeats (CRISPR) editing has transformed our influence over all DNA-carrying entities, heralding global CRISPRization. This is evident in biomedical research where the ease and low-cost of CRISPR editing has made it the preferred method of manipulating the mouse genome, facilitating rapid discovery of genome function in an in vivo context. Here, CRISPR genome editing components are updated for elucidating lncRNA function in mice. Various strategies are highlighted for understanding the function of lncRNAs residing in intergenic sequence space, as host genes that harbor microRNAs or other genes, and as natural antisense, overlapping or intronic genes. Also discussed is CRISPR editing of mice carrying human lncRNAs as well as the editing of competing endogenous RNAs. The information described herein should assist labs in the rigorous design of experiments that interrogate lncRNA function in mice where complex disease processes can be modeled thus accelerating translational discovery.
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Affiliation(s)
- Joseph M Miano
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America.
| | - Xiaochun Long
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, United States of America
| | - Qing Lyu
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
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25
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Lee HK, Willi M, Smith HE, Miller SM, Liu DR, Liu C, Hennighausen L. Simultaneous targeting of linked loci in mouse embryos using base editing. Sci Rep 2019; 9:1662. [PMID: 30733567 PMCID: PMC6367434 DOI: 10.1038/s41598-018-33533-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/24/2018] [Indexed: 12/30/2022] Open
Abstract
A particular challenge in genome engineering has been the simultaneous introduction of mutations into linked (located on the same chromosome) loci. Although CRISPR/Cas9 has been widely used to mutate individual sites, its application in simultaneously targeting of linked loci is limited as multiple nearby double-stranded DNA breaks created by Cas9 routinely result in the deletion of sequences between the cleavage sites. Base editing is a newer form of genome editing that directly converts C∙G-to-T∙A, or A∙T-to-G∙C, base pairs without introducing double-stranded breaks, thus opening the possibility to generate linked mutations without disrupting the entire locus. Through the co-injection of two base editors and two sgRNAs into mouse zygotes, we introduced C∙G-to-T∙A transitions into two cytokine-sensing transcription factor binding sites separated by 9 kb. We determined that one enhancer activates the two flanking genes in mammary tissue during pregnancy and lactation. The ability to introduce linked mutations simultaneously in one step into the mammalian germline has implications for a wide range of applications, including the functional analysis of linked cis-elements creating disease models and correcting pathogenic mutations.
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Affiliation(s)
- Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, 20892, USA.
| | - Michaela Willi
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Harold E Smith
- Genomics Core, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Shannon M Miller
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, 20892, USA.
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26
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Lee HK, Willi M, Miller SM, Kim S, Liu C, Liu DR, Hennighausen L. Targeting fidelity of adenine and cytosine base editors in mouse embryos. Nat Commun 2018; 9:4804. [PMID: 30442934 PMCID: PMC6238002 DOI: 10.1038/s41467-018-07322-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/25/2018] [Indexed: 11/09/2022] Open
Abstract
Base editing directly converts a target base pair into a different base pair in the genome of living cells without introducing double-stranded DNA breaks. While cytosine base editors (CBE) and adenine base editors (ABE) are used to install and correct point mutations in a wide range of organisms, the extent and distribution of off-target edits in mammalian embryos have not been studied in detail. We analyze on-target and proximal off-target editing at 13 loci by a variety of CBEs and ABE in more than 430 alleles generated from mouse zygotic injections using newly generated and published sequencing data. ABE predominantly generates anticipated A•T-to-G•C edits. Among CBEs, SaBE3 and BE4, result in the highest frequencies of anticipated C•G-to-T•A products relative to editing byproducts. Together, these findings highlight the remarkable fidelity of ABE in mouse embryos and identify preferred CBE variants when fidelity in vivo is critical.
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Affiliation(s)
- Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Michaela Willi
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shannon M Miller
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Sojung Kim
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, 20892, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD, 20892, USA.
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27
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Quillen EE, Norton HL, Parra EJ, Lona-Durazo F, Ang KC, Illiescu FM, Pearson LN, Shriver MD, Lasisi T, Gokcumen O, Starr I, Lin YL, Martin AR, Jablonski NG. Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 168 Suppl 67:4-26. [PMID: 30408154 DOI: 10.1002/ajpa.23737] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023]
Abstract
Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.
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Affiliation(s)
- Ellen E Quillen
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina.,Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio
| | - Esteban J Parra
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Frida Lona-Durazo
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Khai C Ang
- Department of Pathology and Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania
| | - Florin Mircea Illiescu
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Centro de Estudios Interculturales e Indígenas - CIIR, P. Universidad Católica de Chile, Santiago, Chile
| | - Laurel N Pearson
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Tina Lasisi
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Izzy Starr
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Yen-Lung Lin
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nina G Jablonski
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
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28
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Song Y, Zhang Y, Chen M, Deng J, Sui T, Lai L, Li Z. Functional validation of the albinism-associated tyrosinase T373K SNP by CRISPR/Cas9-mediated homology-directed repair (HDR) in rabbits. EBioMedicine 2018; 36:517-525. [PMID: 30274819 PMCID: PMC6197749 DOI: 10.1016/j.ebiom.2018.09.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/19/2018] [Accepted: 09/23/2018] [Indexed: 02/06/2023] Open
Abstract
Background Oculocutaneous albinism (OCA) is a group of autosomal recessive disorders characterized by reduced melanin that are caused by mutations in the gene encoding tyrosinase (TYR), which is the rate-limiting enzyme in the production of the pigment melanin. Many studies or meta-analyses have suggested an association between the TYR T373K SNP and OCA1, but there is limited biochemical and genetic evidence to support this association. Methods We overexpressed TYR-WT and TYR-T373K mutants on HK293T cells and tested the changes of melanin production and tyrosinase activity. Then we generated TYR-K373T knock-in (KI) rabbits by microinjection of ssDNA and synthesized RNAs targeting C1118A using CRISPR/Cas9-HDR to observe the formation of melanin. Findings We demonstrated that the T373K mutation in TYR can reduce tyrosinase activity, leading to an absence of melanin synthesis at the cell-level. The gene-edited TYR-K373T rabbits exhibited rescued melanin production in hair follicles and irises, as inferred from the evident decrease in pigmentation in TYR-T373K rabbits, thus providing functional validation of the albinism-associated T373K SNP at the animal level. Interpretation Our study provides the first animal-level functional validation of the albinism-associated TYR K373T SNP in rabbits, and these results will facilitate gene therapy of OCA1 in pre-clinical settings in the future. Fund The National Key Research and Development Program of China Stem Cell and Translational Research, the Strategic Priority Research Program of the Chinese Academy of Sciences, the Guangdong Province Science and Technology Plan Project, and the Program for JLU Science and Technology Innovative Research Team.
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Affiliation(s)
- Yuning Song
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun 130062, China
| | - Yuxin Zhang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun 130062, China
| | - Mao Chen
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun 130062, China
| | - Jichao Deng
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun 130062, China
| | - Tingting Sui
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun 130062, China
| | - Liangxue Lai
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun 130062, China; Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China.
| | - Zhanjun Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun 130062, China.
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29
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Montoliu L, Whitelaw CBA. Unexpected mutations were expected and unrelated to CRISPR-Cas9 activity. Transgenic Res 2018; 27:315-319. [PMID: 29855762 DOI: 10.1007/s11248-018-0081-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/26/2018] [Indexed: 12/26/2022]
Abstract
The scientific journal Nature Methods have just retracted a publication that reported numerous unexpected mutations after a CRISPR-Cas9 experiment based on collecting whole genome sequencing information from one control and two experimental genome edited mice. In the intervening 10 months since publication the data presented have been strongly contested and criticized by the scientific and biotech communities, through publications, open science channels and social networks. The criticism focused on the animal used as control, which was derived from the same mouse strain as the experimental individuals but from an unrelated sub-colony, hence control and experimental mice were genetically divergent. The most plausible explanation for the vast majority of the reported unexpected mutations were the expected underlying genetic polymorphisms that normally accumulate in two different colonies of the same mouse strain which occur as a result of spontaneous mutations and genetic drift. Therefore, the reported mutations were most likely not related to CRISPR-Cas9 activity.
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Affiliation(s)
- Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC), Biomedical Research Networking Centre Consortium on Rare Diseases (CIBERER-ISCIII), Darwin 3, 28049, Madrid, Spain.
| | - C Bruce A Whitelaw
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.
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30
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Abstract
Prokaryotic type II adaptive immune systems have been developed into the versatile CRISPR technology, which has been widely applied in site-specific genome editing and has revolutionized biomedical research due to its superior efficiency and flexibility. Recent studies have greatly diversified CRISPR technologies by coupling it with various DNA repair mechanisms and targeting strategies. These new advances have significantly expanded the generation of genetically modified animal models, either by including species in which targeted genetic modification could not be achieved previously, or through introducing complex genetic modifications that take multiple steps and cost years to achieve using traditional methods. Herein, we review the recent developments and applications of CRISPR-based technology in generating various animal models, and discuss the everlasting impact of this new progress on biomedical research.
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Affiliation(s)
- Xun Ma
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Avery Sum-Yu Wong
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Hei-Yin Tam
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Samuel Yung-Kin Tsui
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Dittman Lai-Shun Chung
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Bo Feng
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Guangdong 510530, China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen Guangdong 518057, China
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31
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CRISPR-based strategies for studying regulatory elements and chromatin structure in mammalian gene control. Mamm Genome 2018; 29:205-228. [PMID: 29196861 PMCID: PMC9881389 DOI: 10.1007/s00335-017-9727-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/27/2017] [Indexed: 01/31/2023]
Abstract
The development of high-throughput methods has enabled the genome-wide identification of putative regulatory elements in a wide variety of mammalian cells at an unprecedented resolution. Extensive genomic studies have revealed the important role of regulatory elements and genetic variation therein in disease formation and risk. In most cases, there is only correlative evidence for the roles of these elements and non-coding changes within these elements in pathogenesis. With the advent of genome- and epigenome-editing tools based on the CRISPR technology, it is now possible to test the functional relevance of the regulatory elements and alterations on a genomic scale. Here, we review the various CRISPR-based strategies that have been developed to functionally validate the candidate regulatory elements in mammals as well as the non-coding genetic variants found to be associated with human disease. We also discuss how these synthetic biology tools have helped to elucidate the role of three-dimensional nuclear architecture and higher-order chromatin organization in shaping functional genome and controlling gene expression.
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32
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Carbonell A, Fueyo R, Izquierdo-Bouldstridge A, Moreta C, Jordan A. Epigenetic mechanisms in health and disease: BCEC 2017. Epigenetics 2018; 13:331-341. [PMID: 29384431 DOI: 10.1080/15592294.2018.1434391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The Barcelona Conference on Epigenetics and Cancer (BCEC) entitled "Epigenetic Mechanisms in Health and Disease" was held in Barcelona, October 26-26, 2017. The 2017 BCEC was the fifth and last edition of a series of annual conferences organized as a joint effort of five leading Barcelona research institutes together with B-Debate. This edition was organized by Albert Jordan from the Molecular Biology Institute of Barcelona (IBMB-CSIC) and Marcus Bushbeck from the Josep Carreras Leukaemia Research Institute (IJC). Jordi Bernués, Marian Martínez-Balbás, and Ferran Azorín were also part of the scientific committee. In 22 talks and 51 posters, researchers presented their latest results in the fields of histone variants, epigenetic regulation, and chromatin 3D organization to an audience of around 250 participants from 16 countries. This year, a broad number of talks focused on the epigenetic causes and possible related treatments of complex diseases such as cancer. Participants at the 2017 BCEC elegantly closed the series, discussing progress made in the field of epigenetics and highlighting its role in human health and disease.
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Affiliation(s)
- Albert Carbonell
- a Department of Molecular Genomics , Molecular Biology Institute of Barcelona (IBMB-CSIC) , Baldiri i Reixac 4-8, 08028 Barcelona , Catalonia , Spain.,b Institute for Research in Biomedicine, IRB Barcelona , The Barcelona Institute for Science and Technology , Baldiri i Reixac, 10, 08028 Barcelona , Catalonia , Spain
| | - Raquel Fueyo
- a Department of Molecular Genomics , Molecular Biology Institute of Barcelona (IBMB-CSIC) , Baldiri i Reixac 4-8, 08028 Barcelona , Catalonia , Spain
| | - Andrea Izquierdo-Bouldstridge
- a Department of Molecular Genomics , Molecular Biology Institute of Barcelona (IBMB-CSIC) , Baldiri i Reixac 4-8, 08028 Barcelona , Catalonia , Spain
| | - Cristina Moreta
- c Germans Trias i Pujol Research Institute (IGTP) , Can Ruti Campus , 08916 , Badalona , Catalonia , Spain
| | - Albert Jordan
- a Department of Molecular Genomics , Molecular Biology Institute of Barcelona (IBMB-CSIC) , Baldiri i Reixac 4-8, 08028 Barcelona , Catalonia , Spain
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33
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Wolter F, Puchta H. Application of CRISPR/Cas to Understand Cis- and Trans-Regulatory Elements in Plants. Methods Mol Biol 2018; 1830:23-40. [PMID: 30043362 DOI: 10.1007/978-1-4939-8657-6_2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The recent emergence of the CRISPR/Cas system as a genome editing tool enables simple, fast, and efficient induction of DNA double-strand breaks at precise positions in the genome. This has proven extremely useful for analysis and modification of protein-coding sequences. Regulatory sequences have received much less attention, but can now be quickly and easily disrupted as well. Editing of cis-regulatory elements (CRE) offers considerable potential for crop improvement via fine-tuning of gene expression that cannot be achieved by simple KO mutations, but its widespread application is still hampered by a lack of precise knowledge about functional motifs in CRE. As demonstrated for mammalian cells, CRISPR/Cas is also extremely useful for the identification and analysis of CRE in their native environment on a large scale using tiling screens. Transcriptional complexes are another promising target for crop genome editing, as demonstrated for pathogen resistance and regulation of flowering. The development of more diverse and sophisticated CRISPR/Cas tools for genome editing will allow even more efficient and powerful approaches for editing of regulatory sequences in the future.
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Affiliation(s)
- Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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34
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Shrock E, Güell M. CRISPR in Animals and Animal Models. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 152:95-114. [PMID: 29150007 DOI: 10.1016/bs.pmbts.2017.07.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CRISPR-Cas9 has revolutionized the generation of transgenic animals. This system has demonstrated an unprecedented efficiency, multiplexability, and ease of use, thereby reducing the time and cost required for genome editing and enabling the production of animals with more extensive genetic modifications. It has also been shown to be applicable to a wide variety of animals, from early-branching metazoans to primates. Genome-wide screens in model organisms have been performed, accurate models of human diseases have been constructed, and potential therapies have been tested and validated in animal models. Several achievements in genetic modification of animals have been translated into products for the agricultural and pharmaceutical industries. Based on the remarkable progress to date, one may anticipate that in the future, CRISPR-Cas9 technology will enable additional far-reaching advances, including understanding the bases of diseases with complex genetic origins, engineering animals to produce organs for human transplantation, and genetically transforming entire populations of organisms to prevent the spread of disease.
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Affiliation(s)
- Ellen Shrock
- Biological and Biomedical Sciences, Harvard University, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Marc Güell
- Harvard Medical School, Boston, MA, United States; Pompeu Fabra University, Barcelona, Spain.
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35
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Identification and characterization of the tyrosinase gene (TYR) and its transcript variants (TYR_1 and TYR_2) in the crab-eating macaque (Macaca fascicularis). Gene 2017; 630:21-27. [PMID: 28756020 DOI: 10.1016/j.gene.2017.07.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/18/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
Abstract
Tyrosinase is a copper-containing enzyme that regulates melanin biosynthesis and is encoded by the tyrosinase (TYR) gene. Previous studies demonstrated that mutations in TYR could lead to oculocutaneous albinism type 1 (OCA1) owing to the failure of melanin formation. Although a previous study found that albinism in the rhesus monkey was derived from a mutation in TYR, the identification and characterization of this gene in non-human primates has not been achieved thus far. Thus, using the rapid amplification of cDNA ends (RACE) and internal reverse transcription PCR (RT-PCR) we identified the full-length sequence of TYR in the crab-eating macaque, and two different transcript variants (TYR_1 and TYR_2). While TYR_1 comprised five exons and its coding sequence was highly similar to that of humans, TYR_2 comprised four exons and was generated by a third-exon-skipping event. Interestingly, these two transcripts were also present in the African green monkey (Old World monkey) and the common marmoset (New World monkey). Deduced amino acid sequence analyses revealed that TYR_2 had a shorter C-terminal region than TYR_1 owing to the exon-skipping event. Thus, the present study is the first to identify and characterize a full-length TYR gene in a non-human primate, while the further validation of the third-exon-skipping in TYR indicates that this event is well conserved in the primate lineage. Therefore, this study provides useful and important information for the study of albinism using non-human primate models.
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36
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Fernández A, Josa S, Montoliu L. A history of genome editing in mammals. Mamm Genome 2017; 28:237-246. [DOI: 10.1007/s00335-017-9699-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/31/2017] [Indexed: 12/28/2022]
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37
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Shin HY, Wang C, Lee HK, Yoo KH, Zeng X, Kuhns T, Yang CM, Mohr T, Liu C, Hennighausen L. CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome. Nat Commun 2017; 8:15464. [PMID: 28561021 PMCID: PMC5460021 DOI: 10.1038/ncomms15464] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 03/31/2017] [Indexed: 12/29/2022] Open
Abstract
Although CRISPR/Cas9 genome editing has provided numerous opportunities to interrogate the functional significance of any given genomic site, there is a paucity of data on the extent of molecular scars inflicted on the mouse genome. Here we interrogate the molecular consequences of CRISPR/Cas9-mediated deletions at 17 sites in four loci of the mouse genome. We sequence targeted sites in 632 founder mice and analyse 54 established lines. While the median deletion size using single sgRNAs is 9 bp, we also obtain large deletions of up to 600 bp. Furthermore, we show unreported asymmetric deletions and large insertions of middle repetitive sequences. Simultaneous targeting of distant loci results in the removal of the intervening sequences. Reliable deletion of juxtaposed sites is only achieved through two-step targeting. Our findings also demonstrate that an extended analysis of F1 genotypes is required to obtain conclusive information on the exact molecular consequences of targeting events.
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Affiliation(s)
- Ha Youn Shin
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Chaochen Wang
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Cell and Developmental Biology & Dental Research Institute, Seoul National University, Seoul 110-749, Republic of Korea
| | - Kyung Hyun Yoo
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Life Systems, Sookmyung Women's University, Seoul 140-742, Republic of Korea
| | - Xianke Zeng
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tyler Kuhns
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chul Min Yang
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Teresa Mohr
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
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38
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Canver MC, Bauer DE, Orkin SH. Functional interrogation of non-coding DNA through CRISPR genome editing. Methods 2017; 121-122:118-129. [PMID: 28288828 PMCID: PMC5483188 DOI: 10.1016/j.ymeth.2017.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/18/2017] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA.
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Affiliation(s)
| | - Daniel E Bauer
- Harvard Medical School, Boston, MA 02115, United States; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States.
| | - Stuart H Orkin
- Harvard Medical School, Boston, MA 02115, United States; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States; Howard Hughes Medical Institute, Boston, MA 02115, United States.
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39
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Song Y, Xu Y, Deng J, Chen M, Lu Y, Wang Y, Yao H, Zhou L, Liu Z, Lai L, Li Z. CRISPR/Cas9-mediated mutation of tyrosinase (Tyr) 3' UTR induce graying in rabbit. Sci Rep 2017; 7:1569. [PMID: 28484254 PMCID: PMC5431497 DOI: 10.1038/s41598-017-01727-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/03/2017] [Indexed: 01/08/2023] Open
Abstract
The 3' untranslated regions (UTRs), located at the end of mRNA molecules, are believed to play a role in RNA replication and/or protein translation. Mutations in the tyrosinase (Tyr) gene are known to cause recessive albinism in humans and other species. In this study, to test whether the CRISPR/Cas9 system works on the mutation of the UTRs regulatory region in rabbit, the 3' UTR of the rabbit Tyr gene was deleted by a dual sgRNA directed CRISPR/Cas9 system. As expected, gray coat color and reduced melanin in hair follicles and irises was found in the mutated rabbit, thus increasing confidence in the association of the mutation of the Tyr 3' UTR with graying in rabbit. The graying phenotype was also found in the F1 generation, suggesting that the mutated allele can be stably inherited by the offspring. Thus, we provide the first evidence that reduced melanin and graying can be caused by deletion of the Tyr 3' UTR in rabbits. Additionally, CRISPR/Cas9-mediated large fragment deletions can facilitate genotype to phenotype studies of UTRs or non-coding RNAs in future.
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Affiliation(s)
- Yuning Song
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Yuxin Xu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Jichao Deng
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Mao Chen
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Yi Lu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Yong Wang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Haobin Yao
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Lina Zhou
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Zhiquan Liu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China.
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Zhanjun Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China.
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40
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Creation of mutant mice with megabase-sized deletions containing custom-designed breakpoints by means of the CRISPR/Cas9 system. Sci Rep 2017; 7:59. [PMID: 28246396 PMCID: PMC5427885 DOI: 10.1038/s41598-017-00140-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/09/2017] [Indexed: 12/17/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a useful tool for creation of mutant mice with mutations mirroring those in human patients. Various methods have been developed for this purpose, including deletions, inversions, and translocations. So far, mutant mice with deletions of up to 1.2 megabases (Mb) have been generated by microinjection of the CRISPR/Cas9 system into fertilized eggs; however, a method for generation of mutant mice with a deletion of more than several Mb size is necessary because such deletions have often been identified as possible causes of human diseases. With an aim to enable the generation of disease models carrying large deletions with a breakpoint in custom-designed sequences, we developed a method for induction of an Mb-sized deletion by microinjection of a pair of sgRNAs, Cas9, and a donor plasmid into fertilized eggs. Using this method, we efficiently and rapidly generated mutant mice carrying deletions up to 5 Mb.
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Pulido-Quetglas C, Aparicio-Prat E, Arnan C, Polidori T, Hermoso T, Palumbo E, Ponomarenko J, Guigo R, Johnson R. Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. PLoS Comput Biol 2017; 13:e1005341. [PMID: 28253259 PMCID: PMC5333799 DOI: 10.1371/journal.pcbi.1005341] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/30/2016] [Indexed: 11/23/2022] Open
Abstract
CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling of individual loci, to parallelized loss-of-function screens of thousands of regulatory elements. However, no solution has been presented for the unique bioinformatic design requirements of CRISPR deletion. We here present CRISPETa, a pipeline for flexible and scalable paired sgRNA design based on an empirical scoring model. Multiple sgRNA pairs are returned for each target, and any number of targets can be analyzed in parallel, making CRISPETa equally useful for focussed or high-throughput studies. Fast run-times are achieved using a pre-computed off-target database. sgRNA pair designs are output in a convenient format for visualisation and oligonucleotide ordering. We present pre-designed, high-coverage library designs for entire classes of protein-coding and non-coding elements in human, mouse, zebrafish, Drosophila melanogaster and Caenorhabditis elegans. In human cells, we reproducibly observe deletion efficiencies of ≥50% for CRISPETa designs targeting an enhancer and exonic fragment of the MALAT1 oncogene. In the latter case, deletion results in production of desired, truncated RNA. CRISPETa will be useful for researchers seeking to harness CRISPR for targeted genomic deletion, in a variety of model organisms, from single-target to high-throughput scales.
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Affiliation(s)
- Carlos Pulido-Quetglas
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Estel Aparicio-Prat
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Carme Arnan
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Taisia Polidori
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Toni Hermoso
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Emilio Palumbo
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Rory Johnson
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
- Department of Clinical Research, University of Bern, Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, Bern, Switzerland
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Josa S, Seruggia D, Fernández A, Montoliu L. Concepts and tools for gene editing. Reprod Fertil Dev 2017; 29:1-7. [DOI: 10.1071/rd16396] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Gene editing is a relatively recent concept in the molecular biology field. Traditional genetic modifications in animals relied on a classical toolbox that, aside from some technical improvements and additions, remained unchanged for many years. Classical methods involved direct delivery of DNA sequences into embryos or the use of embryonic stem cells for those few species (mice and rats) where it was possible to establish them. For livestock, the advent of somatic cell nuclear transfer platforms provided alternative, but technically challenging, approaches for the genetic alteration of loci at will. However, the entire landscape changed with the appearance of different classes of genome editors, from initial zinc finger nucleases, to transcription activator-like effector nucleases and, most recently, with the development of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas). Gene editing is currently achieved by CRISPR–Cas-mediated methods, and this technological advancement has boosted our capacity to generate almost any genetically altered animal that can be envisaged.
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A Transgenic Core Facility’s Experience in Genome Editing Revolution. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1016:75-90. [DOI: 10.1007/978-3-319-63904-8_4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Cao HX, Wang W, Le HTT, Vu GTH. The Power of CRISPR-Cas9-Induced Genome Editing to Speed Up Plant Breeding. Int J Genomics 2016; 2016:5078796. [PMID: 28097123 PMCID: PMC5206445 DOI: 10.1155/2016/5078796] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/17/2016] [Accepted: 11/01/2016] [Indexed: 12/26/2022] Open
Abstract
Genome editing with engineered nucleases enabling site-directed sequence modifications bears a great potential for advanced plant breeding and crop protection. Remarkably, the RNA-guided endonuclease technology (RGEN) based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) is an extremely powerful and easy tool that revolutionizes both basic research and plant breeding. Here, we review the major technical advances and recent applications of the CRISPR-Cas9 system for manipulation of model and crop plant genomes. We also discuss the future prospects of this technology in molecular plant breeding.
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Affiliation(s)
- Hieu X. Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466 Stadt Seeland, Germany
| | - Wenqin Wang
- School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Hien T. T. Le
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi, Vietnam
| | - Giang T. H. Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466 Stadt Seeland, Germany
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45
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CRISPR/Cas9 Immune System as a Tool for Genome Engineering. Arch Immunol Ther Exp (Warsz) 2016; 65:233-240. [PMID: 27699445 PMCID: PMC5434172 DOI: 10.1007/s00005-016-0427-5] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 09/16/2016] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) adaptive immune systems constitute a bacterial defence against invading nucleic acids derived from bacteriophages or plasmids. This prokaryotic system was adapted in molecular biology and became one of the most powerful and versatile platforms for genome engineering. CRISPR/Cas9 is a simple and rapid tool which enables the efficient modification of endogenous genes in various species and cell types. Moreover, a modified version of the CRISPR/Cas9 system with transcriptional repressors or activators allows robust transcription repression or activation of target genes. The simplicity of CRISPR/Cas9 has resulted in the widespread use of this technology in many fields, including basic research, biotechnology and biomedicine.
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Mojica FJ, Montoliu L. On the Origin of CRISPR-Cas Technology: From Prokaryotes to Mammals. Trends Microbiol 2016; 24:811-820. [DOI: 10.1016/j.tim.2016.06.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/02/2016] [Accepted: 06/10/2016] [Indexed: 12/21/2022]
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Song Y, Yuan L, Wang Y, Chen M, Deng J, Lv Q, Sui T, Li Z, Lai L. Efficient dual sgRNA-directed large gene deletion in rabbit with CRISPR/Cas9 system. Cell Mol Life Sci 2016; 73:2959-68. [PMID: 26817461 PMCID: PMC11108552 DOI: 10.1007/s00018-016-2143-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 12/21/2022]
Abstract
The CRISPR RNA-guided Cas9 nuclease gene-targeting system has been extensively used to edit the genome of several organisms. However, most mutations reported to date have been are indels, resulting in multiple mutations and numerous alleles in targeted genes. In the present study, a large deletion of 105 kb in the TYR (tyrosinase) gene was generated in rabbit via a dual sgRNA-directed CRISPR/Cas9 system. The typical symptoms of albinism accompanied significantly decreased expression of TYR in the TYR knockout rabbits. Furthermore, the same genotype and albinism phenotype were found in the F1 generation, suggesting that large-fragment deletions can be efficiently transmitted to the germline and stably inherited in offspring. Taken together, our data demonstrate that mono and biallelic large deletions can be achieved using the dual sgRNA-directed CRISPR/Cas9 system. This system produces no mosaic mutations or off-target effects, making it an efficient tool for large-fragment deletions in rabbit and other organisms.
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Affiliation(s)
- Yuning Song
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Lin Yuan
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Yong Wang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Mao Chen
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Jichao Deng
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Qingyan Lv
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Tingting Sui
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China
| | - Zhanjun Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China.
| | - Liangxue Lai
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun, 130062, China.
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Oliveros JC, Franch M, Tabas-Madrid D, San-León D, Montoliu L, Cubas P, Pazos F. Breaking-Cas-interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes. Nucleic Acids Res 2016; 44:W267-71. [PMID: 27166368 PMCID: PMC4987939 DOI: 10.1093/nar/gkw407] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 12/31/2022] Open
Abstract
The CRISPR/Cas technology is enabling targeted genome editing in multiple organisms with unprecedented accuracy and specificity by using RNA-guided nucleases. A critical point when planning a CRISPR/Cas experiment is the design of the guide RNA (gRNA), which directs the nuclease and associated machinery to the desired genomic location. This gRNA has to fulfil the requirements of the nuclease and lack homology with other genome sites that could lead to off-target effects. Here we introduce the Breaking-Cas system for the design of gRNAs for CRISPR/Cas experiments, including those based in the Cas9 nuclease as well as others recently introduced. The server has unique features not available in other tools, including the possibility of using all eukaryotic genomes available in ENSEMBL (currently around 700), placing variable PAM sequences at 5' or 3' and setting the guide RNA length and the scores per nucleotides. It can be freely accessed at: http://bioinfogp.cnb.csic.es/tools/breakingcas, and the code is available upon request.
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Affiliation(s)
- Juan C Oliveros
- National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain
| | - Mònica Franch
- National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain
| | - Daniel Tabas-Madrid
- National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain
| | - David San-León
- National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain
| | - Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain CIBERER, ISCIII, Madrid, Spain
| | - Pilar Cubas
- National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain
| | - Florencio Pazos
- National Centre for Biotechnology (CNB-CSIC), c/ Darwin 3, 28049 Madrid, Spain
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49
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Miano JM, Zhu QM, Lowenstein CJ. A CRISPR Path to Engineering New Genetic Mouse Models for Cardiovascular Research. Arterioscler Thromb Vasc Biol 2016; 36:1058-75. [PMID: 27102963 PMCID: PMC4882230 DOI: 10.1161/atvbaha.116.304790] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/06/2016] [Indexed: 12/26/2022]
Abstract
Previous efforts to target the mouse genome for the addition, subtraction, or substitution of biologically informative sequences required complex vector design and a series of arduous steps only a handful of laboratories could master. The facile and inexpensive clustered regularly interspaced short palindromic repeats (CRISPR) method has now superseded traditional means of genome modification such that virtually any laboratory can quickly assemble reagents for developing new mouse models for cardiovascular research. Here, we briefly review the history of CRISPR in prokaryotes, highlighting major discoveries leading to its formulation for genome modification in the animal kingdom. Core components of CRISPR technology are reviewed and updated. Practical pointers for 2-component and 3-component CRISPR editing are summarized with many applications in mice including frameshift mutations, deletion of enhancers and noncoding genes, nucleotide substitution of protein-coding and gene regulatory sequences, incorporation of loxP sites for conditional gene inactivation, and epitope tag integration. Genotyping strategies are presented and topics of genetic mosaicism and inadvertent targeting discussed. Finally, clinical applications and ethical considerations are addressed as the biomedical community eagerly embraces this astonishing innovation in genome editing to tackle previously intractable questions.
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Affiliation(s)
- Joseph M Miano
- From the Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY (J.M.M., Q.M.Z., C.J.L.); and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA (Q.M.Z.).
| | - Qiuyu Martin Zhu
- From the Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY (J.M.M., Q.M.Z., C.J.L.); and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA (Q.M.Z.)
| | - Charles J Lowenstein
- From the Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY (J.M.M., Q.M.Z., C.J.L.); and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA (Q.M.Z.)
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50
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Novel Hypomorphic Alleles of the Mouse Tyrosinase Gene Induced by CRISPR-Cas9 Nucleases Cause Non-Albino Pigmentation Phenotypes. PLoS One 2016; 11:e0155812. [PMID: 27224051 PMCID: PMC4880214 DOI: 10.1371/journal.pone.0155812] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/04/2016] [Indexed: 11/20/2022] Open
Abstract
Tyrosinase is a key enzyme in melanin biosynthesis. Mutations in the gene encoding tyrosinase (Tyr) cause oculocutaneous albinism (OCA1) in humans. Alleles of the Tyr gene have been useful in studying pigment biology and coat color formation. Over 100 different Tyr alleles have been reported in mice, of which ≈24% are spontaneous mutations, ≈60% are radiation-induced, and the remaining alleles were obtained by chemical mutagenesis and gene targeting. Therefore, most mutations were random and could not be predicted a priori. Using the CRISPR-Cas9 system, we targeted two distinct regions of exon 1 to induce pigmentation changes and used an in vivo visual phenotype along with heteroduplex mobility assays (HMA) as readouts of CRISPR-Cas9 activity. Most of the mutant alleles result in complete loss of tyrosinase activity leading to an albino phenotype. In this study, we describe two novel in-frame deletion alleles of Tyr, dhoosara (Sanskrit for gray) and chandana (Sanskrit for sandalwood). These alleles are hypomorphic and show lighter pigmentation phenotypes of the body and eyes. This study demonstrates the utility of CRISPR-Cas9 system in generating domain-specific in-frame deletions and helps gain further insights into structure-function of Tyr gene.
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