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Zhang R, He Z, Shi Y, Sun X, Chen X, Wang G, Zhang Y, Gao P, Wu Y, Lu S, Duan J, Sun S, Yang N, Fan W, Zhao K, Yang B, Xia Y, Zhang Y, Zhang Y, Yin H. Amplification editing enables efficient and precise duplication of DNA from short sequence to megabase and chromosomal scale. Cell 2024:S0092-8674(24)00637-8. [PMID: 38936359 DOI: 10.1016/j.cell.2024.05.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/24/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024]
Abstract
Duplication is a foundation of molecular evolution and a driver of genomic and complex diseases. Here, we develop a genome editing tool named Amplification Editing (AE) that enables programmable DNA duplication with precision at chromosomal scale. AE can duplicate human genomes ranging from 20 bp to 100 Mb, a size comparable to human chromosomes. AE exhibits activity across various cell types, encompassing diploid, haploid, and primary cells. AE exhibited up to 73.0% efficiency for 1 Mb and 3.4% for 100 Mb duplications, respectively. Whole-genome sequencing and deep sequencing of the junctions of edited sequences confirm the precision of duplication. AE can create chromosomal microduplications within disease-relevant regions in embryonic stem cells, indicating its potential for generating cellular and animal models. AE is a precise and efficient tool for chromosomal engineering and DNA duplication, broadening the landscape of precision genome editing from an individual genetic locus to the chromosomal scale.
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Affiliation(s)
- Ruiwen Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China; Department of Rheumatology and Immunology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Zhou He
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yajing Shi
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiangkun Sun
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xinyu Chen
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Guoquan Wang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yizhou Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Pan Gao
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Ying Wu
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Shuhan Lu
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Junyi Duan
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Shangwu Sun
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Na Yang
- Center for Gene Diagnosis and Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Wei Fan
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Kaitao Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Yan Zhang
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ying Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China; Department of Rheumatology and Immunology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Hao Yin
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China.
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2
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Darbellay F, Ramisch A, Lopez-Delisle L, Kosicki M, Rauseo A, Jouini Z, Visel A, Andrey G. Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development. Nat Commun 2024; 15:4820. [PMID: 38844479 PMCID: PMC11156918 DOI: 10.1038/s41467-024-49203-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
Chondrocyte differentiation controls skeleton development and stature. Here we provide a comprehensive map of chondrocyte-specific enhancers and show that they provide a mechanistic framework through which non-coding genetic variants can influence skeletal development and human stature. Working with fetal chondrocytes isolated from mice bearing a Col2a1 fluorescent regulatory sensor, we identify 780 genes and 2'704 putative enhancers specifically active in chondrocytes using a combination of RNA-seq, ATAC-seq and H3K27ac ChIP-seq. Most of these enhancers (74%) show pan-chondrogenic activity, with smaller populations being restricted to limb (18%) or trunk (8%) chondrocytes only. Notably, genetic variations overlapping these enhancers better explain height differences than those overlapping non-chondrogenic enhancers. Finally, targeted deletions of identified enhancers at the Fgfr3, Col2a1, Hhip and, Nkx3-2 loci confirm their role in regulating cognate genes. This enhancer map provides a framework for understanding how genes and non-coding variations influence bone development and diseases.
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Affiliation(s)
- Fabrice Darbellay
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA
| | - Anna Ramisch
- Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA
| | - Antonella Rauseo
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland
| | - Zahra Jouini
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, CA, 95343, USA
| | - Guillaume Andrey
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland.
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland.
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3
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Bassani S, Chrast J, Ambrosini G, Voisin N, Schütz F, Brusco A, Sirchia F, Turban L, Schubert S, Abou Jamra R, Schlump JU, DeMille D, Bayrak-Toydemir P, Nelson GR, Wong KN, Duncan L, Mosera M, Gilissen C, Vissers LELM, Pfundt R, Kersseboom R, Yttervik H, Hansen GÅM, Smeland MF, Butler KM, Lyons MJ, Carvalho CMB, Zhang C, Lupski JR, Potocki L, Flores-Gallegos L, Morales-Toquero R, Petit F, Yalcin B, Tuttle A, Elloumi HZ, McCormick L, Kukolich M, Klaas O, Horvath J, Scala M, Iacomino M, Operto F, Zara F, Writzl K, Maver A, Haanpää MK, Pohjola P, Arikka H, Kievit AJA, Calandrini C, Iseli C, Guex N, Reymond A. Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles. Genome Med 2024; 16:72. [PMID: 38811945 PMCID: PMC11137988 DOI: 10.1186/s13073-024-01339-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/19/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney, caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpression in zebrafish provided evidence for a dominant-negative mode of action, wherein an increased level of AFF3 resulted in pathological effects. METHODS Evolutionary constraints suggest that other modes-of-inheritance could be at play. We challenged this hypothesis by screening ID cohorts for individuals with predicted-to-be damaging variants in AFF3. We used both animal and cellular models to assess the deleteriousness of the identified variants. RESULTS We identified an individual with a KINSSHIP-like phenotype carrying a de novo partial duplication of AFF3 further strengthening the hypothesis that an increased level of AFF3 is pathological. We also detected seventeen individuals displaying a milder syndrome with either heterozygous Loss-of-Function (LoF) or biallelic missense variants in AFF3. Consistent with semi-dominance, we discovered three patients with homozygous LoF and one compound heterozygote for a LoF and a missense variant, who presented more severe phenotypes than their heterozygous parents. Matching zebrafish knockdowns exhibit neurological defects that could be rescued by expressing human AFF3 mRNA, confirming their association with the ablation of aff3. Conversely, some of the human AFF3 mRNAs carrying missense variants identified in affected individuals did not rescue these phenotypes. Overexpression of mutated AFF3 mRNAs in zebrafish embryos produced a significant increase of abnormal larvae compared to wild-type overexpression further demonstrating deleteriousness. To further assess the effect of AFF3 variation, we profiled the transcriptome of fibroblasts from affected individuals and engineered isogenic cells harboring + / + , KINSSHIP/KINSSHIP, LoF/ + , LoF/LoF or KINSSHIP/LoF AFF3 genotypes. The expression of more than a third of the AFF3 bound loci is modified in either the KINSSHIP/KINSSHIP or the LoF/LoF lines. While the same pathways are affected, only about one third of the differentially expressed genes are common to the homozygote datasets, indicating that AFF3 LoF and KINSSHIP variants largely modulate transcriptomes differently, e.g. the DNA repair pathway displayed opposite modulation. CONCLUSIONS Our results and the high pleiotropy shown by variation at this locus suggest that minute changes in AFF3 function are deleterious.
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Affiliation(s)
- Sissy Bassani
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, CH, 1015, Switzerland
- Present address: Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, CH, 1015, Switzerland
| | - Giovanna Ambrosini
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Norine Voisin
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, CH, 1015, Switzerland
- Present address: Sophia Genetics, St Sulpice, Switzerland
| | - Frédéric Schütz
- Biostatistics Platform, University of Lausanne, Lausanne, Switzerland
| | - Alfredo Brusco
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126, Turin, Italy
- Medical Genetics Unit, Città Della Salute E Della Scienza University Hospital, 10126, Turin, Italy
| | - Fabio Sirchia
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126, Turin, Italy
- Medical Genetics Unit, Città Della Salute E Della Scienza University Hospital, 10126, Turin, Italy
- Present address: Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Present address: Medical Genetics Unit, IRCCS San Matteo Foundation, Pavia, Italy
| | - Lydia Turban
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Susanna Schubert
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Jan-Ulrich Schlump
- Department of Pediatrics, Centre for Neuromedicine, Gemeinschaftskrankenhaus Herdecke Gerhard-Kienle-Weg, Herdecke, Germany
| | - Desiree DeMille
- Genomics Analysis 396, ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Gary Rex Nelson
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kristen Nicole Wong
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Laura Duncan
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, TN, USA
- Present address: Mayo Clinic, Rochester, MN, USA
| | - Mackenzie Mosera
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christian Gilissen
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rogier Kersseboom
- Center for Genetic Developmental Disorders Southwest, Zuidwester, Middelharnis, The Netherlands
| | - Hilde Yttervik
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | | | | | | | | | - Claudia M B Carvalho
- Pacific Northwest Research Institute (PNRI), Broadway, Seattle, WA, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chaofan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | | | | | | | - Binnaz Yalcin
- Inserm UMR1231, University of Burgundy, 21000, Dijon, France
| | | | | | - Lane McCormick
- Department of Genetics, Cook Children's Medical Center, Cook Children's Health Care System, Fort Worth, TX, USA
| | - Mary Kukolich
- Department of Genetics, Cook Children's Medical Center, Cook Children's Health Care System, Fort Worth, TX, USA
| | - Oliver Klaas
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Judit Horvath
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Marcello Scala
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, 16132, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Michele Iacomino
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Francesca Operto
- Department of Medicine, Child and Adolescent Neuropsychiatry Unit, Surgery and Dentistry, University of Salerno, Salerno, Italy
| | - Federico Zara
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, 16132, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maria K Haanpää
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Pia Pohjola
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Harri Arikka
- Department of Pediatric Neurology, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Anneke J A Kievit
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Camilla Calandrini
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, CH, 1015, Switzerland.
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4
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Hurtado A, Mota-Gómez I, Lao M, Real FM, Jedamzick J, Burgos M, Lupiáñez DG, Jiménez R, Barrionuevo FJ. Complete male-to-female sex reversal in XY mice lacking the miR-17~92 cluster. Nat Commun 2024; 15:3809. [PMID: 38714644 PMCID: PMC11076593 DOI: 10.1038/s41467-024-47658-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 04/04/2024] [Indexed: 05/10/2024] Open
Abstract
Mammalian sex determination is controlled by antagonistic gene cascades operating in embryonic undifferentiated gonads. The expression of the Y-linked gene SRY is sufficient to trigger the testicular pathway, whereas its absence in XX embryos leads to ovarian differentiation. Yet, the potential involvement of non-coding regulation in this process remains unclear. Here we show that the deletion of a single microRNA cluster, miR-17~92, induces complete primary male-to-female sex reversal in XY mice. Sry expression is delayed in XY knockout gonads, which develop as ovaries. Sertoli cell differentiation is reduced, delayed and unable to sustain testicular development. Pre-supporting cells in mutant gonads undergo a transient state of sex ambiguity which is subsequently resolved towards the ovarian fate. The miR-17~92 predicted target genes are upregulated, affecting the fine regulation of gene networks controlling gonad development. Thus, microRNAs emerge as key components for mammalian sex determination, controlling Sry expression timing and Sertoli cell differentiation.
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Grants
- P20-00583 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)
- P20-00583 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)
- P11-CVI-7291 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)
- P20-00583 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)
- IRTG2403 Deutsche Forschungsgemeinschaft (German Research Foundation)
- IRTG2403 Deutsche Forschungsgemeinschaft (German Research Foundation)
- IRTG2403 Deutsche Forschungsgemeinschaft (German Research Foundation)
- IRTG2403 Deutsche Forschungsgemeinschaft (German Research Foundation)
- grant no. 101045439, 3D-REVOLUTION EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- Ministerio de Ciencia e Innovación. Agencia Estatal de Investigación. Grant No. PID2022-139302NB-I00
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Affiliation(s)
- Alicia Hurtado
- Department of Genetics and Institute of Biotechnology, Labs. 127 and A105, Centre for Biomedical Research, University of Granada, Armilla, Granada, Spain
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC/UPO/JA, Seville, Spain
| | - Irene Mota-Gómez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Miguel Lao
- Department of Genetics and Institute of Biotechnology, Labs. 127 and A105, Centre for Biomedical Research, University of Granada, Armilla, Granada, Spain
| | - Francisca M Real
- Research Group Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Johanna Jedamzick
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Miguel Burgos
- Department of Genetics and Institute of Biotechnology, Labs. 127 and A105, Centre for Biomedical Research, University of Granada, Armilla, Granada, Spain
| | - Darío G Lupiáñez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC/UPO/JA, Seville, Spain.
| | - Rafael Jiménez
- Department of Genetics and Institute of Biotechnology, Labs. 127 and A105, Centre for Biomedical Research, University of Granada, Armilla, Granada, Spain.
| | - Francisco J Barrionuevo
- Department of Genetics and Institute of Biotechnology, Labs. 127 and A105, Centre for Biomedical Research, University of Granada, Armilla, Granada, Spain.
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5
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Morimoto K, Suzuki H, Kuno A, Daitoku Y, Tanimoto Y, Kato K, Murata K, Sugiyama F, Mizuno S. Regional random mutagenesis driven by multiple sgRNAs and diverse on-target genome editing events to identify functionally important elements in non-coding regions. Open Biol 2024; 14:240007. [PMID: 38565160 PMCID: PMC10987234 DOI: 10.1098/rsob.240007] [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: 01/05/2024] [Accepted: 02/06/2024] [Indexed: 04/04/2024] Open
Abstract
Functional regions that regulate biological phenomena are interspersed throughout eukaryotic genomes. The most definitive approach for identifying such regions is to confirm the phenotype of cells or organisms in which specific regions have been mutated or removed from the genome. This approach is invaluable for the functional analysis of genes with a defined functional element, the protein-coding sequence. By contrast, no functional analysis platforms have been established for the study of cis-elements or microRNA cluster regions consisting of multiple microRNAs with functional overlap. Whole-genome mutagenesis approaches, such as via N-ethyl-N-nitrosourea and gene trapping, have greatly contributed to elucidating the function of coding genes. These methods almost never induce deletions of genomic regions or multiple mutations within a narrow region. In other words, cis-elements and microRNA clusters cannot be effectively targeted in such a manner. Herein, we established a novel region-specific random mutagenesis method named CRISPR- and transposase-based regional mutagenesis (CTRL-mutagenesis). We demonstrate that CTRL-mutagenesis randomly induces diverse mutations within target regions in murine embryonic stem cells. Comparative analysis of mutants harbouring subtly different mutations within the same region would facilitate the further study of cis-element and microRNA clusters.
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Affiliation(s)
- Kento Morimoto
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Hayate Suzuki
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Akihiro Kuno
- Department of Anatomy and Embryology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Daitoku
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Tanimoto
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kanako Kato
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kazuya Murata
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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6
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Wang S, Gong X, Xiao F, Yang Y. Recent advances in host-focused molecular tools for investigating host-gut microbiome interactions. Front Microbiol 2024; 15:1335036. [PMID: 38605718 PMCID: PMC11007152 DOI: 10.3389/fmicb.2024.1335036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Microbial communities in the human gut play a significant role in regulating host gene expression, influencing a variety of biological processes. To understand the molecular mechanisms underlying host-microbe interactions, tools that can dissect signaling networks are required. In this review, we discuss recent advances in molecular tools used to study this interplay, with a focus on those that explore how the microbiome regulates host gene expression. These tools include CRISPR-based whole-body genetic tools for deciphering host-specific genes involved in the interaction process, Cre-loxP based tissue/cell-specific gene editing approaches, and in vitro models of host-derived organoids. Overall, the application of these molecular tools is revolutionizing our understanding of how host-microbiome interactions contribute to health and disease, paving the way for improved therapies and interventions that target microbial influences on the host.
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Affiliation(s)
- Siyao Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, China
| | - Xu Gong
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, China
| | - Fei Xiao
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Yun Yang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, China
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7
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Pinglay S, Lalanne JB, Daza RM, Koeppel J, Li X, Lee DS, Shendure J. Multiplex generation and single cell analysis of structural variants in a mammalian genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576756. [PMID: 38405830 PMCID: PMC10888807 DOI: 10.1101/2024.01.22.576756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The functional consequences of structural variants (SVs) in mammalian genomes are challenging to study. This is due to several factors, including: 1) their numerical paucity relative to other forms of standing genetic variation such as single nucleotide variants (SNVs) and short insertions or deletions (indels); 2) the fact that a single SV can involve and potentially impact the function of more than one gene and/or cis regulatory element; and 3) the relative immaturity of methods to generate and map SVs, either randomly or in targeted fashion, in in vitro or in vivo model systems. Towards addressing these challenges, we developed Genome-Shuffle-seq, a straightforward method that enables the multiplex generation and mapping of several major forms of SVs (deletions, inversions, translocations) throughout a mammalian genome. Genome-Shuffle-seq is based on the integration of "shuffle cassettes" to the genome, wherein each shuffle cassette contains components that facilitate its site-specific recombination (SSR) with other integrated shuffle cassettes (via Cre-loxP), its mapping to a specific genomic location (via T7-mediated in vitro transcription or IVT), and its identification in single-cell RNA-seq (scRNA-seq) data (via T7-mediated in situ transcription or IST). In this proof-of-concept, we apply Genome-Shuffle-seq to induce and map thousands of genomic SVs in mouse embryonic stem cells (mESCs) in a single experiment. Induced SVs are rapidly depleted from the cellular population over time, possibly due to Cre-mediated toxicity and/or negative selection on the rearrangements themselves. Leveraging T7 IST of barcodes whose positions are already mapped, we further demonstrate that we can efficiently genotype which SVs are present in association with each of many single cell transcriptomes in scRNA-seq data. Finally, preliminary evidence suggests our method may be a powerful means of generating extrachromosomal circular DNAs (ecDNAs). Looking forward, we anticipate that Genome-Shuffle-seq may be broadly useful for the systematic exploration of the functional consequences of SVs on gene expression, the chromatin landscape, and 3D nuclear architecture. We further anticipate potential uses for in vitro modeling of ecDNAs, as well as in paving the path to a minimal mammalian genome.
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Affiliation(s)
- Sudarshan Pinglay
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | | | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | | | - Xiaoyi Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David S Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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8
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Nuttle X, Burt ND, Currall B, Moysés-Oliveira M, Mohajeri K, Bhavsar R, Lucente D, Yadav R, Tai DJC, Gusella JF, Talkowski ME. Parallelized engineering of mutational models using piggyBac transposon delivery of CRISPR libraries. CELL REPORTS METHODS 2024; 4:100672. [PMID: 38091988 PMCID: PMC10831954 DOI: 10.1016/j.crmeth.2023.100672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/14/2023] [Accepted: 11/21/2023] [Indexed: 01/25/2024]
Abstract
New technologies and large-cohort studies have enabled novel variant discovery and association at unprecedented scale, yet functional characterization of these variants remains paramount to deciphering disease mechanisms. Approaches that facilitate parallelized genome editing of cells of interest or induced pluripotent stem cells (iPSCs) have become critical tools toward this goal. Here, we developed an approach that incorporates libraries of CRISPR-Cas9 guide RNAs (gRNAs) together with inducible Cas9 into a piggyBac (PB) transposon system to engineer dozens to hundreds of genomic variants in parallel against isogenic cellular backgrounds. This method empowers loss-of-function (LoF) studies through the introduction of insertions or deletions (indels) and copy-number variants (CNVs), though generating specific nucleotide changes is possible with prime editing. The ability to rapidly establish high-quality mutational models at scale will facilitate the development of isogenic cellular collections and catalyze comparative functional genomic studies investigating the roles of hundreds of genes and mutations in development and disease.
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Affiliation(s)
- Xander Nuttle
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
| | - Nicholas D Burt
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Benjamin Currall
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Mariana Moysés-Oliveira
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Kiana Mohajeri
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; PhD program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Riya Bhavsar
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Diane Lucente
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Rachita Yadav
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Derek J C Tai
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - James F Gusella
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Michael E Talkowski
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
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9
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Bassani S, Chrast J, Ambrosini G, Voisin N, Schütz F, Brusco A, Sirchia F, Turban L, Schubert S, Jamra RA, Schlump JU, DeMille D, Bayrak-Toydemir P, Nelson GR, Wong KN, Duncan L, Mosera M, Gilissen C, Vissers LE, Pfundt R, Kersseboom R, Yttervik H, Hansen GÅM, Falkenberg Smeland M, Butler KM, Lyons MJ, Carvalho CM, Zhang C, Lupski JR, Potocki L, Flores-Gallegos L, Morales-Toquero R, Petit F, Yalcin B, Tuttle A, Elloumi HZ, Mccormick L, Kukolich M, Klaas O, Horvath J, Scala M, Iacomino M, Operto F, Zara F, Writzl K, Maver A, Haanpää MK, Pohjola P, Arikka H, Iseli C, Guex N, Reymond A. Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.14.24301100. [PMID: 38293053 PMCID: PMC10827271 DOI: 10.1101/2024.01.14.24301100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpression in zebrafish provided evidence for a dominant-negative (DN) mode-of-action, wherein an increased level of AFF3 resulted in pathological effects. Methods Evolutionary constraints suggest that other mode-of-inheritance could be at play. We challenged this hypothesis by screening ID cohorts for individuals with predicted-to-be deleterious variants in AFF3. We used both animal and cellular models to assess the deleteriousness of the identified variants. Results We identified an individual with a KINSSHIP-like phenotype carrying a de novo partial duplication of AFF3 further strengthening the hypothesis that an increased level of AFF3 is pathological. We also detected seventeen individuals displaying a milder syndrome with either heterozygous LoF or biallelic missense variants in AFF3. Consistent with semi-dominance, we discovered three patients with homozygous LoF and one compound heterozygote for a LoF and a missense variant, who presented more severe phenotypes than their heterozygous parents. Matching zebrafish knockdowns exhibit neurological defects that could be rescued by expressing human AFF3 mRNA, confirming their association with the ablation of aff3. Conversely, some of the human AFF3 mRNAs carrying missense variants identified in affected individuals did not complement. Overexpression of mutated AFF3 mRNAs in zebrafish embryos produced a significant increase of abnormal larvae compared to wild-type overexpression further demonstrating deleteriousness. To further assess the effect of AFF3 variation, we profiled the transcriptome of fibroblasts from affected individuals and engineered isogenic cells harboring +/+, DN/DN, LoF/+, LoF/LoF or DN/LoF AFF3 genotypes. The expression of more than a third of the AFF3 bound loci is modified in either the DN/DN or the LoF/LoF lines. While the same pathways are affected, only about one-third of the differentially expressed genes are common to these homozygote datasets, indicating that AFF3 LoF and DN variants largely modulate transcriptomes differently, e.g. the DNA repair pathway displayed opposite modulation. Conclusions Our results and the high pleiotropy shown by variation at this locus suggest that minute changes in AFF3 function are deleterious.
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Affiliation(s)
- Sissy Bassani
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Giovanna Ambrosini
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Norine Voisin
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Frédéric Schütz
- Biostatistics platform, University of Lausanne, Lausanne, Switzerland
| | - Alfredo Brusco
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Fabio Sirchia
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Lydia Turban
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Susanna Schubert
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Jan-Ulrich Schlump
- Department of Pediatrics, Centre for Neuromedicine, Gemeinschaftskrankenhaus Herdecke Gerhard-Kienle-Weg, Herdecke, Germany
| | - Desiree DeMille
- Genomics Analysis 396, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Pinar Bayrak-Toydemir
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Gary Rex Nelson
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Kristen Nicole Wong
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Laura Duncan
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mackenzie Mosera
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christian Gilissen
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lisenka E.L.M. Vissers
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rogier Kersseboom
- Center for genetic developmental disorders southwest, Zuidwester, Middelharnis, The Netherlands
| | - Hilde Yttervik
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | | | | | | | | | - Claudia M.B. Carvalho
- Pacific Northwest Research Institute (PNRI), Broadway, Seattle, Washington, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Chaofan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | | | | | | | - Binnaz Yalcin
- Inserm UMR1231, University of Burgundy, 21000 Dijon, France
| | | | | | - Lane Mccormick
- Department of Genetics, Cook Children’s Medical Center, Cook Children’s Health Care System, Fort Worth, Texas, USA
| | - Mary Kukolich
- Department of Genetics, Cook Children’s Medical Center, Cook Children’s Health Care System, Fort Worth, Texas, USA
| | - Oliver Klaas
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Judit Horvath
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Michele Iacomino
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Francesca Operto
- Child and Adolescent Neuropsychiatry Unit, Department of Medicine, Surgery and Dentistry, University of Salerno, Salerno, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maria K. Haanpää
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Pia Pohjola
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Harri Arikka
- Department of Pediatric Neurology, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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10
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Mehryar MM, Shi X, Li J, Wu Q. DNA polymerases in precise and predictable CRISPR/Cas9-mediated chromosomal rearrangements. BMC Biol 2023; 21:288. [PMID: 38066536 PMCID: PMC10709867 DOI: 10.1186/s12915-023-01784-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Recent studies have shown that, owning to its cohesive cleavage, Cas9-mediated CRISPR gene editing outcomes at junctions of chromosomal rearrangements or DNA-fragment editing are precise and predictable; however, the underlying mechanisms are poorly understood due to lack of suitable assay system and analysis tool. RESULTS Here we developed a customized computer program to take account of staggered or cohesive Cas9 cleavage and to rapidly process large volumes of junctional sequencing reads from chromosomal rearrangements or DNA-fragment editing, including DNA-fragment inversions, duplications, and deletions. We also established a sensitive assay system using HPRT1 and DCK as reporters for cell growth during DNA-fragment editing by Cas9 with dual sgRNAs and found prominent large resections or long deletions at junctions of chromosomal rearrangements. In addition, we found that knockdown of PolQ (encoding Polθ polymerase), which has a prominent role in theta-mediated end joining (TMEJ) or microhomology-mediated end joining (MMEJ), results in increased large resections but decreased small deletions. We also found that the mechanisms for generating small deletions of 1bp and >1bp during DNA-fragment editing are different with regard to their opposite dependencies on Polθ and Polλ (encoded by the PolL gene). Specifically, Polθ suppresses 1bp deletions but promotes >1bp deletions, whereas Polλ promotes 1bp deletions but suppresses >1bp deletions. Finally, we found that Polλ is the main DNA polymerase responsible for fill-in of the 5' overhangs of staggered Cas9 cleavage ends. CONCLUSIONS These findings contribute to our understanding of the molecular mechanisms of CRISPR/Cas9-mediated DNA-fragment editing and have important implications for controllable, precise, and predictable gene editing.
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Affiliation(s)
- Mohammadreza M Mehryar
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Xin Shi
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Jingwei Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- WLA Laboratories, Shanghai, 201203, China.
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11
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Huang X, Henck J, Qiu C, Sreenivasan VKA, Balachandran S, Amarie OV, Hrabě de Angelis M, Behncke RY, Chan WL, Despang A, Dickel DE, Duran M, Feuchtinger A, Fuchs H, Gailus-Durner V, Haag N, Hägerling R, Hansmeier N, Hennig F, Marshall C, Rajderkar S, Ringel A, Robson M, Saunders LM, da Silva-Buttkus P, Spielmann N, Srivatsan SR, Ulferts S, Wittler L, Zhu Y, Kalscheuer VM, Ibrahim DM, Kurth I, Kornak U, Visel A, Pennacchio LA, Beier DR, Trapnell C, Cao J, Shendure J, Spielmann M. Single-cell, whole-embryo phenotyping of mammalian developmental disorders. Nature 2023; 623:772-781. [PMID: 37968388 PMCID: PMC10665194 DOI: 10.1038/s41586-023-06548-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/16/2023] [Indexed: 11/17/2023]
Abstract
Mouse models are a critical tool for studying human diseases, particularly developmental disorders1. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse2. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing3 to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6 million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions4,5. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be 'decomposable' through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution.
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Affiliation(s)
- Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Jana Henck
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck & Kiel University, Lübeck, Germany
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Varun K A Sreenivasan
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck & Kiel University, Lübeck, Germany
| | - Saranya Balachandran
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck & Kiel University, Lübeck, Germany
| | - Oana V Amarie
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Rose Yinghan Behncke
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Wing-Lee Chan
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Alexandra Despang
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Diane E Dickel
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Annette Feuchtinger
- Core Facility Pathology & Tissue Analytics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Natja Haag
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Rene Hägerling
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Nils Hansmeier
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | | | - Cooper Marshall
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | | | - Alessa Ringel
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
| | - Michael Robson
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lauren M Saunders
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Patricia da Silva-Buttkus
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Nadine Spielmann
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Sanjay R Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sascha Ulferts
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Yiwen Zhu
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | | | - Daniel M Ibrahim
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Uwe Kornak
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - David R Beier
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Junyue Cao
- Laboratory of Single-Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Malte Spielmann
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck & Kiel University, Lübeck, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany.
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12
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Zhang Y, Chen S, Yang L, Zhang Q. Application progress of CRISPR/Cas9 genome-editing technology in edible fungi. Front Microbiol 2023; 14:1169884. [PMID: 37303782 PMCID: PMC10248459 DOI: 10.3389/fmicb.2023.1169884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/26/2023] [Indexed: 06/13/2023] Open
Abstract
Edible fungi are not only delicious but are also rich in nutritional and medicinal value, which is highly sought after by consumers. As the edible fungi industry continues to rapidly advance worldwide, particularly in China, the cultivation of superior and innovative edible fungi strains has become increasingly pivotal. Nevertheless, conventional breeding techniques for edible fungi can be arduous and time-consuming. CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9) is a powerful tool for molecular breeding due to its ability to mediate high-efficiency and high-precision genome modification, which has been successfully applied to many kinds of edible fungi. In this review, we briefly summarized the working mechanism of the CRISPR/Cas9 system and highlighted the application progress of CRISPR/Cas9-mediated genome-editing technology in edible fungi, including Agaricus bisporus, Ganoderma lucidum, Flammulina filiformis, Ustilago maydis, Pleurotus eryngii, Pleurotus ostreatus, Coprinopsis cinerea, Schizophyllum commune, Cordyceps militaris, and Shiraia bambusicola. Additionally, we discussed the limitations and challenges encountered using CRISPR/Cas9 technology in edible fungi and provided potential solutions. Finally, the applications of CRISPR/Cas9 system for molecular breeding of edible fungi in the future are explored.
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13
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Paranjape N, Lin YHT, Flores-Ramirez Q, Sarin V, Johnson AB, Chu J, Paredes M, Wiita AP. A CRISPR-engineered isogenic model of the 22q11.2 A-B syndromic deletion. Sci Rep 2023; 13:7689. [PMID: 37169815 PMCID: PMC10175260 DOI: 10.1038/s41598-023-34325-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
22q11.2 deletion syndrome, associated with congenital and neuropsychiatric anomalies, is the most common copy number variant (CNV)-associated syndrome. Patient-derived, induced pluripotent stem cell (iPS) models have provided insight into this condition. However, patient-derived iPS cells may harbor underlying genetic heterogeneity that can confound analysis. Furthermore, almost all available models reflect the commonly-found ~ 3 Mb "A-D" deletion at this locus. The ~ 1.5 Mb "A-B" deletion, a variant of the 22q11.2 deletion which may lead to different syndromic features, and is much more frequently inherited than the A-D deletion, remains under-studied due to lack of relevant models. Here we leveraged a CRISPR-based strategy to engineer isogenic iPS models of the 22q11.2 "A-B" deletion. Differentiation to excitatory neurons with subsequent characterization by transcriptomics and cell surface proteomics identified deletion-associated alterations in proliferation and adhesion. To illustrate in vivo applications of this model, we further implanted neuronal progenitor cells into the cortex of neonatal mice and found potential alterations in neuronal maturation. The isogenic models generated here will provide a unique resource to study this less-common variant of the 22q11.2 microdeletion syndrome.
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Affiliation(s)
- Neha Paranjape
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yu-Hsiu T Lin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Quetzal Flores-Ramirez
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Vishesh Sarin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amanda Brooke Johnson
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- San Francisco State University, San Francisco, CA, USA
| | - Julia Chu
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Mercedes Paredes
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
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14
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Cova G, Glaser J, Schöpflin R, Prada-Medina CA, Ali S, Franke M, Falcone R, Federer M, Ponzi E, Ficarella R, Novara F, Wittler L, Timmermann B, Gentile M, Zuffardi O, Spielmann M, Mundlos S. Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve split-hand/foot malformation type 3. Nat Commun 2023; 14:1475. [PMID: 36928426 PMCID: PMC10020157 DOI: 10.1038/s41467-023-37057-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
Split-Hand/Foot Malformation type 3 (SHFM3) is a congenital limb malformation associated with tandem duplications at the LBX1/FGF8 locus. Yet, the disease patho-mechanism remains unsolved. Here we investigate the functional consequences of SHFM3-associated rearrangements on chromatin conformation and gene expression in vivo in transgenic mice. We show that the Lbx1/Fgf8 locus consists of two separate, but interacting, regulatory domains. Re-engineering of a SHFM3-associated duplication and a newly reported inversion in mice results in restructuring of the chromatin architecture. This leads to ectopic activation of the Lbx1 and Btrc genes in the apical ectodermal ridge (AER) in an Fgf8-like pattern induced by AER-specific enhancers of Fgf8. We provide evidence that the SHFM3 phenotype is the result of a combinatorial effect on gene misexpression in the developing limb. Our results reveal insights into the molecular mechanism underlying SHFM3 and provide conceptual framework for how genomic rearrangements can cause gene misexpression and disease.
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Affiliation(s)
- Giulia Cova
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany.
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany.
- Department of Pathology, New York University School of Medicine, Langone Health Medical Center, New York, NY, 10016, USA.
| | - Juliane Glaser
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Cesar Augusto Prada-Medina
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
| | - Salaheddine Ali
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Martin Franke
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, 41013, Spain
| | - Rita Falcone
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
| | - Miriam Federer
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Universität Innsbruck, Innsbruck, 6020, Austria
| | - Emanuela Ponzi
- Medical Genetics Unit, Department of Reproductive Medicine, ASL Bari, Bari, 70131, Italy
| | - Romina Ficarella
- Medical Genetics Unit, Department of Reproductive Medicine, ASL Bari, Bari, 70131, Italy
| | | | - Lars Wittler
- Department of Developmental Genetics, Transgenic Unit, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Mattia Gentile
- Medical Genetics Unit, Department of Reproductive Medicine, ASL Bari, Bari, 70131, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, 27100, Italy
| | - Malte Spielmann
- Institute of Human Genetics, Universitätsklinikum Schleswig Holstein Campus Kiel and Christian-Albrechts-Universität, Kiel, 24118, Germany
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany.
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany.
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, 13353, Germany.
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15
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Jiang YF, Wang S, Wang CL, Xu RH, Wang WW, Jiang Y, Wang MS, Jiang L, Dai LH, Wang JR, Chu XH, Zeng YQ, Fang LZ, Wu DD, Zhang Q, Ding XD. Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs. iScience 2023; 26:106119. [PMID: 36852268 PMCID: PMC9958381 DOI: 10.1016/j.isci.2023.106119] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.
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Affiliation(s)
- Yi-Fan Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Chong-Long Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ru-Hai Xu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wen-Wen Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Yao Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Li-He Dai
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jie-Ru Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiao-Hong Chu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yong-Qing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Ling-Zhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Xiang-Dong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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16
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Payne ZL, Penny GM, Turner TN, Dutcher SK. A gap-free genome assembly of Chlamydomonas reinhardtii and detection of translocations induced by CRISPR-mediated mutagenesis. PLANT COMMUNICATIONS 2023; 4:100493. [PMID: 36397679 PMCID: PMC10030371 DOI: 10.1016/j.xplc.2022.100493] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/26/2022] [Accepted: 11/15/2022] [Indexed: 05/04/2023]
Abstract
Genomic assemblies of the unicellular green alga Chlamydomonas reinhardtii have provided important resources for researchers. However, assembly errors, large gaps, and unplaced scaffolds as well as strain-specific variants currently impede many types of analysis. By combining PacBio HiFi and Oxford Nanopore long-read technologies, we generated a de novo genome assembly for strain CC-5816, derived from crosses of strains CC-125 and CC-124. Multiple methods of evaluating genome completeness and base-pair error rate suggest that the final telomere-to-telomere assembly is highly accurate. The CC-5816 assembly enabled previously difficult analyses that include characterization of the 17 centromeres, rDNA arrays on three chromosomes, and 56 insertions of organellar DNA into the nuclear genome. Using Nanopore sequencing, we identified sites of cytosine (CpG) methylation, which are enriched at centromeres. We analyzed CRISPR-Cas9 insertional mutants in the PF23 gene. Two of the three alleles produced progeny that displayed patterns of meiotic inviability that suggested the presence of a chromosomal aberration. Mapping Nanopore reads from pf23-2 and pf23-3 onto the CC-5816 genome showed that these two strains each carry a translocation that was initiated at the PF23 gene locus on chromosome 11 and joined with chromosomes 5 or 3, respectively. The translocations were verified by demonstrating linkage between loci on the two translocated chromosomes in meiotic progeny. The three pf23 alleles display the expected short-cilia phenotype, and immunoblotting showed that pf23-2 lacks the PF23 protein. Our CC-5816 genome assembly will undoubtedly provide an important tool for the Chlamydomonas research community.
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Affiliation(s)
- Zachary L Payne
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Gervette M Penny
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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17
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Schaeffer L, Lindner L, Pavlovic G, Hérault Y, Birling MC. CRISMERE Chromosome Engineering in Mouse and Rat. Methods Mol Biol 2023; 2631:277-297. [PMID: 36995673 DOI: 10.1007/978-1-0716-2990-1_12] [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
CRISPR/Cas9 technology is a versatile tool for engineering biology that has dramatically transformed our ability to manipulate genomes. In this protocol, we use its capacity to generate two double-strand breaks simultaneously, at precise positions in the genome, to generate mouse or rat lines with deletion, inversion, and duplication of a specific genomic segment. The technic is called CRISMERE for CRISpr-MEdiated REarrangement. This protocol describes the different steps to generate and validate the different chromosomal rearrangements that can be obtained with the technology. These new genetic configurations can be useful to model rare diseases with copy number variation, understand the genomic organization, or provide genetic tools (like balancer chromosome) to keep lethal mutations.
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Affiliation(s)
- Laurence Schaeffer
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Loic Lindner
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Guillaume Pavlovic
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Yann Hérault
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France
| | - Marie-Christine Birling
- Université de Strasbourg, CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Illkirch, France.
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18
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Inoue Y, Tsuchida N, Okamoto N, Shuichi S, Ohashi K, Saitoh S, Ogawa A, Hamada K, Sakamoto M, Miyake N, Hamanaka K, Fujita A, Koshimizu E, Miyatake S, Mizuguchi T, Ogata K, Uchiyama Y, Matsumoto N. Three KINSSHIP syndrome patients with mosaic and germline AFF3 variants. Clin Genet 2022; 103:590-595. [PMID: 36576140 DOI: 10.1111/cge.14292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022]
Abstract
AFF3 at 2q11.2 encodes the nuclear transcriptional activator AF4/FMR2 Family Member 3. AFF3 constitutes super elongation complex like 3, which plays a role in promoting the expression of genes involved in neurogenesis and development. The degron motif in AFF3 with nine highly conserved amino acids is recognized by E3 ubiquitin ligase to induce protein degradation. Recently, AFF3 missense variants in this region and variants featuring deletion including this region were identified and shown to cause KINSSHIP syndrome. In this study, we identified two novel and one previously reported missense variants in the degron of AFF3 in three unrelated Japanese patients. Notably, two of these three variants exhibited mosaicism in the examined tissues. This study suggests that mosaic variants also cause KINSSHIP syndrome, showing various phenotypes.
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Affiliation(s)
- Yuta Inoue
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Shimakawa Shuichi
- Department of Pediatrics, Osaka Medical and Pharmaceutical University Hospital, Osaka, Japan
| | - Kei Ohashi
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Atsushi Ogawa
- Department of Pediatrics, Chikushi Hospital, Fukuoka University, Fukuoka, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masamune Sakamoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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19
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Ringel AR, Szabo Q, Chiariello AM, Chudzik K, Schöpflin R, Rothe P, Mattei AL, Zehnder T, Harnett D, Laupert V, Bianco S, Hetzel S, Glaser J, Phan MHQ, Schindler M, Ibrahim DM, Paliou C, Esposito A, Prada-Medina CA, Haas SA, Giere P, Vingron M, Wittler L, Meissner A, Nicodemi M, Cavalli G, Bantignies F, Mundlos S, Robson MI. Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes. Cell 2022; 185:3689-3704.e21. [PMID: 36179666 PMCID: PMC9567273 DOI: 10.1016/j.cell.2022.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/03/2022] [Accepted: 08/30/2022] [Indexed: 01/26/2023]
Abstract
Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.
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Affiliation(s)
- Alessa R Ringel
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Quentin Szabo
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Konrad Chudzik
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Patricia Rothe
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandra L Mattei
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Tobias Zehnder
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Dermot Harnett
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Verena Laupert
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Sara Hetzel
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Juliane Glaser
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Mai H Q Phan
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Magdalena Schindler
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Daniel M Ibrahim
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Christina Paliou
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Cesar A Prada-Medina
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Stefan A Haas
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Peter Giere
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexander Meissner
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Giacomo Cavalli
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Frédéric Bantignies
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany.
| | - Michael I Robson
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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20
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D’Annibale OM, Phua YL, Van’t Land C, Karunanidhi A, Dorenbaum A, Mohsen AW, Vockley J. Treatment of VLCAD-Deficient Patient Fibroblasts with Peroxisome Proliferator-Activated Receptor δ Agonist Improves Cellular Bioenergetics. Cells 2022; 11:2635. [PMID: 36078043 PMCID: PMC9454759 DOI: 10.3390/cells11172635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/15/2022] [Accepted: 08/20/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency is an autosomal recessive disease that prevents the body from utilizing long-chain fatty acids for energy, most needed during stress and fasting. Symptoms can appear from infancy through childhood and adolescence or early adulthood, and include hypoglycemia, recurrent rhabdomyolysis, myopathy, hepatopathy, and cardiomyopathy. REN001 is a peroxisome-proliferator-activated receptor delta (PPARδ) agonist that modulates the expression of the genes coding for fatty acid β-oxidation enzymes and proteins involved in oxidative phosphorylation. Here, we assessed the effect of REN001 on VLCAD-deficient patient fibroblasts. Methods: VLCAD-deficient patient and control fibroblasts were treated with REN001. Cells were harvested for gene expression analysis, protein content, VLCAD enzyme activity, cellular bioenergetics, and ATP production. Results: VLCAD-deficient cell lines responded differently to REN001 based on genotype. All cells had statistically significant increases in ACADVL gene expression. Small increases in VLCAD protein and enzyme activity were observed and were cell-line- and dose-dependent. Even with these small increases, cellular bioenergetics improved in all cell lines in the presence of REN001, as demonstrated by the oxygen consumption rate and ATP production. VLCAD-deficient cell lines containing missense mutations responded better to REN001 treatment than one containing a duplication mutation in ACADVL. Discussion: Treating VLCAD-deficient fibroblasts with the REN001 PPARδ agonist results in an increase in VLCAD protein and enzyme activity, and a decrease in cellular stress. These results establish REN001 as a potential therapy for VLCADD as enhanced expression may provide a therapeutic increase in total VLCAD activity, but suggest the need for mutation-specific treatment augmented by other treatment measures.
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Affiliation(s)
- Olivia M. D’Annibale
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
| | - Yu Leng Phua
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Clinton Van’t Land
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Anuradha Karunanidhi
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Alejandro Dorenbaum
- Reneo Pharmaceuticals, Inc., 18575 Jamboree Road Suite 275-S, Irvine, CA 92612, USA
| | - Al-Walid Mohsen
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
| | - Jerry Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
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21
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In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation. Nat Genet 2022; 54:1026-1036. [PMID: 35817979 PMCID: PMC9279147 DOI: 10.1038/s41588-022-01117-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 05/31/2022] [Indexed: 01/05/2023]
Abstract
Vertebrate genomes organize into topologically associating domains, delimited by boundaries that insulate regulatory elements from nontarget genes. However, how boundary function is established is not well understood. Here, we combine genome-wide analyses and transgenic mouse assays to dissect the regulatory logic of clustered-CCCTC-binding factor (CTCF) boundaries in vivo, interrogating their function at multiple levels: chromatin interactions, transcription and phenotypes. Individual CTCF binding site (CBS) deletions revealed that the characteristics of specific sites can outweigh other factors such as CBS number and orientation. Combined deletions demonstrated that CBSs cooperate redundantly and provide boundary robustness. We show that divergent CBS signatures are not strictly required for effective insulation and that chromatin loops formed by nonconvergently oriented sites could be mediated by a loop interference mechanism. Further, we observe that insulation strength constitutes a quantitative modulator of gene expression and phenotypes. Our results highlight the modular nature of boundaries and their control over developmental processes.
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22
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Pinglay S, Bulajić M, Rahe DP, Huang E, Brosh R, Mamrak NE, King BR, German S, Cadley JA, Rieber L, Easo N, Lionnet T, Mahony S, Maurano MT, Holt LJ, Mazzoni EO, Boeke JD. Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation. Science 2022; 377:eabk2820. [PMID: 35771912 PMCID: PMC9648154 DOI: 10.1126/science.abk2820] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Precise Hox gene expression is crucial for embryonic patterning. Intra-Hox transcription factor binding and distal enhancer elements have emerged as the major regulatory modules controlling Hox gene expression. However, quantifying their relative contributions has remained elusive. Here, we introduce "synthetic regulatory reconstitution," a conceptual framework for studying gene regulation, and apply it to the HoxA cluster. We synthesized and delivered variant rat HoxA clusters (130 to 170 kilobases) to an ectopic location in the mouse genome. We found that a minimal HoxA cluster recapitulated correct patterns of chromatin remodeling and transcription in response to patterning signals, whereas the addition of distal enhancers was needed for full transcriptional output. Synthetic regulatory reconstitution could provide a generalizable strategy for deciphering the regulatory logic of gene expression in complex genomes.
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Affiliation(s)
- Sudarshan Pinglay
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Milica Bulajić
- Department of Biology, New York University, New York, NY 10003, USA
| | - Dylan P. Rahe
- Department of Biology, New York University, New York, NY 10003, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Nicholas E. Mamrak
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Benjamin R. King
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Sergei German
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - John A. Cadley
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Lila Rieber
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Nicole Easo
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Timothée Lionnet
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Cell Biology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew T. Maurano
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Liam J. Holt
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | | | - Jef D. Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
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23
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Liu X, Dong J, Liao J, Tian L, Qiu H, Wu T, Ge F, Zhu J, Shi L, Jiang A, Yu H, Zhao M, Ren A. Establishment of CRISPR/Cas9 Genome-Editing System Based on Dual sgRNAs in Flammulina filiformis. J Fungi (Basel) 2022; 8:jof8070693. [PMID: 35887449 PMCID: PMC9318071 DOI: 10.3390/jof8070693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 02/01/2023] Open
Abstract
Flammulina filiformis, previously known as Asian Flammulina velutipes, is one of the most commercially important edible fungi, with nutritional value and medicinal properties worldwide. However, precision genome editing using CRISPR/Cas9, which is a revolutionary technology and provides a powerful tool for molecular breeding, has not been established in F. filiformis. Here, plasmids harboring expression cassettes of Basidiomycete codon-optimized Cas9 and dual sgRNAs targeting pyrG under the control of the gpd promoter and FfU6 promoter, respectively, were delivered into protoplasts of F. filiformis Dan3 strain through PEG-mediated transformation. The results showed that an efficient native U6 promoter of F. filiformis was identified, and ultimately several pyrG mutants exhibiting 5-fluorooric acid (5-FOA) resistance were obtained. Additionally, diagnostic PCR followed by Sanger sequencing revealed that fragment deletion between the two sgRNA target sites or small insertions and deletions (indels) were introduced in these pyrG mutants through the nonhomologous end joining (NHEJ) pathway, resulting in heritable changes in genomic information. Taken together, this is the first report in which a successful CRISPR/Cas9 genome-editing system based on dual sgRNAs was established in F. filiformis, which broadens the application of this advanced tool in Basidiomycetes.
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Affiliation(s)
- Xiaotian Liu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
| | - Jianghan Dong
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
| | - Jian Liao
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
| | - Li Tian
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
| | - Hao Qiu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
| | - Tao Wu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
| | - Feng Ge
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
| | - Jing Zhu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
| | - Liang Shi
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
| | - Ailiang Jiang
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
| | - Hanshou Yu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
| | - Mingwen Zhao
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
| | - Ang Ren
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (J.D.); (J.L.); (L.T.); (H.Q.); (T.W.); (F.G.); (J.Z.); (L.S.); (A.J.); (H.Y.); (M.Z.)
- Sanya Institute of Nanjing Agricultural University, Sanya 572025, China
- Institute of Biology, Guizhou Academy of Sciences, Guiyang 550009, China
- Correspondence: ; Tel./Fax: +86-25-84395602
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24
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Yoshiki A, Ballard G, Perez AV. Genetic quality: a complex issue for experimental study reproducibility. Transgenic Res 2022; 31:413-430. [PMID: 35751794 PMCID: PMC9489590 DOI: 10.1007/s11248-022-00314-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022]
Abstract
Laboratory animal research involving mice, requires consideration of many factors to be controlled. Genetic quality is one factor that is often overlooked but is essential for the generation of reproducible experimental results. Whether experimental research involves inbred mice, spontaneous mutant, or genetically modified strains, exercising genetic quality through careful breeding, good recordkeeping, and prudent quality control steps such as validation of the presence of mutations and verification of the genetic background, will help ensure that experimental results are accurate and that reference controls are representative for the particular experiment. In this review paper, we will discuss various techniques used for the generation of genetically altered mice, and the different aspects to be considered regarding genetic quality, including inbred strains and substrains used, quality check controls during and after genetic manipulation and breeding. We also provide examples for when to use the different techniques and considerations on genetic quality checks. Further, we emphasize on the importance of establishing an in-house genetic quality program.
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Affiliation(s)
- Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, 3050074, Japan.
| | - Gregory Ballard
- Comparative Medicine and Quality, The Jackson Laboratory, Bar Harbor, ME 04609, USA
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25
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Context-dependent enhancer function revealed by targeted inter-TAD relocation. Nat Commun 2022; 13:3488. [PMID: 35715427 PMCID: PMC9205857 DOI: 10.1038/s41467-022-31241-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/09/2022] [Indexed: 11/08/2022] Open
Abstract
The expression of some genes depends on large, adjacent regions of the genome that contain multiple enhancers. These regulatory landscapes frequently align with Topologically Associating Domains (TADs), where they integrate the function of multiple similar enhancers to produce a global, TAD-specific regulation. We asked if an individual enhancer could overcome the influence of one of these landscapes, to drive gene transcription. To test this, we transferred an enhancer from its native location, into a nearby TAD with a related yet different functional specificity. We used the biphasic regulation of Hoxd genes during limb development as a paradigm. These genes are first activated in proximal limb cells by enhancers located in one TAD, which is then silenced when the neighboring TAD activates its enhancers in distal limb cells. We transferred a distal limb enhancer into the proximal limb TAD and found that its new context suppresses its normal distal specificity, even though it is bound by HOX13 transcription factors, which are responsible for the distal activity. This activity can be rescued only when a large portion of the surrounding environment is removed. These results indicate that, at least in some cases, the functioning of enhancer elements is subordinated to the host chromatin context, which can exert a dominant control over its activity. Here the authors show that a strong enhancer sequence can be controlled by the chromatin environment provided by a topologically associated domain (TAD) located nearby. An enhancer relocated by homologous recombination takes all the hallmarks of its new neighboring enhancers located in the recipient TAD.
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26
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Pulido-Quetglas C, Johnson R. Designing libraries for pooled CRISPR functional screens of long noncoding RNAs. Mamm Genome 2022; 33:312-327. [PMID: 34533605 PMCID: PMC9114037 DOI: 10.1007/s00335-021-09918-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/09/2021] [Indexed: 02/01/2023]
Abstract
Human and other genomes encode tens of thousands of long noncoding RNAs (lncRNAs), the vast majority of which remain uncharacterised. High-throughput functional screening methods, notably those based on pooled CRISPR-Cas perturbations, promise to unlock the biological significance and biomedical potential of lncRNAs. Such screens are based on libraries of single guide RNAs (sgRNAs) whose design is critical for success. Few off-the-shelf libraries are presently available, and lncRNAs tend to have cell-type-specific expression profiles, meaning that library design remains in the hands of researchers. Here we introduce the topic of pooled CRISPR screens for lncRNAs and guide readers through the three key steps of library design: accurate annotation of transcript structures, curation of optimal candidate sets, and design of sgRNAs. This review is a starting point and reference for researchers seeking to design custom CRISPR screening libraries for lncRNAs.
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Affiliation(s)
- Carlos Pulido-Quetglas
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012, Bern, Switzerland
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland.
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland.
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
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27
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Kraft K, Yost KE, Murphy SE, Magg A, Long Y, Corces MR, Granja JM, Wittler L, Mundlos S, Cech TR, Boettiger AN, Chang HY. Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation. Proc Natl Acad Sci U S A 2022; 119:e2201883119. [PMID: 35617427 PMCID: PMC9295753 DOI: 10.1073/pnas.2201883119] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Polycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction. This process is essential for embryonic stem cell (ESC) pluripotency, differentiation, and development. Polycomb repressive complex 2 (PRC2) can both read and write H3K27me3, enabling progressive spreading of H3K27me3 on the linear genome. Long-range Polycomb-associated DNA contacts have also been described, but their regulation and role in gene silencing remain unclear. Here, we apply H3K27me3 HiChIP, a protein-directed chromosome conformation method, and optical reconstruction of chromatin architecture to profile long-range Polycomb-associated DNA loops that span tens to hundreds of megabases across multiple topological associated domains in mouse ESCs and human induced pluripotent stem cells. We find that H3K27me3 loop anchors are enriched for Polycomb nucleation points and coincide with key developmental genes. Genetic deletion of H3K27me3 loop anchors results in disruption of spatial contact between distant loci and altered H3K27me3 in cis, both locally and megabases away on the same chromosome. In mouse embryos, loop anchor deletion leads to ectopic activation of the partner gene, suggesting that Polycomb-associated loops control gene silencing during development. Further, we find that alterations in PRC2 occupancy resulting from an RNA binding–deficient EZH2 mutant are accompanied by loss of Polycomb-associated DNA looping. Together, these results suggest PRC2 uses RNA binding to enhance long-range chromosome folding and H3K27me3 spreading. Developmental gene loci have unique roles in Polycomb spreading, emerging as important architectural elements of the epigenome.
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Affiliation(s)
- Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305
| | - Kathryn E. Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Andreas Magg
- Research Group of Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin, 10117 Berlin, Germany
| | - Yicheng Long
- HHMI, University of Colorado, Boulder, CO 80309
- Department of Biochemistry, University of Colorado, Boulder, CO 80309
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309
| | - M. Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305
| | - Jeffrey M. Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Stefan Mundlos
- Research Group of Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin, 10117 Berlin, Germany
| | - Thomas R. Cech
- HHMI, University of Colorado, Boulder, CO 80309
- Department of Biochemistry, University of Colorado, Boulder, CO 80309
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309
| | | | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305
- HHMI, Stanford University School of Medicine, Stanford, CA 94305
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28
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Abstract
One of the most fundamental questions in developmental biology is how one fertilized cell can give rise to a fully mature organism and how gene regulation governs this process. Precise spatiotemporal gene expression is required for development and is believed to be achieved through a complex interplay of sequence-specific information, epigenetic modifications, trans-acting factors, and chromatin folding. Here we review the role of chromatin folding during development, the mechanisms governing 3D genome organization, and how it is established in the embryo. Furthermore, we discuss recent advances and debated questions regarding the contribution of the 3D genome to gene regulation during organogenesis. Finally, we describe the mechanisms that can reshape the 3D genome, including disease-causing structural variations and the emerging view that transposable elements contribute to chromatin organization.
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Affiliation(s)
- Juliane Glaser
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Stefan Mundlos
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
- Charité - Universitätsmedizin Berlin, BCRT - Berlin Institute of Health Center for Regenerative Therapies, 10178 Berlin, Germany
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29
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Abstract
Over the past decade, CRISPR has become as much a verb as it is an acronym, transforming biomedical research and providing entirely new approaches for dissecting all facets of cell biology. In cancer research, CRISPR and related tools have offered a window into previously intractable problems in our understanding of cancer genetics, the noncoding genome and tumour heterogeneity, and provided new insights into therapeutic vulnerabilities. Here, we review the progress made in the development of CRISPR systems as a tool to study cancer, and the emerging adaptation of these technologies to improve diagnosis and treatment.
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Affiliation(s)
- Alyna Katti
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Bianca J Diaz
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Christina M Caragine
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Neville E Sanjana
- Department of Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
| | - Lukas E Dow
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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30
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Banas K, Modarai S, Rivera-Torres N, Yoo BC, Bialk PA, Barrett C, Batish M, Kmiec EB. Exon skipping induced by CRISPR-directed gene editing regulates the response to chemotherapy in non-small cell lung carcinoma cells. Gene Ther 2022; 29:357-367. [PMID: 35314779 PMCID: PMC9203268 DOI: 10.1038/s41434-022-00324-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 01/26/2022] [Accepted: 02/14/2022] [Indexed: 11/17/2022]
Abstract
We have been developing CRISPR-directed gene editing as an augmentative therapy for the treatment of non-small cell lung carcinoma (NSCLC) by genetic disruption of Nuclear Factor Erythroid 2-Related Factor 2 (NRF2). NRF2 promotes tumor cell survival in response to therapeutic intervention and thus its disablement should restore or enhance effective drug action. Here, we report how NRF2 disruption leads to collateral damage in the form of CRISPR-mediated exon skipping. Heterogeneous populations of transcripts and truncated proteins produce a variable response to chemotherapy, dependent on which functional domain is missing. We identify and characterize predicted and unpredicted transcript populations and discover that several types of transcripts arise through exon skipping; wherein one or two NRF2 exons are missing. In one specific case, the presence or absence of a single nucleotide determines whether an exon is skipped or not by reorganizing Exonic Splicing Enhancers (ESEs). We isolate and characterize the diversity of clones induced by CRISPR activity in a NSCLC tumor cell population, a critical and often overlooked genetic byproduct of this exciting technology. Finally, gRNAs must be designed with care to avoid altering gene expression patterns that can account for variable responses to solid tumor therapy.
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Affiliation(s)
- Kelly Banas
- Gene Editing Institute, ChristianaCare, Newark, DE, USA
| | | | | | | | - Pawel A Bialk
- Gene Editing Institute, ChristianaCare, Newark, DE, USA
| | - Connor Barrett
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, USA
| | - Mona Batish
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, USA
| | - Eric B Kmiec
- Gene Editing Institute, ChristianaCare, Newark, DE, USA.
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31
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Abdelnour SA, Xie L, Hassanin AA, Zuo E, Lu Y. The Potential of CRISPR/Cas9 Gene Editing as a Treatment Strategy for Inherited Diseases. Front Cell Dev Biol 2022; 9:699597. [PMID: 34977000 PMCID: PMC8715006 DOI: 10.3389/fcell.2021.699597] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) is a promising innovative technology for genomic editing that offers scientists the chance to edit DNA structures and change gene function. It has several possible uses consisting of editing inherited deficiencies, treating, and reducing the spread of disorders. Recently, reports have demonstrated the creation of synthetic RNA molecules and supplying them alongside Cas9 into genome of eukaryotes, since distinct specific regions of the genome can be manipulated and targeted. The therapeutic potential of CRISPR/Cas9 technology is great, especially in gene therapy, in which a patient-specific mutation is genetically edited, or in the treating of human disorders that are untreatable with traditional treatments. This review focused on numerous, in vivo, in vitro, and ex vivo uses of the CRISPR/Cas9 technology in human inherited diseases, discovering the capability of this versatile in medicine and examining some of the main limitations for its upcoming use in patients. In addition to introducing a brief impression of the biology of the CRISPR/Cas9 scheme and its mechanisms, we presented the utmost recent progress in the uses of CRISPR/Cas9 technology in editing and treating of human genetic diseases.
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Affiliation(s)
- Sameh A Abdelnour
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China.,Animal Production Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Long Xie
- Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Abdallah A Hassanin
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Erwei Zuo
- Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yangqing Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
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32
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Kuno A, Ikeda Y, Ayabe S, Kato K, Sakamoto K, Suzuki SR, Morimoto K, Wakimoto A, Mikami N, Ishida M, Iki N, Hamada Y, Takemura M, Daitoku Y, Tanimoto Y, Dinh TTH, Murata K, Hamada M, Muratani M, Yoshiki A, Sugiyama F, Takahashi S, Mizuno S. DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes. PLoS Biol 2022; 20:e3001507. [PMID: 35041655 PMCID: PMC8765641 DOI: 10.1371/journal.pbio.3001507] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
Genome editing can introduce designed mutations into a target genomic site. Recent research has revealed that it can also induce various unintended events such as structural variations, small indels, and substitutions at, and in some cases, away from the target site. These rearrangements may result in confounding phenotypes in biomedical research samples and cause a concern in clinical or agricultural applications. However, current genotyping methods do not allow a comprehensive analysis of diverse mutations for phasing and mosaic variant detection. Here, we developed a genotyping method with an on-target site analysis software named Determine Allele mutations and Judge Intended genotype by Nanopore sequencer (DAJIN) that can automatically identify and classify both intended and unintended diverse mutations, including point mutations, deletions, inversions, and cis double knock-in at single-nucleotide resolution. Our approach with DAJIN can handle approximately 100 samples under different editing conditions in a single run. With its high versatility, scalability, and convenience, DAJIN-assisted multiplex genotyping may become a new standard for validating genome editing outcomes.
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Affiliation(s)
- Akihiro Kuno
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Yoshihisa Ikeda
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Kanako Kato
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kotaro Sakamoto
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
| | - Sayaka R. Suzuki
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kento Morimoto
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Arata Wakimoto
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Natsuki Mikami
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Miyuki Ishida
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Natsumi Iki
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yuko Hamada
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Megumi Takemura
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoko Daitoku
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoko Tanimoto
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Tra Thi Huong Dinh
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuya Murata
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Michito Hamada
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
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33
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Mayran A, Bolt CC. Transgenic Model Systems Have Revolutionized the Study of Disease. DNA Cell Biol 2021; 41:49-52. [PMID: 34941457 PMCID: PMC8787710 DOI: 10.1089/dna.2021.0514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The current pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected most of the world in a profound way. As an indirect consequence, the general public has been put into direct contact with the research process, almost in real time. Justifiably, a lot of this focus has been targeted toward research directly linked to coronavirus disease 2019 (COVID-19). In this opinion article, we want to highlight to a general audience the value of having a diverse “portfolio” of research approaches for society as a whole. In this study, we will focus on our field of research, namely the study of gene regulation through the use of transgenesis. We will highlight how this type of research can also be used to provide a better understanding as well as tools to fight SARS-CoV-2 and other future challenges.
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Affiliation(s)
- Alexandre Mayran
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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34
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Lassègue B, Kumar S, Mandavilli R, Wang K, Tsai M, Kang DW, Demos C, Hernandes MS, San Martín A, Taylor WR, Jo H, Griendling KK. Characterization of Poldip2 knockout mice: Avoiding incorrect gene targeting. PLoS One 2021; 16:e0247261. [PMID: 34928942 PMCID: PMC8687530 DOI: 10.1371/journal.pone.0247261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 11/17/2021] [Indexed: 01/11/2023] Open
Abstract
POLDIP2 is a multifunctional protein whose roles are only partially understood. Our laboratory previously reported physiological studies performed using a mouse gene trap model, which suffered from three limitations: perinatal lethality in homozygotes, constitutive Poldip2 inactivation and inadvertent downregulation of the adjacent Tmem199 gene. To overcome these limitations, we developed a new conditional floxed Poldip2 model. The first part of the present study shows that our initial floxed mice were affected by an unexpected mutation, which was not readily detected by Southern blotting and traditional PCR. It consisted of a 305 kb duplication around Poldip2 with retention of the wild type allele and could be traced back to the original targeted ES cell clone. We offer simple suggestions to rapidly detect similar accidents, which may affect genome editing using both traditional and CRISPR-based methods. In the second part of the present study, correctly targeted floxed Poldip2 mice were generated and used to produce a new constitutive knockout line by crossing with a Cre deleter. In contrast to the gene trap model, many homozygous knockout mice were viable, in spite of having no POLDIP2 expression. To further characterize the effects of Poldip2 ablation in the vasculature, RNA-seq and RT-qPCR experiments were performed in constitutive knockout arteries. Results show that POLDIP2 inactivation affects multiple cellular processes and provide new opportunities for future in-depth study of its functions.
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Affiliation(s)
- Bernard Lassègue
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
| | - Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Rohan Mandavilli
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
| | - Keke Wang
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
| | - Michelle Tsai
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
| | - Dong-Won Kang
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Catherine Demos
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Marina S. Hernandes
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
| | - Alejandra San Martín
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
| | - W. Robert Taylor
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, United States of America
- Division of Cardiology, Atlanta VA Medical Center, Decatur, GA, United States of America
| | - Hanjoong Jo
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Kathy K. Griendling
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States of America
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35
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Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer. Nat Commun 2021; 12:7235. [PMID: 34903763 PMCID: PMC8668926 DOI: 10.1038/s41467-021-27492-1] [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: 03/25/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022] Open
Abstract
Developmental genes are frequently controlled by multiple enhancers sharing similar specificities. As a result, deletions of such regulatory elements have often failed to reveal their full function. Here, we use the Pitx1 testbed locus to characterize in detail the regulatory and cellular identity alterations following the deletion of one of its enhancers (Pen). By combining single cell transcriptomics and an in-embryo cell tracing approach, we observe an increased fraction of Pitx1 non/low-expressing cells and a decreased fraction of Pitx1 high-expressing cells. We find that the over-representation of Pitx1 non/low-expressing cells originates from a failure of the Pitx1 locus to coordinate enhancer activities and 3D chromatin changes. This locus mis-activation induces a localized heterochrony and a concurrent loss of irregular connective tissue, eventually leading to a clubfoot phenotype. This data suggests that, in some cases, redundant enhancers may be used to locally enforce a robust activation of their host regulatory landscapes.
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36
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Zhou S, Wu Y, Xie ZX, Jia B, Yuan YJ. Directed genome evolution driven by structural rearrangement techniques. Chem Soc Rev 2021; 50:12788-12807. [PMID: 34651628 DOI: 10.1039/d1cs00722j] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Directed genome evolution simulates the process of natural evolution at the genomic level in the laboratory to generate desired phenotypes. Here we review the applications of recent technological advances in genome writing and editing to directed genome evolution, with a focus on structural rearrangement techniques. We highlight how these techniques can be used to generate diverse genotypes, and to accelerate the evolution of phenotypic traits. We also discuss the perspectives of directed genome evolution.
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Affiliation(s)
- Sijie Zhou
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yi Wu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Ze-Xiong Xie
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Bin Jia
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Ying-Jin Yuan
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
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37
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Niu F, Jiang Q, Sun X, Hu Z, Wang L, Zhang H. Large DNA fragment deletion in lncRNA77580 regulates neighboring gene expression in soybean (Glycine max). FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:1139-1147. [PMID: 34585661 DOI: 10.1071/fp20400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) affect gene expressions via a wide range of mechanisms and are considered important regulators of numerous essential biological processes, including abiotic stress responses. However, the biological functions of most lncRNAs are yet to be determined. Moreover, to date, no effective methods have been developed to study the function of plant lncRNAs. We previously discovered a salt stress-related lncRNA, lncRNA77580 in soybean (Glycine max L.). In this study, we cloned the full-length lncRNA77580 and found that it shows nuclear-specific localisation. Furthermore, we employed CRISPR/Cas9 technology to induce large DNA fragment deletions in lncRNA77580 in soybean using a dual-single guide RNA/Cas9 design. As a result, we obtained deletion mutant soybean roots with targeted genomic fragment deletion in lncRNA77580. Deletion and overexpression of lncRNA77580 were found to alter the expression of several neighboring protein-coding genes associated with the response to salt stress. The longer the deleted DNA fragment in lncRNA77580, the greater the influence on the expression of lncRNA77580 itself and neighboring genes. Collectively, the findings of this study revealed that large DNA fragment deletion in lncRNAs using the CRISPR/Cas9 system is a powerful method to obtain functional mutations of soybean lncRNAs that could benefit future research on lncRNA function in soybean.
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Affiliation(s)
- Fengjuan Niu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | | | - Xianjun Sun
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Zheng Hu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Lixia Wang
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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38
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Socha M, Sowińska-Seidler A, Melo US, Kragesteen BK, Franke M, Heinrich V, Schöpflin R, Nagel I, Gruchy N, Mundlos S, Sreenivasan VK, López C, Vingron M, Bukowska-Olech E, Spielmann M, Jamsheer A. Position effects at the FGF8 locus are associated with femoral hypoplasia. Am J Hum Genet 2021; 108:1725-1734. [PMID: 34433009 DOI: 10.1016/j.ajhg.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022] Open
Abstract
Copy-number variations (CNVs) are a common cause of congenital limb malformations and are interpreted primarily on the basis of their effect on gene dosage. However, recent studies show that CNVs also influence the 3D genome chromatin organization. The functional interpretation of whether a phenotype is the result of gene dosage or a regulatory position effect remains challenging. Here, we report on two unrelated families with individuals affected by bilateral hypoplasia of the femoral bones, both harboring de novo duplications on chromosome 10q24.32. The ∼0.5 Mb duplications include FGF8, a key regulator of limb development and several limb enhancer elements. To functionally characterize these variants, we analyzed the local chromatin architecture in the affected individuals' cells and re-engineered the duplications in mice by using CRISPR-Cas9 genome editing. We found that the duplications were associated with ectopic chromatin contacts and increased FGF8 expression. Transgenic mice carrying the heterozygous tandem duplication including Fgf8 exhibited proximal shortening of the limbs, resembling the human phenotype. To evaluate whether the phenotype was a result of gene dosage, we generated another transgenic mice line, carrying the duplication on one allele and a concurrent Fgf8 deletion on the other allele, as a control. Surprisingly, the same malformations were observed. Capture Hi-C experiments revealed ectopic interaction with the duplicated region and Fgf8, indicating a position effect. In summary, we show that duplications at the FGF8 locus are associated with femoral hypoplasia and that the phenotype is most likely the result of position effects altering FGF8 expression rather than gene dosage effects.
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39
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Aquino-Jarquin G. Current advances in overcoming obstacles of CRISPR/Cas9 off-target genome editing. Mol Genet Metab 2021; 134:77-86. [PMID: 34391646 DOI: 10.1016/j.ymgme.2021.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022]
Abstract
CRISPR/Cas9-based technology has revolutionized biomedical research by providing a high-fidelity gene-editing method, foreshadowing a significant impact on the therapeutics of many human genetic disorders previously considered untreatable. However, off-target events represent a critical hurdle before genome editing can be fully established in clinical practice. This mini-review recapitulates some recent advances for detecting and overcoming off-target effects mediated by the CRISPR/Cas9 system that could increase the likelihood of clinical success of the CRISPR-based approaches.
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Affiliation(s)
- Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico; Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, Mexico.
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40
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D'Annibale OM, Koppes EA, Alodaib AN, Kochersperger C, Karunanidhi A, Mohsen AW, Vockley J. Characterization of variants of uncertain significance in isovaleryl-CoA dehydrogenase identified through newborn screening: An approach for faster analysis. Mol Genet Metab 2021; 134:29-36. [PMID: 34535384 PMCID: PMC8578405 DOI: 10.1016/j.ymgme.2021.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Clinical standard of care for newborn screening (NBS) is acylcarnitine metabolites quantitation by tandem mass spectrometry (MS/MS) from dried blood spots. Follow up sequencing often results in identification of one or more variants of uncertain significance (VUS). Isovaleric acidemia (IVA) is an autosomal recessive inborn error of metabolism caused by deficiency of isovaleryl-CoA dehydrogenase (IVDH) in the Leu catabolism pathway. Many IVD mutations are characterized as VUS complicating IVA clinical diagnoses and treatment. We present a testing platform approach to confirm the functional implication of VUS identified in newborns with IVA applicable to multiple inborn errors of metabolism identified by NBS. METHODS An IVD null HEK293T cell culture model was generated by using a dual sgRNA CRISPR/Cas9 genome-editing strategy targeting IVD exons 2-3. Clonal cell lines were confirmed by a combination of genomic breakpoint sequencing and droplet digital PCR. The IVD null model had no IVDH antigen signal and 96% reduction in IVDH enzyme activity. The IVD null model was transfected with vectors containing control or variant IVD and functional assays were performed to determine variant pathogenicity. RESULTS c.149G > C (p.Arg50Pro; precursor numbering), c.986T > C (p.Met329Thr), and c.1010G > A (p.Arg337Gln), c.1179del394 f. mutant proteins had reduced IVDH protein and activity. c.932C > T (p.Ala311Val), c.707C > T (p.Thr236Ile), and c.1232G > A (p.Arg411Gln) had stable IVDH protein, but no enzyme activity. c.521T > G (p.Val174Gly) had normal IVDH protein and activity. IVD variant transfection results confirmed results from IVA fibroblasts containing the same variants. CONCLUSIONS We have developed an IVD null HEK293T cell line to rapidly allow determination of VUS pathogenicity following identification of novel alleles by clinical sequencing following positive NBS results for suspected IVA. We suggest similar models can be generated via genome-editing for high throughput assessment of VUS function for a multitude of inborn errors of metabolism and can ideally supplement NBS programs.
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Affiliation(s)
- Olivia M D'Annibale
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
| | - Erik A Koppes
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Ahmad N Alodaib
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Catherine Kochersperger
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Anuradha Karunanidhi
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Al-Walid Mohsen
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
| | - Jerry Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA.
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41
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Takeda I, Araki M, Ishiguro KI, Ohga T, Takada K, Yamaguchi Y, Hashimoto K, Kai T, Nakagata N, Imasaka M, Yoshinobu K, Araki K. Gene trapping reveals a new transcriptionally active genome element: The chromosome-specific clustered trap region. Genes Cells 2021; 26:874-890. [PMID: 34418226 DOI: 10.1111/gtc.12890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/01/2022]
Abstract
Nearly half of the human genome consists of repetitive sequences such as long interspersed nuclear elements. The relationship between these repeating sequences and diseases has remained unclear. Gene trapping is a useful technique for disrupting a gene and expressing a reporter gene by using the promoter activity of the gene. The analysis of trapped genes revealed a new genome element-the chromosome-specific clustered trap (CSCT) region. For any examined sequence within this region, an equivalent was found using the BLAT of the University of California, Santa Cruz (UCSC) Genome Browser. CSCT13 mapped to chromosome 13 and contained only three genes. To elucidate its in vivo function, the whole CSCT13 region (1.6 Mbp) was deleted using the CRISPR/Cas9 system in mouse embryonic stem cells, and subsequently, a CSCT13 knockout mouse line was established. The rate of homozygotes was significantly lower than expected according to Mendel's laws. In addition, the number of offspring obtained by mating homozygotes was significantly smaller than that obtained by crossing controls. Furthermore, CSCT13 might have an effect on meiotic homologous recombination. This study identifies a transcriptionally active CSCT with an important role in mouse development.
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Affiliation(s)
- Iyo Takeda
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Masatake Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Kei-Ichiro Ishiguro
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Toshinori Ohga
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Kouki Takada
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Yusuke Yamaguchi
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Koichi Hashimoto
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Takuma Kai
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Naomi Nakagata
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Mai Imasaka
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Kumiko Yoshinobu
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
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42
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Villoutreix R, Ayala D, Joron M, Gompert Z, Feder JL, Nosil P. Inversion breakpoints and the evolution of supergenes. Mol Ecol 2021; 30:2738-2755. [PMID: 33786937 PMCID: PMC7614923 DOI: 10.1111/mec.15907] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/04/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The coexistence of discrete morphs that differ in multiple traits is common within natural populations of many taxa. Such morphs are often associated with chromosomal inversions, presumably because the recombination suppressing effects of inversions help maintain alternate adaptive combinations of alleles across the multiple loci affecting these traits. However, inversions can also harbour selected mutations at their breakpoints, leading to their rise in frequency in addition to (or independent from) their role in recombination suppression. In this review, we first describe the different ways that breakpoints can create mutations. We then critically examine the evidence for the breakpoint-mutation and recombination suppression hypotheses for explaining the existence of discrete morphs associated with chromosomal inversions. We find that the evidence that inversions are favoured due to recombination suppression is often indirect. The evidence that breakpoints harbour mutations that are adaptive is also largely indirect, with the characterization of inversion breakpoints at the sequence level being incomplete in most systems. Direct tests of the role of suppressed recombination and breakpoint mutations in inversion evolution are thus needed. Finally, we emphasize how the two hypotheses of recombination suppression and breakpoint mutation can act in conjunction, with implications for understanding the emergence of supergenes and their evolutionary dynamics. We conclude by discussing how breakpoint characterization could improve our understanding of complex, discrete phenotypic forms in nature.
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Affiliation(s)
- Romain Villoutreix
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
| | - Diego Ayala
- UMR MIVEGEC, Univ. Montpellier, CNRS, IRD, 34934 Montpellier, France
| | - Mathieu Joron
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
| | | | - Jeffrey L. Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame,
Indiana 46556, USA
| | - Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
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43
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Maino E, Wojtal D, Evagelou SL, Farheen A, Wong TWY, Lindsay K, Scott O, Rizvi SZ, Hyatt E, Rok M, Visuvanathan S, Chiodo A, Schneeweiss M, Ivakine EA, Cohn RD. Targeted genome editing in vivo corrects a Dmd duplication restoring wild-type dystrophin expression. EMBO Mol Med 2021; 13:e13228. [PMID: 33724658 PMCID: PMC8103086 DOI: 10.15252/emmm.202013228] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 02/06/2021] [Accepted: 02/10/2021] [Indexed: 12/26/2022] Open
Abstract
Tandem duplication mutations are increasingly found to be the direct cause of many rare heritable diseases, accounting for up to 10% of cases. Unfortunately, animal models recapitulating such mutations are scarce, limiting our ability to study them and develop genome editing therapies. Here, we describe the generation of a novel duplication mouse model, harboring a multi-exonic tandem duplication in the Dmd gene which recapitulates a human mutation. Duplication correction of this mouse was achieved by implementing a single-guide RNA (sgRNA) CRISPR/Cas9 approach. This strategy precisely removed a duplication mutation in vivo, restored full-length dystrophin expression, and was accompanied by improvements in both histopathological and clinical phenotypes. We conclude that CRISPR/Cas9 represents a powerful tool to accurately model and treat tandem duplication mutations. Our findings will open new avenues of research for exploring the study and therapeutics of duplication disorders.
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Affiliation(s)
- Eleonora Maino
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Daria Wojtal
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Sonia L Evagelou
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
| | - Aiman Farheen
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
| | - Tatianna W Y Wong
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Kyle Lindsay
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
| | - Ori Scott
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
- Institute of Medical ScienceUniversity of TorontoTorontoONCanada
- Department of Pediatricsthe Hospital for Sick ChildrenTorontoONCanada
| | - Samar Z Rizvi
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Elzbieta Hyatt
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
| | - Matthew Rok
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Shagana Visuvanathan
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
| | - Amanda Chiodo
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
| | - Michelle Schneeweiss
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
| | - Evgueni A Ivakine
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
- Department of PhysiologyUniversity of TorontoTorontoONCanada
| | - Ronald D Cohn
- Program in Genetics and Genome Biologythe Hospital for Sick Children Research InstituteTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
- Institute of Medical ScienceUniversity of TorontoTorontoONCanada
- Department of Pediatricsthe Hospital for Sick ChildrenTorontoONCanada
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44
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Voisin N, Schnur RE, Douzgou S, Hiatt SM, Rustad CF, Brown NJ, Earl DL, Keren B, Levchenko O, Geuer S, Verheyen S, Johnson D, Zarate YA, Hančárová M, Amor DJ, Bebin EM, Blatterer J, Brusco A, Cappuccio G, Charrow J, Chatron N, Cooper GM, Courtin T, Dadali E, Delafontaine J, Del Giudice E, Doco M, Douglas G, Eisenkölbl A, Funari T, Giannuzzi G, Gruber-Sedlmayr U, Guex N, Heron D, Holla ØL, Hurst ACE, Juusola J, Kronn D, Lavrov A, Lee C, Lorrain S, Merckoll E, Mikhaleva A, Norman J, Pradervand S, Prchalová D, Rhodes L, Sanders VR, Sedláček Z, Seebacher HA, Sellars EA, Sirchia F, Takenouchi T, Tanaka AJ, Taska-Tench H, Tønne E, Tveten K, Vitiello G, Vlčková M, Uehara T, Nava C, Yalcin B, Kosaki K, Donnai D, Mundlos S, Brunetti-Pierri N, Chung WK, Reymond A. Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy. Am J Hum Genet 2021; 108:857-873. [PMID: 33961779 DOI: 10.1016/j.ajhg.2021.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/29/2021] [Indexed: 12/27/2022] Open
Abstract
The ALF transcription factor paralogs, AFF1, AFF2, AFF3, and AFF4, are components of the transcriptional super elongation complex that regulates expression of genes involved in neurogenesis and development. We describe an autosomal dominant disorder associated with de novo missense variants in the degron of AFF3, a nine amino acid sequence important for its binding to ubiquitin ligase, or with de novo deletions of this region. The sixteen affected individuals we identified, along with two previously reported individuals, present with a recognizable pattern of anomalies, which we named KINSSHIP syndrome (KI for horseshoe kidney, NS for Nievergelt/Savarirayan type of mesomelic dysplasia, S for seizures, H for hypertrichosis, I for intellectual disability, and P for pulmonary involvement), partially overlapping the AFF4-associated CHOPS syndrome. Whereas homozygous Aff3 knockout mice display skeletal anomalies, kidney defects, brain malformations, and neurological anomalies, knockin animals modeling one of the microdeletions and the most common of the missense variants identified in affected individuals presented with lower mesomelic limb deformities like KINSSHIP-affected individuals and early lethality, respectively. Overexpression of AFF3 in zebrafish resulted in body axis anomalies, providing some support for the pathological effect of increased amount of AFF3. The only partial phenotypic overlap of AFF3- and AFF4-associated syndromes and the previously published transcriptome analyses of ALF transcription factors suggest that these factors are not redundant and each contributes uniquely to proper development.
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Affiliation(s)
- Norine Voisin
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
| | - Rhonda E Schnur
- GeneDx, Gaithersburg, MD 20877, USA; Cooper Medical School of Rowan University, Division of Genetics, Camden, NJ 08103, USA
| | - Sofia Douzgou
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9NT, UK
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Flemington Road, Parkville, VIC 3052, Australia; Murdoch Children's Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia
| | | | - Boris Keren
- Department of Genetics, Pitié-Salpêtrière Hospital, Assistance Publique - Hôpitaux de Paris, Groupe de Recherche Clinique Déficience Intellectuelle et Autisme UPMC, Paris 75013, France
| | - Olga Levchenko
- Research Centre for Medical Genetics, Moscow 115522, Russia
| | - Sinje Geuer
- Max Planck Institute for Molecular Genetics, Berlin 14195, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Sarah Verheyen
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria
| | - Diana Johnson
- Sheffield Clinical Genetics Service, Sheffield S10 2TQ, UK
| | - Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR 72701, USA
| | - Miroslava Hančárová
- Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - David J Amor
- Murdoch Children's Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia
| | - E Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jasmin Blatterer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino 10126, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino 10126, Italy
| | - Gerarda Cappuccio
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples 80131, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Naples 80078, Italy
| | - Joel Charrow
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Nicolas Chatron
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Genetics Department, Lyon University Hospital, Lyon 69007, France
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Thomas Courtin
- Department of Genetics, Pitié-Salpêtrière Hospital, Assistance Publique - Hôpitaux de Paris, Groupe de Recherche Clinique Déficience Intellectuelle et Autisme UPMC, Paris 75013, France
| | - Elena Dadali
- Research Centre for Medical Genetics, Moscow 115522, Russia
| | | | - Ennio Del Giudice
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples 80131, Italy
| | - Martine Doco
- Secteur Génétique, CHU Reims, EA3801, SFR CAPSANTE, 51092 Reims, France
| | | | - Astrid Eisenkölbl
- Department of Pediatrics and Adolescent Medicine, Johannes Kepler University, Kepler University Hospital Linz, Krankenhausstraße 26-30, 4020 Linz, Austria
| | | | - Giuliana Giannuzzi
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
| | - Ursula Gruber-Sedlmayr
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Nicolas Guex
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Bioinformatics Competence Center, University of Lausanne, Lausanne 1015, Switzerland
| | - Delphine Heron
- Department of Genetics, Pitié-Salpêtrière Hospital, Assistance Publique - Hôpitaux de Paris, Groupe de Recherche Clinique Déficience Intellectuelle et Autisme UPMC, Paris 75013, France
| | - Øystein L Holla
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | | | - David Kronn
- New York Medical College, Valhalla, NY 10595, USA
| | | | - Crystle Lee
- Victorian Clinical Genetics Services, Flemington Road, Parkville, VIC 3052, Australia
| | - Séverine Lorrain
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Protein Analysis Facility, University of Lausanne, Lausanne 1015, Switzerland
| | - Else Merckoll
- Department of Radiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Anna Mikhaleva
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
| | | | - Sylvain Pradervand
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste 34100, Italy
| | - Darina Prchalová
- Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | | | - Victoria R Sanders
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Zdeněk Sedláček
- Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Heidelis A Seebacher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria
| | - Elizabeth A Sellars
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR 72701, USA
| | - Fabio Sirchia
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste 34100, Italy
| | - Toshiki Takenouchi
- Center for Medical Genetics, Department of Pediatrics, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Akemi J Tanaka
- Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Heidi Taska-Tench
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Elin Tønne
- Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Giuseppina Vitiello
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples 80131, Italy
| | - Markéta Vlčková
- Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Tomoko Uehara
- Center for Medical Genetics, Department of Pediatrics, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Caroline Nava
- Department of Genetics, Pitié-Salpêtrière Hospital, Assistance Publique - Hôpitaux de Paris, Groupe de Recherche Clinique Déficience Intellectuelle et Autisme UPMC, Paris 75013, France
| | - Binnaz Yalcin
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France
| | - Kenjiro Kosaki
- Center for Medical Genetics, Department of Pediatrics, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Dian Donnai
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9NT, UK
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin 14195, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples 80131, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Naples 80078, Italy
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland.
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Clark JF, Dinsmore CJ, Soriano P. A most formidable arsenal: genetic technologies for building a better mouse. Genes Dev 2021; 34:1256-1286. [PMID: 33004485 PMCID: PMC7528699 DOI: 10.1101/gad.342089.120] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this review, Clark et al. summarize the history of mice in genetic studies and the development of classic approaches to genome modification, and how they have been used and improved in recent years. They also discuss the recent surge of nuclease-mediated techniques and how they are changing the field of mouse genetics. The mouse is one of the most widely used model organisms for genetic study. The tools available to alter the mouse genome have developed over the preceding decades from forward screens to gene targeting in stem cells to the recent influx of CRISPR approaches. In this review, we first consider the history of mice in genetic study, the development of classic approaches to genome modification, and how such approaches have been used and improved in recent years. We then turn to the recent surge of nuclease-mediated techniques and how they are changing the field of mouse genetics. Finally, we survey common classes of alleles used in mice and discuss how they might be engineered using different methods.
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Affiliation(s)
- James F Clark
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Colin J Dinsmore
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Philippe Soriano
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
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Saito R, Miyoshi C, Koebis M, Kushima I, Nakao K, Mori D, Ozaki N, Funato H, Yanagisawa M, Aiba A. Two novel mouse models mimicking minor deletions in 22q11.2 deletion syndrome revealed the contribution of each deleted region to psychiatric disorders. Mol Brain 2021; 14:68. [PMID: 33845872 PMCID: PMC8042712 DOI: 10.1186/s13041-021-00778-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/03/2021] [Indexed: 12/02/2022] Open
Abstract
22q11.2 deletion syndrome (22q11.2DS) is a disorder caused by the segmental deletion of human chromosome 22. This chromosomal deletion is known as high genetic risk factors for various psychiatric disorders. The different deletion types are identified in 22q11.2DS patients, including the most common 3.0-Mb deletion, and the less-frequent 1.5-Mb and 1.4-Mb deletions. In previous animal studies of psychiatric disorders associated with 22q11.2DS mainly focused on the 1.5-Mb deletion and model mice mimicking the human 1.5-Mb deletion have been established with diverse genetic backgrounds, which resulted in the contradictory phenotypes. On the other hand, the contribution of the genes in 1.4-Mb region to psychiatric disorders is poorly understood. In this study, we generated two mouse lines that reproduced the 1.4-Mb and 1.5-Mb deletions of 22q11.2DS [Del(1.4 Mb)/+ and Del(1.5 Mb)/+] on the pure C57BL/6N genetic background. These mutant mice were analyzed comprehensively by behavioral tests, such as measurement of locomotor activity, sociability, prepulse inhibition and fear-conditioning memory. Del(1.4 Mb)/+ mice displayed decreased locomotor activity, but no abnormalities were observed in all other behavioral tests. Del(1.5 Mb)/+ mice showed reduction of prepulse inhibition and impairment of contextual- and cued-dependent fear memory, which is consistent with previous reports. Furthermore, apparently intact social recognition in Del(1.4 Mb)/+ and Del(1.5 Mb)/+ mice suggests that the impaired social recognition observed in Del(3.0 Mb)/+ mice mimicking the human 3.0-Mb deletion requires mutations both in 1.4-Mb and 1.5 Mb regions. Our previous study has shown that Del(3.0 Mb)/+ mice presented disturbance of behavioral circadian rhythm. Therefore, we further evaluated sleep/wakefulness cycles in Del(3.0 Mb)/+ mice by electroencephalogram (EEG) and electromyogram (EMG) recording. EEG/EMG analysis revealed the disturbed wakefulness and non-rapid eye moving sleep (NREMS) cycles in Del(3.0 Mb)/+ mice, suggesting that Del(3.0 Mb)/+ mice may be unable to maintain their wakefulness. Together, our mouse models deepen our understanding of genetic contributions to schizophrenic phenotypes related to 22q11.2DS.
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Affiliation(s)
- Ryo Saito
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Chika Miyoshi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575 Japan
| | - Michinori Koebis
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan
- Medical Genomics Center, Nagoya University Hospital, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan
| | - Kazuki Nakao
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Daisuke Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan
- Brain and Mind Research Center, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550 Japan
| | - Hiromasa Funato
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575 Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575 Japan
| | - Atsu Aiba
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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47
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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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48
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Allou L, Balzano S, Magg A, Quinodoz M, Royer-Bertrand B, Schöpflin R, Chan WL, Speck-Martins CE, Carvalho DR, Farage L, Lourenço CM, Albuquerque R, Rajagopal S, Nampoothiri S, Campos-Xavier B, Chiesa C, Niel-Bütschi F, Wittler L, Timmermann B, Spielmann M, Robson MI, Ringel A, Heinrich V, Cova G, Andrey G, Prada-Medina CA, Pescini-Gobert R, Unger S, Bonafé L, Grote P, Rivolta C, Mundlos S, Superti-Furga A. Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator. Nature 2021; 592:93-98. [DOI: 10.1038/s41586-021-03208-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/07/2021] [Indexed: 11/09/2022]
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49
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Sharma G, Sharma AR, Bhattacharya M, Lee SS, Chakraborty C. CRISPR-Cas9: A Preclinical and Clinical Perspective for the Treatment of Human Diseases. Mol Ther 2021; 29:571-586. [PMID: 33238136 PMCID: PMC7854284 DOI: 10.1016/j.ymthe.2020.09.028] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/12/2020] [Accepted: 09/16/2020] [Indexed: 12/21/2022] Open
Abstract
At present, the idea of genome modification has revolutionized the modern therapeutic research era. Genome modification studies have traveled a long way from gene modifications in primary cells to genetic modifications in animals. The targeted genetic modification may result in the modulation (i.e., either upregulation or downregulation) of the predefined gene expression. Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated nuclease 9 (Cas9) is a promising genome-editing tool that has therapeutic potential against incurable genetic disorders by modifying their DNA sequences. In comparison with other genome-editing techniques, CRISPR-Cas9 is simple, efficient, and very specific. This enabled CRISPR-Cas9 genome-editing technology to enter into clinical trials against cancer. Besides therapeutic potential, the CRISPR-Cas9 tool can also be applied to generate genetically inhibited animal models for drug discovery and development. This comprehensive review paper discusses the origin of CRISPR-Cas9 systems and their therapeutic potential against various genetic disorders, including cancer, allergy, immunological disorders, Duchenne muscular dystrophy, cardiovascular disorders, neurological disorders, liver-related disorders, cystic fibrosis, blood-related disorders, eye-related disorders, and viral infection. Finally, we discuss the different challenges, safety concerns, and strategies that can be applied to overcome the obstacles during CRISPR-Cas9-mediated therapeutic approaches.
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Affiliation(s)
- Garima Sharma
- Neuropsychopharmacology and Toxicology Program, College of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea
| | - Manojit Bhattacharya
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea.
| | - Chiranjib Chakraborty
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea; Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126, India.
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50
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Antao AM, Karapurkar JK, Lee DR, Kim KS, Ramakrishna S. Disease modeling and stem cell immunoengineering in regenerative medicine using CRISPR/Cas9 systems. Comput Struct Biotechnol J 2020; 18:3649-3665. [PMID: 33304462 PMCID: PMC7710510 DOI: 10.1016/j.csbj.2020.11.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022] Open
Abstract
CRISPR/Cas systems are popular genome editing tools that belong to a class of programmable nucleases and have enabled tremendous progress in the field of regenerative medicine. We here outline the structural and molecular frameworks of the well-characterized type II CRISPR system and several computational tools intended to facilitate experimental designs. The use of CRISPR tools to generate disease models has advanced research into the molecular aspects of disease conditions, including unraveling the molecular basis of immune rejection. Advances in regenerative medicine have been hindered by major histocompatibility complex-human leukocyte antigen (HLA) genes, which pose a major barrier to cell- or tissue-based transplantation. Based on progress in CRISPR, including in recent clinical trials, we hypothesize that the generation of universal donor immune-engineered stem cells is now a realistic approach to tackling a multitude of disease conditions.
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Affiliation(s)
- Ainsley Mike Antao
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | | | - Dong Ryul Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, South Korea.,CHA Stem Cell Institute, CHA University, Seoul, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea.,College of Medicine, Hanyang University, Seoul, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea.,College of Medicine, Hanyang University, Seoul, South Korea
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