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Garcia-Gonzalez I, Rocha SF, Hamidi A, Garcia-Ortega L, Regano A, Sanchez-Muñoz M, Lytvyn M, Garcia-Cabero A, Roig-Soucase S, Schoofs H, Castro M, Sabata H, Potente M, Graupera M, Makinen T, Benedito R. iSuRe-HadCre is an essential tool for effective conditional genetics. Nucleic Acids Res 2024; 52:e56. [PMID: 38850155 PMCID: PMC11260470 DOI: 10.1093/nar/gkae472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/04/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024] Open
Abstract
Methods for modifying gene function at high spatiotemporal resolution in mice have revolutionized biomedical research, with Cre-loxP being the most widely used technology. However, the Cre-loxP technology has several drawbacks, including weak activity, leakiness, toxicity, and low reliability of existing Cre-reporters. This is mainly because different genes flanked by loxP sites (floxed) vary widely in their sensitivity to Cre-mediated recombination. Here, we report the generation, validation, and utility of iSuRe-HadCre, a new dual Cre-reporter and deleter mouse line that avoids these drawbacks. iSuRe-HadCre achieves this through a novel inducible dual-recombinase genetic cascade that ensures that cells expressing a fluorescent reporter had only transient Cre activity, that is nonetheless sufficient to effectively delete floxed genes. iSuRe-HadCre worked reliably in all cell types and for the 13 floxed genes tested. This new tool will enable the precise, efficient, and trustworthy analysis of gene function in entire mouse tissues or in single cells.
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Affiliation(s)
- Irene Garcia-Gonzalez
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Susana F Rocha
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Anahita Hamidi
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Lourdes Garcia-Ortega
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Alvaro Regano
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Maria S Sanchez-Muñoz
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Mariya Lytvyn
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Aroa Garcia-Cabero
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Sergi Roig-Soucase
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Hans Schoofs
- Uppsala University, Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden
| | - Marco Castro
- Angiogenesis & Metabolism Laboratory, Center of Vascular Biomedicine, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Helena Sabata
- Endothelial Pathobiology and Microenviroment Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Michael Potente
- Angiogenesis & Metabolism Laboratory, Center of Vascular Biomedicine, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Mariona Graupera
- Endothelial Pathobiology and Microenviroment Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029 Madrid, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Pg. Lluís Companys 23, Barcelona, Spain
| | - Taija Makinen
- Uppsala University, Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden
- Translational Cancer Medicine Program, Research Programs Unit, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Wihuri Research Institute, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Rui Benedito
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
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Hosur V, Erhardt V, Hartig E, Lorenzo K, Megathlin H, Tarchini B. Large-Scale Genome-Wide Optimization and Prediction of the Cre Recombinase System for Precise Genome Manipulation in Mice. RESEARCH SQUARE 2024:rs.3.rs-4595968. [PMID: 39011108 PMCID: PMC11247941 DOI: 10.21203/rs.3.rs-4595968/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The Cre-Lox recombination system is a powerful tool in mouse genetics, offering spatial-temporal control over gene expression and facilitating the large-scale generation of conditional knockout mice. Its versatility also extends to other research models, such as rats, pigs, and zebrafish. However, the Cre-Lox technology presents a set of challenges that includes high costs, a time-intensive process, and the occurrence of unpredictable recombination events, which can lead to unexpected phenotypic outcomes. To better understand factors affecting recombination, we embarked on a systematic and genome-wide analysis of Cre-mediated recombination in mice. To ensure uniformity and reproducibility, we generated 11 novel strains with conditional alleles at the ROSA26 locus, utilizing a single inbred mouse strain background, C57BL/6J. We examined several factors influencing Cre-recombination, including the inter-loxP distance, mutant loxP sites, the zygosity of the conditional alleles, chromosomal location, and the age of the breeders. We discovered that the selection of the Cre-driver strain profoundly impacts recombination efficiency. We also found that successful and complete recombination is best achieved when loxP sites are spaced between 1 to 4 kb apart, with mutant loxP sites facilitating recombination at distances of 1 to 3 kb. Furthermore, we demonstrate that complete recombination does not occur at an inter-loxP distance of ≥ 15 kb with wildtype loxP sites, nor at a distance of ≥ 7 kb with mutant lox71/66 sites. Interestingly, the age of the Cre-driver mouse at the time of breeding emerged as a critical factor in recombination efficiency, with best results observed between 8 and 20 weeks old. Moreover, crossing heterozygous floxed alleles with the Cre-driver strain resulted in more efficient recombination than using homozygous floxed alleles. Lastly, maintaining an inter-loxP distance of 4 kb or less ensures efficient recombination of the conditional allele, regardless of the chromosomal location. While CRISPR/Cas has revolutionized genome editing in mice, Cre-Lox technology remains a cornerstone for the generation of sophisticated alleles and for precise control of gene expression in mice. The knowledge gained here will enable investigators to select a Cre-Lox approach that is most efficient for their desired outcome in the generation of both germline and non-germline mouse models of human disease, thereby reducing time and cost of Cre-Lox technology-mediated genome modification.
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Affiliation(s)
| | | | - Elli Hartig
- The Jackson Laboratory for Mammalian Genetics
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Erhardt V, Hartig E, Lorenzo K, Megathlin HR, Tarchini B, Hosur V. Large-Scale Genome-Wide Optimization and Prediction of the Cre Recombinase System for Precise Genome Manipulation in Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599022. [PMID: 38948742 PMCID: PMC11212873 DOI: 10.1101/2024.06.14.599022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The Cre-Lox recombination system is a powerful tool in mouse genetics, offering spatial-temporal control over gene expression and facilitating the large-scale generation of conditional knockout mice. Its versatility also extends to other research models, such as rats, pigs, and zebrafish. However, the Cre-Lox technology presents a set of challenges that includes high costs, a time-intensive process, and the occurrence of unpredictable recombination events, which can lead to unexpected phenotypic outcomes. To better understand factors affecting recombination, we embarked on a systematic and genome-wide analysis of Cre-mediated recombination in mice. To ensure uniformity and reproducibility, we generated 11 novel strains with conditional alleles at the ROSA26 locus, utilizing a single inbred mouse strain background, C57BL/6J. We examined several factors influencing Cre-recombination, including the inter-loxP distance, mutant loxP sites, the zygosity of the conditional alleles, chromosomal location, and the age of the breeders. We discovered that the selection of the Cre-driver strain profoundly impacts recombination efficiency. We also found that successful and complete recombination is best achieved when loxP sites are spaced between 1 to 4 kb apart, with mutant loxP sites facilitating recombination at distances of 1 to 3 kb. Furthermore, we demonstrate that complete recombination does not occur at an inter-loxP distance of ≥ 15 kb with wildtype loxP sites, nor at a distance of ≥ 7 kb with mutant lox71/66 sites. Interestingly, the age of the Cre-driver mouse at the time of breeding emerged as a critical factor in recombination efficiency, with best results observed between 8 and 20 weeks old. Moreover, crossing heterozygous floxed alleles with the Cre-driver strain resulted in more efficient recombination than using homozygous floxed alleles. Lastly, maintaining an inter-loxP distance of 4 kb or less ensures efficient recombination of the conditional allele, regardless of the chromosomal location. While CRISPR/Cas has revolutionized genome editing in mice, Cre-Lox technology remains a cornerstone for the generation of sophisticated alleles and for precise control of gene expression in mice. The knowledge gained here will enable investigators to select a Cre-Lox approach that is most efficient for their desired outcome in the generation of both germline and non-germline mouse models of human disease, thereby reducing time and cost of Cre-Lox technology-mediated genome modification.
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Affiliation(s)
- Valerie Erhardt
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME
| | - Elli Hartig
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME
- Tufts University School of Medicine, Boston, MA
| | - Kristian Lorenzo
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME
- The Roux Institute at Northeastern University, Portland, ME
| | - Hannah R Megathlin
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME
- Graduate School of Biomedical Sciences and Engineering, UMaine, Orono, ME
| | - Basile Tarchini
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME
- Tufts University School of Medicine, Boston, MA
| | - Vishnu Hosur
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME
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4
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Volk Robertson K, Schleh MW, Harrison FE, Hasty AH. Microglial-specific knockdown of iron import gene, Slc11a2, blunts LPS-induced neuroinflammatory responses in a sex-specific manner. Brain Behav Immun 2024; 116:370-384. [PMID: 38141840 PMCID: PMC10874246 DOI: 10.1016/j.bbi.2023.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023] Open
Abstract
Neuroinflammation and microglial iron load are significant hallmarks found in several neurodegenerative diseases. In in vitro systems, microglia preferentially upregulate the iron importer, divalent metal transporter 1 (DMT1, gene name Slc11a2) in response to inflammatory stimuli, and it has been shown that iron can augment cellular inflammation, suggesting a feed-forward loop between mechanisms involved in iron import and inflammatory signaling. However, it is not understood how microglial iron import mechanisms contribute to inflammation in vivo, or whether altering a microglial iron-related gene affects the inflammatory response. These studies aimed to determine the effect of knocking down microglial iron import gene Slc11a2 on the inflammatory response in vivo. We generated a novel model of tamoxifen-inducible, microglial-specific Slc11a2 knockdown using Cx3cr1Cre-ERT2 mice. Transgenic male and female mice were administered intraperitoneal saline or lipopolysaccharide (LPS) and assessed for sickness behavior post-injection. Plasma cytokines and microglial bulk RNA sequencing (RNASeq) analyses were performed at 4 h post-LPS, and microglia were collected for gene expression analysis after 24 h. A subset of mice was assessed in a behavioral test battery following LPS-induced sickness recovery. Control male, but not female, mice significantly upregulated microglial Slc11a2 at 4 and 24 h following LPS. In Slc11a2 knockdown mice, we observed an improvement in the acute behavioral sickness response post-LPS in male, but not female, animals. Microglia from male, but not female, knockdown animals exhibited a significant decrease in LPS-provoked pro-inflammatory cytokine expression after 24 h. RNASeq data from male knockdown microglia 4 h post-LPS revealed a robust downregulation in inflammatory genes including Il6, Tnfα, and Il1β, and an increase in anti-inflammatory and homeostatic markers (e.g., Tgfbr1, Cx3cr1, and Trem2). This corresponded with a profound decrease in plasma pro-inflammatory cytokines 4 h post-LPS. At 4 h, male knockdown microglia also upregulated expression of markers of iron export, iron recycling, and iron homeostasis and decreased iron storage and import genes, along with pro-oxidant markers such as Cybb, Nos2, and Hif1α. Overall, this work elucidates how manipulating a specific gene involved in iron import in microglia alters acute inflammatory signaling and overall cell activation state in male mice. These data highlight a sex-specific link between a microglial iron import gene and the pro-inflammatory response to LPS in vivo, providing further insight into the mechanisms driving neuroinflammatory disease.
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Affiliation(s)
- Katrina Volk Robertson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Michael W Schleh
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Fiona E Harrison
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Alyssa H Hasty
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; VA Tennessee Valley Healthcare System, Nashville, TN, USA.
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5
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Minami Y, Yuan Y, Ueda HR. High-throughput Genetically Modified Animal Experiments Achieved by Next-generation Mammalian Genetics. J Biol Rhythms 2022; 37:135-151. [PMID: 35137623 DOI: 10.1177/07487304221075002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Animal models are essential tools for modern scientists to conduct biological experiments and investigate their hypotheses in vivo. However, for the past decade, raising the throughput of such animal experiments has been a great challenge. Conventionally, in vivo high-throughput assay was achieved through large-scale mutagen-driven forward genetic screening, which took years to find causal genes. In contrast, reverse genetics accelerated the causal gene identification process, but its throughput was also limited by 2 barriers, that is, the genome modification step and the time-consuming crossing step. Defined as genetics without crossing, next-generation genetics is able to produce gene-modified animals that can be analyzed at the founder generation (F0). This method is or can be accomplished through recent technological advances in gene editing and virus-based efficient gene modifications. Notably, next-generation genetics has accelerated the process of cross-species studies, and it will be a useful technique during animal experiments as it can provide genetic perturbation at an individual level without crossing. In this review, we begin by introducing the history of animal-based high-throughput analysis, with a specific focus on chronobiology. We then describe ways that gene modification efficiency during animal experiments was enhanced and why crossing remained a barrier to reaching higher efficiency. Moreover, we mention the Triple CRISPR as a critical technique for achieving next-generation genetics. Finally, we discuss the potential applications and limitations of next-generation mammalian genetics.
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Affiliation(s)
- Yoichi Minami
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yufei Yuan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Japan
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6
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Hoersten J, Ruiz-Gómez G, Lansing F, Rojo-Romanos T, Schmitt L, Sonntag J, Pisabarro M, Buchholz F. Pairing of single mutations yields obligate Cre-type site-specific recombinases. Nucleic Acids Res 2022; 50:1174-1186. [PMID: 34951450 PMCID: PMC8789052 DOI: 10.1093/nar/gkab1240] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/24/2021] [Accepted: 12/06/2021] [Indexed: 12/28/2022] Open
Abstract
Tyrosine site-specific recombinases (SSRs) represent a versatile genome editing tool with considerable therapeutic potential. Recent developments to engineer and evolve SSRs into heterotetramers to improve target site flexibility signified a critical step towards their broad utility in genome editing. However, SSR monomers can form combinations of different homo- and heterotetramers in cells, increasing their off-target potential. Here, we discover that two paired mutations targeting residues implicated in catalysis lead to simple obligate tyrosine SSR systems, where the presence of all distinct subunits to bind as a heterotetramer is obligatory for catalysis. Therefore, only when the paired mutations are applied as single mutations on each recombinase subunit, the engineered SSRs can efficiently recombine the intended target sequence, while the subunits carrying the point mutations expressed in isolation are inactive. We demonstrate the utility of the obligate SSR system to improve recombination specificity of a designer-recombinase for a therapeutic target in human cells. Furthermore, we show that the mutations render the naturally occurring SSRs, Cre and Vika, obligately heteromeric for catalytic proficiency, providing a straight-forward approach to improve their applied properties. These results facilitate the development of safe and effective therapeutic designer-recombinases and advance our mechanistic understanding of SSR catalysis.
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Affiliation(s)
- Jenna Hoersten
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Gloria Ruiz-Gómez
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Felix Lansing
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Teresa Rojo-Romanos
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Lukas Theo Schmitt
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Jan Sonntag
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - M Teresa Pisabarro
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
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Sinsheimer A, Mohsen AW, Bloom K, Karunanidhi A, Bharathi S, Wu YL, Schiff M, Wang Y, Goetzman ES, Ghaloul-Gonzalez L, Vockley J. Development and characterization of a mouse model for Acad9 deficiency. Mol Genet Metab 2021; 134:156-163. [PMID: 34556413 PMCID: PMC8588265 DOI: 10.1016/j.ymgme.2021.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 11/27/2022]
Abstract
Acyl CoA Dehydrogenase 9 (ACAD9) is a member of the family of flavoenzymes that catalyze the dehydrogenation of acyl-CoAs to 2,3 enoyl-CoAs in mitochondrial fatty acid oxidation (FAO). Inborn errors of metabolism of all family members, including ACAD9, have been described in humans, and represent significant causes of morbidity and mortality particularly in children. ACAD9 deficiency leads to a combined defect in fatty acid oxidation and oxidative phosphorylation (OXPHOS) due to a dual role in the pathways. In addition to its function in mitochondrial FAO, ACAD9 has a second function as one of 14 factors responsible for assembly of complex I of the electron transport chain (ETC). Considerable controversy remains over the relative role of these two functions in normal physiology and the disparate clinical findings described in patients with ACAD9 deficiency. To better understand the normal function of ACAD9 and the pathophysiology of its deficiency, several knock out mouse models were developed. Homozygous total body knock out appeared to be lethal as no ACAD9 animals were obtained. Cre-lox technology was then used to generate tissue-specific deletion of the gene. Cardiac-specific ACAD9 deficient animals had severe neonatal cardiomyopathy and died by 17 days of age. They had severe mitochondrial dysfunction in vitro. Muscle-specific mutants were viable but exhibited muscle weakness. Additional studies of heart muscle from the cardiac specific deficient animals were used to examine the evolutionarily conserved signaling Intermediate in toll pathway (ECSIT) protein, a known binding partner of ACAD9 in the electron chain complex I assembly pathway. As expected, ECSIT levels were significantly reduced in the absence of ACAD9 protein, consistent with the demonstrated impairment of the complex I assembly. The various ACAD9 deficient animals should serve as useful models for development of novel therapeutics for this disorder.
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Affiliation(s)
- Andrew Sinsheimer
- University of Pittsburgh, Graduate School of Public Health, Human Genetics, Pittsburgh, PA, United States of America
| | - Al-Walid Mohsen
- University of Pittsburgh, Graduate School of Public Health, Human Genetics, Pittsburgh, PA, United States of America; University of Pittsburgh, School of Medicine, Pediatrics, Pittsburgh, PA, United States of America
| | - Kailyn Bloom
- University of Pittsburgh, School of Medicine, Pediatrics, Pittsburgh, PA, United States of America
| | - Anuradha Karunanidhi
- University of Pittsburgh, School of Medicine, Pediatrics, Pittsburgh, PA, United States of America
| | - Sivakama Bharathi
- University of Pittsburgh, School of Medicine, Pediatrics, Pittsburgh, PA, United States of America
| | - Yijen L Wu
- Department of Developmental Biology, University of Pittsburgh, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States of America
| | - Manuel Schiff
- University of Pittsburgh, School of Medicine, Pediatrics, Pittsburgh, PA, United States of America; Inserm UMR_S1163, Institut Imagine, Paris, France
| | - Yudong Wang
- University of Pittsburgh, School of Medicine, Pediatrics, Pittsburgh, PA, United States of America
| | - Eric S Goetzman
- University of Pittsburgh, Graduate School of Public Health, Human Genetics, Pittsburgh, PA, United States of America; University of Pittsburgh, School of Medicine, Pediatrics, Pittsburgh, PA, United States of America
| | - Lina Ghaloul-Gonzalez
- University of Pittsburgh, Graduate School of Public Health, Human Genetics, Pittsburgh, PA, United States of America; University of Pittsburgh, School of Medicine, Pediatrics, Pittsburgh, PA, United States of America
| | - Jerry Vockley
- University of Pittsburgh, Graduate School of Public Health, Human Genetics, Pittsburgh, PA, United States of America; University of Pittsburgh, School of Medicine, Pediatrics, Pittsburgh, PA, United States of America.
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Abstract
PURPOSE OF REVIEW Conditional or inducible recombinase-based genetics is still the gold standard to analyse gene function, given its high specificity, temporal control, limited toxicity and the many available genetic tools. However, it is based on methods that have inherent limitations and shortcomings. The purpose of this review is to summarize and contrast the different available methods used to perform conditional gene function analysis to better inform the community about their particularities and the need to use better methods. RECENT FINDINGS As any other biomedical field, the vascular biology field has moved from using and analysing standard gene knockout (KO) mice, to use conditional genetics to delete a given gene only at a given time point, cell-type or organ of interest. This is the only way to accurately understand a gene function and avoid other confounding factors. Therefore, nowadays the majority of laboratories working with mice use CreERT2-tamoxifen-inducible genetics. However, this necessary transition from the relatively simple KO genetics to the more sophisticated conditional genetics brought a series of additional methodological issues that are often overlooked or unappreciated. Recent findings from several laboratories have shown how important is to know what to expect from and control for in conditional genetics. Without this a priori knowledge, the quality, robustness, time and costs of conditional genetic experiments can be significantly compromised. SUMMARY We start this review by discussing the intricacies of the most simple and widely used methods to perform conditional genetics and then extend on the need of novel and more advanced methods to increase the ease, efficiency and reliability of conditional mutagenesis and gene function analysis.
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Affiliation(s)
- Irene Garcia-Gonzalez
- Molecular Genetics of Angiogenesis Laboratory, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
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9
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Tian X, Zhou B. Strategies for site-specific recombination with high efficiency and precise spatiotemporal resolution. J Biol Chem 2021; 296:100509. [PMID: 33676891 PMCID: PMC8050033 DOI: 10.1016/j.jbc.2021.100509] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/04/2023] Open
Abstract
Site-specific recombinases (SSRs) are invaluable genome engineering tools that have enormously boosted our understanding of gene functions and cell lineage relationships in developmental biology, stem cell biology, regenerative medicine, and multiple diseases. However, the ever-increasing complexity of biomedical research requires the development of novel site-specific genetic recombination technologies that can manipulate genomic DNA with high efficiency and fine spatiotemporal control. Here, we review the latest innovative strategies of the commonly used Cre-loxP recombination system and its combinatorial strategies with other site-specific recombinase systems. We also highlight recent progress with a focus on the new generation of chemical- and light-inducible genetic systems and discuss the merits and limitations of each new and established system. Finally, we provide the future perspectives of combining various recombination systems or improving well-established site-specific genetic tools to achieve more efficient and precise spatiotemporal genetic manipulation.
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Affiliation(s)
- Xueying Tian
- Key Laboratory of Regenerative Medicine of Ministry of Education, College of Life Science and Technology, Jinan University, Guangzhou, China.
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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10
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Buck TM, Vos RM, Alves CH, Wijnholds J. AAV- CRB2 protects against vision loss in an inducible CRB1 retinitis pigmentosa mouse model. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 20:423-441. [PMID: 33575434 PMCID: PMC7848734 DOI: 10.1016/j.omtm.2020.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/21/2020] [Indexed: 01/31/2023]
Abstract
Loss of Crumbs homolog 1 (CRB1) or CRB2 proteins in Müller cells or photoreceptors in the mouse retina results in a CRB dose-dependent retinal phenotype. In this study, we present a novel Müller cell-specific Crb1KOCrb2LowMGC retinitis pigmentosa mouse model (complete loss of CRB1 and reduced levels of CRB2 specifically in Müller cells). The Crb double mutant mice showed deficits in electroretinography, optokinetic head tracking, and retinal morphology. Exposure of retinas to low levels of dl-α-aminoadipate acid induced gliosis and retinal disorganization in Crb1KOCrb2LowMGC retinas but not in wild-type or Crb1-deficient retinas. Crb1KOCrb2LowMGC mice showed a substantial decrease in inner/outer photoreceptor segment length and optokinetic head-tracking response. Intravitreal application of rAAV vectors expressing human CRB2 (hCRB2) in Müller cells of Crb1KOCrb2LowMGC mice subsequently exposed to low levels of dl-α-aminoadipate acid prevented loss of vision, whereas recombinant adeno-associated viral (rAAV) vectors expressing human CRB1 (hCRB1) did not. Both rAAV vectors partially protected the morphology of the retina. The results suggest that hCRB expression in Müller cells is vital for control of retinal cell adhesion at the outer limiting membrane, and that the rAAV-cytomegalovirus (CMV)-hCRB2 vector is more potent than rAAV-minimal CMV (CMVmin)-hCRB1 in protection against loss of vision.
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Affiliation(s)
- Thilo M Buck
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZC Leiden, the Netherlands
| | - Rogier M Vos
- Netherlands Institute of Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), 1105 BA Amsterdam, the Netherlands
| | - C Henrique Alves
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZC Leiden, the Netherlands
| | - Jan Wijnholds
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZC Leiden, the Netherlands.,Netherlands Institute of Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), 1105 BA Amsterdam, the Netherlands
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11
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Mann SN, Hadad N, Nelson Holte M, Rothman AR, Sathiaseelan R, Ali Mondal S, Agbaga MP, Unnikrishnan A, Subramaniam M, Hawse J, Huffman DM, Freeman WM, Stout MB. Health benefits attributed to 17α-estradiol, a lifespan-extending compound, are mediated through estrogen receptor α. eLife 2020; 9:59616. [PMID: 33289482 PMCID: PMC7744101 DOI: 10.7554/elife.59616] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
Metabolic dysfunction underlies several chronic diseases, many of which are exacerbated by obesity. Dietary interventions can reverse metabolic declines and slow aging, although compliance issues remain paramount. 17α-estradiol treatment improves metabolic parameters and slows aging in male mice. The mechanisms by which 17α-estradiol elicits these benefits remain unresolved. Herein, we show that 17α-estradiol elicits similar genomic binding and transcriptional activation through estrogen receptor α (ERα) to that of 17β-estradiol. In addition, we show that the ablation of ERα completely attenuates the beneficial metabolic effects of 17α-E2 in male mice. Our findings suggest that 17α-E2 may act through the liver and hypothalamus to improve metabolic parameters in male mice. Lastly, we also determined that 17α-E2 improves metabolic parameters in male rats, thereby proving that the beneficial effects of 17α-E2 are not limited to mice. Collectively, these studies suggest ERα may be a drug target for mitigating chronic diseases in male mammals.
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Affiliation(s)
- Shivani N Mann
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, United States.,Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, United States.,Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, United States
| | - Niran Hadad
- The Jackson Laboratory, Bar Harbor, United States
| | - Molly Nelson Holte
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Alicia R Rothman
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, United States
| | - Roshini Sathiaseelan
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, United States
| | - Samim Ali Mondal
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, United States
| | - Martin-Paul Agbaga
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, United States.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, United States.,Dean McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, United States
| | - Archana Unnikrishnan
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, United States.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, United States
| | | | - John Hawse
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Derek M Huffman
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, United States
| | - Willard M Freeman
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, United States.,Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, United States.,Oklahoma City Veterans Affairs Medical Center, Oklahoma City, United States
| | - Michael B Stout
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, United States.,Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, United States.,Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, United States
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12
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Garcia-Gonzalez I, Mühleder S, Fernández-Chacón M, Benedito R. Genetic Tools to Study Cardiovascular Biology. Front Physiol 2020; 11:1084. [PMID: 33071802 PMCID: PMC7541935 DOI: 10.3389/fphys.2020.01084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/06/2020] [Indexed: 12/22/2022] Open
Abstract
Progress in biomedical science is tightly associated with the improvement of methods and genetic tools to manipulate and analyze gene function in mice, the most widely used model organism in biomedical research. The joint effort of numerous individual laboratories and consortiums has contributed to the creation of a large genetic resource that enables scientists to image cells, probe signaling pathways activities, or modify a gene function in any desired cell type or time point, à la carte. However, as these tools significantly increase in number and become more sophisticated, it is more difficult to keep track of each tool's possibilities and understand their advantages and disadvantages. Knowing the best currently available genetic technology to answer a particular biological question is key to reach a higher standard in biomedical research. In this review, we list and discuss the main advantages and disadvantages of available mammalian genetic technology to analyze cardiovascular cell biology at higher cellular and molecular resolution. We start with the most simple and classical genetic approaches and end with the most advanced technology available to fluorescently label cells, conditionally target their genes, image their clonal expansion, and decode their lineages.
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Affiliation(s)
| | | | | | - Rui Benedito
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
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13
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Espinosa E, Paly E, Barre FX. High-Resolution Whole-Genome Analysis of Sister-Chromatid Contacts. Mol Cell 2020; 79:857-869.e3. [PMID: 32681820 DOI: 10.1016/j.molcel.2020.06.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]
Abstract
Sister-chromatid cohesion describes the orderly association of newly replicated DNA molecules behind replication forks. It plays an essential role in the maintenance and faithful transmission of genetic information. Cohesion is created by DNA topological links and proteinaceous bridges, whose formation and deposition could be potentially affected by many processes. Current knowledge on cohesion has been mainly gained by fluorescence microscopy observation. However, the resolution limit of microscopy and the restricted number of genomic positions that can be simultaneously visualized considerably hampered progress. Here, we present a high-throughput methodology to monitor sister-chromatid contacts (Hi-SC2). Using the multi-chromosomal Vibrio cholerae bacterium as a model, we show that Hi-SC2 permits to monitor local variations in sister-chromatid cohesion at a high resolution over a whole genome.
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Affiliation(s)
- Elena Espinosa
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Evelyne Paly
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - François-Xavier Barre
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
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14
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Functional Access to Neuron Subclasses in Rodent and Primate Forebrain. Cell Rep 2020; 26:2818-2832.e8. [PMID: 30840900 PMCID: PMC6509701 DOI: 10.1016/j.celrep.2019.02.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 01/08/2019] [Accepted: 02/04/2019] [Indexed: 12/21/2022] Open
Abstract
Viral vectors enable foreign proteins to be expressed in brains of non-genetic species, including non-human primates. However, viruses targeting specific neuron classes have proved elusive. Here we describe viral promoters and strategies for accessing GABAergic interneurons and their molecularly defined subsets in the rodent and primate. Using a set intersection approach, which relies on two co-active promoters, we can restrict heterologous protein expression to cortical and hippocampal somatostatin-positive and parvalbumin-positive interneurons. With an orthogonal set difference method, we can enrich for subclasses of neuropeptide-Y-positive GABAergic interneurons by effectively subtracting the expression pattern of one promoter from that of another. These methods harness the complexity of gene expression patterns in the brain and significantly expand the number of genetically tractable neuron classes across mammals.
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15
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Luo L, Ambrozkiewicz MC, Benseler F, Chen C, Dumontier E, Falkner S, Furlanis E, Gomez AM, Hoshina N, Huang WH, Hutchison MA, Itoh-Maruoka Y, Lavery LA, Li W, Maruo T, Motohashi J, Pai ELL, Pelkey KA, Pereira A, Philips T, Sinclair JL, Stogsdill JA, Traunmüller L, Wang J, Wortel J, You W, Abumaria N, Beier KT, Brose N, Burgess HA, Cepko CL, Cloutier JF, Eroglu C, Goebbels S, Kaeser PS, Kay JN, Lu W, Luo L, Mandai K, McBain CJ, Nave KA, Prado MA, Prado VF, Rothstein J, Rubenstein JL, Saher G, Sakimura K, Sanes JR, Scheiffele P, Takai Y, Umemori H, Verhage M, Yuzaki M, Zoghbi HY, Kawabe H, Craig AM. Optimizing Nervous System-Specific Gene Targeting with Cre Driver Lines: Prevalence of Germline Recombination and Influencing Factors. Neuron 2020; 106:37-65.e5. [PMID: 32027825 PMCID: PMC7377387 DOI: 10.1016/j.neuron.2020.01.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/12/2019] [Accepted: 01/10/2020] [Indexed: 12/17/2022]
Abstract
The Cre-loxP system is invaluable for spatial and temporal control of gene knockout, knockin, and reporter expression in the mouse nervous system. However, we report varying probabilities of unexpected germline recombination in distinct Cre driver lines designed for nervous system-specific recombination. Selective maternal or paternal germline recombination is showcased with sample Cre lines. Collated data reveal germline recombination in over half of 64 commonly used Cre driver lines, in most cases with a parental sex bias related to Cre expression in sperm or oocytes. Slight differences among Cre driver lines utilizing common transcriptional control elements affect germline recombination rates. Specific target loci demonstrated differential recombination; thus, reporters are not reliable proxies for another locus of interest. Similar principles apply to other recombinase systems and other genetically targeted organisms. We hereby draw attention to the prevalence of germline recombination and provide guidelines to inform future research for the neuroscience and broader molecular genetics communities.
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Affiliation(s)
- Lin Luo
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Mateusz C. Ambrozkiewicz
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany,Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Fritz Benseler
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Cui Chen
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Emilie Dumontier
- Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | | | | | | | - Naosuke Hoshina
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Wei-Hsiang Huang
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA,Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montreal, QC H3G 1A4, Canada
| | - Mary Anne Hutchison
- Synapse and Neural Circuit Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yu Itoh-Maruoka
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Laura A. Lavery
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77003, USA,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wei Li
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Tomohiko Maruo
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan,Department of Biochemistry, Tokushima University Graduate School of Medical Sciences, 3-18-15, Kuramoto-cho, Tokushima 770-8503, Japan,Department of Biochemistry, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Junko Motohashi
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Emily Ling-Lin Pai
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA,Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kenneth A. Pelkey
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ariane Pereira
- Department of Neurobiology and Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas Philips
- Department of Neurology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jennifer L. Sinclair
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Jeff A. Stogsdill
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02139, USA
| | | | - Jiexin Wang
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Joke Wortel
- Department of Functional Genomics and Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam and University Medical Center Amsterdam, de Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Wenjia You
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA,Departments of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nashat Abumaria
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China,Department of Laboratory Animal Science, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Kevin T. Beier
- Department of Physiology and Biophysics, Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, CA 92697, USA
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Harold A. Burgess
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Constance L. Cepko
- Departments of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jean-François Cloutier
- Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Cagla Eroglu
- Department of Cell Biology, Department of Neurobiology, and Duke Institute for Brain Sciences, Regeneration Next Initiative, Duke University Medical Center, Durham, NC 27710, USA
| | - Sandra Goebbels
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Pascal S. Kaeser
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeremy N. Kay
- Department of Neurobiology and Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wei Lu
- Synapse and Neural Circuit Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Kenji Mandai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan,Department of Biochemistry, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Chris J. McBain
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Klaus-Armin Nave
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Marco A.M. Prado
- Robarts Research Institute, Department of Anatomy and Cell Biology, and Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada,Brain and Mind Institute, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Vania F. Prado
- Robarts Research Institute, Department of Anatomy and Cell Biology, and Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada,Brain and Mind Institute, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Jeffrey Rothstein
- Department of Neurology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - John L.R. Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA,Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gesine Saher
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Yoshimi Takai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hisashi Umemori
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthijs Verhage
- Department of Functional Genomics and Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam and University Medical Center Amsterdam, de Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Michisuke Yuzaki
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Huda Yahya Zoghbi
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77003, USA,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hiroshi Kawabe
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany; Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Gerontology, Laboratory of Molecular Life Science, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, 2-2 Minatojima-minamimachi Chuo-ku, Kobe, Hyogo 650-0047, Japan.
| | - Ann Marie Craig
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada.
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16
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Lanigan TM, Kopera HC, Saunders TL. Principles of Genetic Engineering. Genes (Basel) 2020; 11:E291. [PMID: 32164255 PMCID: PMC7140808 DOI: 10.3390/genes11030291] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/28/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic engineering is the use of molecular biology technology to modify DNA sequence(s) in genomes, using a variety of approaches. For example, homologous recombination can be used to target specific sequences in mouse embryonic stem (ES) cell genomes or other cultured cells, but it is cumbersome, poorly efficient, and relies on drug positive/negative selection in cell culture for success. Other routinely applied methods include random integration of DNA after direct transfection (microinjection), transposon-mediated DNA insertion, or DNA insertion mediated by viral vectors for the production of transgenic mice and rats. Random integration of DNA occurs more frequently than homologous recombination, but has numerous drawbacks, despite its efficiency. The most elegant and effective method is technology based on guided endonucleases, because these can target specific DNA sequences. Since the advent of clustered regularly interspaced short palindromic repeats or CRISPR/Cas9 technology, endonuclease-mediated gene targeting has become the most widely applied method to engineer genomes, supplanting the use of zinc finger nucleases, transcription activator-like effector nucleases, and meganucleases. Future improvements in CRISPR/Cas9 gene editing may be achieved by increasing the efficiency of homology-directed repair. Here, we describe principles of genetic engineering and detail: (1) how common elements of current technologies include the need for a chromosome break to occur, (2) the use of specific and sensitive genotyping assays to detect altered genomes, and (3) delivery modalities that impact characterization of gene modifications. In summary, while some principles of genetic engineering remain steadfast, others change as technologies are ever-evolving and continue to revolutionize research in many fields.
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Affiliation(s)
- Thomas M. Lanigan
- Biomedical Research Core Facilities, Vector Core, University of Michigan, Ann Arbor, MI 48109, USA; (T.M.L.); (H.C.K.)
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huira C. Kopera
- Biomedical Research Core Facilities, Vector Core, University of Michigan, Ann Arbor, MI 48109, USA; (T.M.L.); (H.C.K.)
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas L. Saunders
- Biomedical Research Core Facilities, Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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17
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Fernández-Chacón M, Casquero-García V, Luo W, Francesca Lunella F, Ferreira Rocha S, Del Olmo-Cabrera S, Benedito R. iSuRe-Cre is a genetic tool to reliably induce and report Cre-dependent genetic modifications. Nat Commun 2019; 10:2262. [PMID: 31118412 PMCID: PMC6531465 DOI: 10.1038/s41467-019-10239-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 04/23/2019] [Indexed: 01/09/2023] Open
Abstract
Most biomedical research aimed at understanding gene function uses the Cre-Lox system, which consists of the Cre recombinase-dependent deletion of genes containing LoxP sites. This system enables conditional genetic modifications because the expression and activity of the recombinase Cre/CreERT2 can be regulated in space by tissue-specific promoters and in time by the ligand tamoxifen. Since the precise Cre-Lox recombination event is invisible, methods were developed to report Cre activity and are widely used. However, numerous studies have shown that expression of a given Cre activity reporter cannot be assumed to indicate deletion of other LoxP-flanked genes of interest. Here, we report the generation of an inducible dual reporter-Cre mouse allele, iSuRe-Cre. By significantly increasing Cre activity in reporter-expressing cells, iSuRe-Cre provides certainty that these cells have completely recombined floxed alleles. This genetic tool increases the ease, efficiency, and reliability of conditional mutagenesis and gene function analysis.
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Affiliation(s)
- Macarena Fernández-Chacón
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain
| | - Verónica Casquero-García
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain
| | - Wen Luo
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain
| | - Federica Francesca Lunella
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain
| | - Susana Ferreira Rocha
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain
| | - Sergio Del Olmo-Cabrera
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain
| | - Rui Benedito
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain.
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18
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Wu SH(S, Lee JH, Koo BK. Lineage Tracing: Computational Reconstruction Goes Beyond the Limit of Imaging. Mol Cells 2019; 42:104-112. [PMID: 30764600 PMCID: PMC6399003 DOI: 10.14348/molcells.2019.0006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 01/18/2018] [Accepted: 01/20/2019] [Indexed: 02/07/2023] Open
Abstract
Tracking the fate of individual cells and their progeny through lineage tracing has been widely used to investigate various biological processes including embryonic development, homeostatic tissue turnover, and stem cell function in regeneration and disease. Conventional lineage tracing involves the marking of cells either with dyes or nucleoside analogues or genetic marking with fluorescent and/or colorimetric protein reporters. Both are imaging-based approaches that have played a crucial role in the field of developmental biology as well as adult stem cell biology. However, imaging-based lineage tracing approaches are limited by their scalability and the lack of molecular information underlying fate transitions. Recently, computational biology approaches have been combined with diverse tracing methods to overcome these limitations and so provide high-order scalability and a wealth of molecular information. In this review, we will introduce such novel computational methods, starting from single-cell RNA sequencing-based lineage analysis to DNA barcoding or genetic scar analysis. These novel approaches are complementary to conventional imaging-based approaches and enable us to study the lineage relationships of numerous cell types during vertebrate, and in particular human, development and disease.
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Affiliation(s)
- Szu-Hsien (Sam) Wu
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna,
Austria
| | - Ji-Hyun Lee
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna,
Austria
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna,
Austria
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19
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Twenty-Seven Tamoxifen-Inducible iCre-Driver Mouse Strains for Eye and Brain, Including Seventeen Carrying a New Inducible-First Constitutive-Ready Allele. Genetics 2019; 211:1155-1177. [PMID: 30765420 PMCID: PMC6456315 DOI: 10.1534/genetics.119.301984] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/11/2019] [Indexed: 12/25/2022] Open
Abstract
To understand gene function, the cre/loxP conditional system is the most powerful available for temporal and spatial control of expression in mouse. However, the research community requires more cre recombinase expressing transgenic mouse strains (cre-drivers) that restrict expression to specific cell types. To address these problems, a high-throughput method for large-scale production that produces high-quality results is necessary. Further, endogenous promoters need to be chosen that drive cell type specific expression, or we need to further focus the expression by manipulating the promoter. Here we test the suitability of using knock-ins at the docking site 5′ of Hprt for rapid development of numerous cre-driver strains focused on expression in adulthood, using an improved cre tamoxifen inducible allele (icre/ERT2), and testing a novel inducible-first, constitutive-ready allele (icre/f3/ERT2/f3). In addition, we test two types of promoters either to capture an endogenous expression pattern (MaxiPromoters), or to restrict expression further using minimal promoter element(s) designed for expression in restricted cell types (MiniPromoters). We provide new cre-driver mouse strains with applicability for brain and eye research. In addition, we demonstrate the feasibility and applicability of using the locus 5′ of Hprt for the rapid generation of substantial numbers of cre-driver strains. We also provide a new inducible-first constitutive-ready allele to further speed cre-driver generation. Finally, all these strains are available to the research community through The Jackson Laboratory.
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20
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Goodwin LO, Splinter E, Davis TL, Urban R, He H, Braun RE, Chesler EJ, Kumar V, van Min M, Ndukum J, Philip VM, Reinholdt LG, Svenson K, White JK, Sasner M, Lutz C, Murray SA. Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis. Genome Res 2019; 29:494-505. [PMID: 30659012 PMCID: PMC6396414 DOI: 10.1101/gr.233866.117] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/14/2019] [Indexed: 01/05/2023]
Abstract
Transgenesis has been a mainstay of mouse genetics for over 30 yr, providing numerous models of human disease and critical genetic tools in widespread use today. Generated through the random integration of DNA fragments into the host genome, transgenesis can lead to insertional mutagenesis if a coding gene or an essential element is disrupted, and there is evidence that larger scale structural variation can accompany the integration. The insertion sites of only a tiny fraction of the thousands of transgenic lines in existence have been discovered and reported, due in part to limitations in the discovery tools. Targeted locus amplification (TLA) provides a robust and efficient means to identify both the insertion site and content of transgenes through deep sequencing of genomic loci linked to specific known transgene cassettes. Here, we report the first large-scale analysis of transgene insertion sites from 40 highly used transgenic mouse lines. We show that the transgenes disrupt the coding sequence of endogenous genes in half of the lines, frequently involving large deletions and/or structural variations at the insertion site. Furthermore, we identify a number of unexpected sequences in some of the transgenes, including undocumented cassettes and contaminating DNA fragments. We demonstrate that these transgene insertions can have phenotypic consequences, which could confound certain experiments, emphasizing the need for careful attention to control strategies. Together, these data show that transgenic alleles display a high rate of potentially confounding genetic events and highlight the need for careful characterization of each line to assure interpretable and reproducible experiments.
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Affiliation(s)
| | | | | | - Rachel Urban
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Hao He
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | | | | | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Max van Min
- Cergentis B.V., 3584 CM Utrecht, The Netherlands
| | - Juliet Ndukum
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | | | - Karen Svenson
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | | | - Cathleen Lutz
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
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21
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Hegde A, Walker JKL. Methods to Investigate the Roles for β-Arrestin-2 in Allergic Inflammatory Airway Disease. Methods Mol Biol 2019; 1957:335-343. [PMID: 30919364 DOI: 10.1007/978-1-4939-9158-7_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Spatial and temporal control of gene expression using cre/loxP technology is a major methodological advance for biomedical research. The ability to alter gene expression after an in vivo disease model has been established and allows researchers the opportunity to examine the impact of that gene on the perpetuation of a disease, a mechanistic insight that is arguably more therapeutically relevant than developmental mechanisms.We used the cre/LoxP technology in mice to show that β-arrestin-2, a gene previously shown to be required for the development of the asthma phenotype, is also required for the perpetuation of, at least, the airway hyperresponsiveness characteristic of that phenotype. Here we describe stepwise methods for the activation of the cre-loxP technology and induction of murine allergic inflammatory airway disease. We comment on the unanticipated problems encountered, which we speculate were a result of interactions between the allergen and β-arrestin-2 gene (Arrb2) regulation and the effect of tamoxifen on the asthma phenotype. The issues encountered here may be generally applicable to cre/loxP utilization in inflammatory disease models, especially if the gene of interest is associated with the inflammatory cascade.
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Affiliation(s)
- Akhil Hegde
- School of Nursing, Duke University Medical Center, Durham, NC, USA
| | - Julia K L Walker
- School of Nursing, Duke University Medical Center, Durham, NC, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.
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22
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Mouse Cre-LoxP system: general principles to determine tissue-specific roles of target genes. Lab Anim Res 2018; 34:147-159. [PMID: 30671100 PMCID: PMC6333611 DOI: 10.5625/lar.2018.34.4.147] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022] Open
Abstract
Genetically engineered mouse models are commonly preferred for studying the human disease due to genetic and pathophysiological similarities between mice and humans. In particular, Cre-loxP system is widely used as an integral experimental tool for generating the conditional. This system has enabled researchers to investigate genes of interest in a tissue/cell (spatial control) and/or time (temporal control) specific manner. A various tissue-specific Cre-driver mouse lines have been generated to date, and new Cre lines are still being developed. This review provides a brief overview of Cre-loxP system and a few commonly used promoters for expression of tissue-specific Cre recombinase. Also, we finally introduce some available links to the Web sites that provides detailed information about Cre mouse lines including their characterization.
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23
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Ade CM, Derbes RS, Wagstaff BJ, Linker SB, White TB, Deharo D, Belancio VP, Ivics Z, Roy-Engel AM. Evaluating different DNA binding domains to modulate L1 ORF2p-driven site-specific retrotransposition events in human cells. Gene 2017; 642:188-198. [PMID: 29154869 DOI: 10.1016/j.gene.2017.11.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 11/11/2017] [Indexed: 12/28/2022]
Abstract
DNA binding domains (DBDs) have been used with great success to impart targeting capabilities to a variety of proteins creating highly useful genomic tools. We evaluated the ability of five types of DBDs and strategies (AAV Rep proteins, Cre, TAL effectors, zinc finger proteins, and Cas9/gRNA system) to target the L1 ORF2 protein to drive retrotransposition of Alu inserts to specific sequences in the human genome. First, we find that the L1 ORF2 protein tolerates the addition of protein domains both at the amino- and carboxy-terminus. Although in some instances retrotransposition efficiencies slightly diminished, all fusion proteins containing an intact ORF2 were capable of driving retrotransposition. Second, the stability of individual ORF2 fusion proteins varies and difficult to predict. Third, DBDs that require the formation of multimers for target recognition are unlikely to modify targeting of ORF2p-driven insertions. Fourth, the more components needed to assemble into a complex to drive targeted retrotransposition, the less likely the strategy will increase targeted insertions. Fifth, abundance of target sequences present in the genome will likely dictate the effectiveness and efficiency of targeted insertions. Lastly, the cleavage capabilities of Cas9 (or a Cas9 nickase variant) are unable to substitute for the L1 ORF2 endonuclease domain functions, suggestive that the endonuclease domain has alternate functions needed for retrotransposition. From these studies, we conclude that the most critical component for the modification of the human L1 ORF2 protein to drive targeted insertions is the selection of the DBD due to the varying functional requirements and impacts on protein stability.
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Affiliation(s)
- Catherine M Ade
- Department of Cellular and Molecular Biology, Tulane University, USA
| | - Rebecca S Derbes
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center and LCRC, 1700 Tulane Ave., New Orleans, LA 70112, USA
| | - Bradley J Wagstaff
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center and LCRC, 1700 Tulane Ave., New Orleans, LA 70112, USA
| | - Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, CA 92037-1002, USA
| | - Travis B White
- Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Dawn Deharo
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Victoria P Belancio
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Astrid M Roy-Engel
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center and LCRC, 1700 Tulane Ave., New Orleans, LA 70112, USA.
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24
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O'Neal WK. Lung Cell-Specific Cre Deleter Mouse Strains: Going Back to Move Forward. Am J Respir Cell Mol Biol 2017; 57:149-150. [PMID: 28762768 DOI: 10.1165/rcmb.2017-0099ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Wanda K O'Neal
- 1 Marsico Lung Institute/UNC Cystic Fibrosis Center University of North Carolina at Chapel Hill Chapel Hill, North Carolina
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25
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Eppig JT. Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. ILAR J 2017; 58:17-41. [PMID: 28838066 PMCID: PMC5886341 DOI: 10.1093/ilar/ilx013] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 03/14/2017] [Accepted: 03/28/2017] [Indexed: 12/13/2022] Open
Abstract
The Mouse Genome Informatics (MGI) Resource supports basic, translational, and computational research by providing high-quality, integrated data on the genetics, genomics, and biology of the laboratory mouse. MGI serves a strategic role for the scientific community in facilitating biomedical, experimental, and computational studies investigating the genetics and processes of diseases and enabling the development and testing of new disease models and therapeutic interventions. This review describes the nexus of the body of growing genetic and biological data and the advances in computer technology in the late 1980s, including the World Wide Web, that together launched the beginnings of MGI. MGI develops and maintains a gold-standard resource that reflects the current state of knowledge, provides semantic and contextual data integration that fosters hypothesis testing, continually develops new and improved tools for searching and analysis, and partners with the scientific community to assure research data needs are met. Here we describe one slice of MGI relating to the development of community-wide large-scale mutagenesis and phenotyping projects and introduce ways to access and use these MGI data. References and links to additional MGI aspects are provided.
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Affiliation(s)
- Janan T. Eppig
- Janan T. Eppig, PhD, is Professor Emeritus at The Jackson Laboratory in Bar Harbor, Maine
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26
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Abstract
Organism-level systems biology in mammals aims to identify, analyze, control, and design molecular and cellular networks executing various biological functions in mammals. In particular, system-level identification and analysis of molecular and cellular networks can be accelerated by next-generation mammalian genetics. Mammalian genetics without crossing, where all production and phenotyping studies of genome-edited animals are completed within a single generation drastically reduce the time, space, and effort of conducting the systems research. Next-generation mammalian genetics is based on recent technological advancements in genome editing and developmental engineering. The process begins with introduction of double-strand breaks into genomic DNA by using site-specific endonucleases, which results in highly efficient genome editing in mammalian zygotes or embryonic stem cells. By using nuclease-mediated genome editing in zygotes, or ~100% embryonic stem cell-derived mouse technology, whole-body knock-out and knock-in mice can be produced within a single generation. These emerging technologies allow us to produce multiple knock-out or knock-in strains in high-throughput manner. In this review, we discuss the basic concepts and related technologies as well as current challenges and future opportunities for next-generation mammalian genetics in organism-level systems biology.
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Affiliation(s)
- Etsuo A Susaki
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, , Bunkyo-ku, Tokyo 113-0033 Japan.,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, , Suita, Osaka 565-0871 Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, , Kawaguchi, Saitama 332-0012 Japan
| | - Hideki Ukai
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, , Suita, Osaka 565-0871 Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, , Bunkyo-ku, Tokyo 113-0033 Japan.,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, , Suita, Osaka 565-0871 Japan
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27
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McLellan MA, Rosenthal NA, Pinto AR. Cre-loxP-Mediated Recombination: General Principles and Experimental Considerations. ACTA ACUST UNITED AC 2017; 7:1-12. [DOI: 10.1002/cpmo.22] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Micheal A. McLellan
- The Jackson Laboratory; Bar Harbor Maine
- Graduate Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University; Boston Massachusetts
| | - Nadia A. Rosenthal
- The Jackson Laboratory; Bar Harbor Maine
- Australian Regenerative Medicine Institute, Monash University; Melbourne Victoria Australia
- National Heart and Lung Institute, Imperial College London; London United Kingdom
| | - Alexander R. Pinto
- The Jackson Laboratory; Bar Harbor Maine
- Australian Regenerative Medicine Institute, Monash University; Melbourne Victoria Australia
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28
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Eppig JT, Smith CL, Blake JA, Ringwald M, Kadin JA, Richardson JE, Bult CJ. Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research. Methods Mol Biol 2017; 1488:47-73. [PMID: 27933520 DOI: 10.1007/978-1-4939-6427-7_3] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Mouse Genome Informatics (MGI), resource ( www.informatics.jax.org ) has existed for over 25 years, and over this time its data content, informatics infrastructure, and user interfaces and tools have undergone dramatic changes (Eppig et al., Mamm Genome 26:272-284, 2015). Change has been driven by scientific methodological advances, rapid improvements in computational software, growth in computer hardware capacity, and the ongoing collaborative nature of the mouse genomics community in building resources and sharing data. Here we present an overview of the current data content of MGI, describe its general organization, and provide examples using simple and complex searches, and tools for mining and retrieving sets of data.
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Affiliation(s)
- Janan T Eppig
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
| | - Cynthia L Smith
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Judith A Blake
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Martin Ringwald
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - James A Kadin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | | | - Carol J Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
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29
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Freudenthal B, Logan J, Croucher PI, Williams GR, Bassett JHD. Rapid phenotyping of knockout mice to identify genetic determinants of bone strength. J Endocrinol 2016; 231:R31-46. [PMID: 27535945 PMCID: PMC5064764 DOI: 10.1530/joe-16-0258] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 08/17/2016] [Indexed: 12/27/2022]
Abstract
The genetic determinants of osteoporosis remain poorly understood, and there is a large unmet need for new treatments in our ageing society. Thus, new approaches for gene discovery in skeletal disease are required to complement the current genome-wide association studies in human populations. The International Knockout Mouse Consortium (IKMC) and the International Mouse Phenotyping Consortium (IMPC) provide such an opportunity. The IKMC generates knockout mice representing each of the known protein-coding genes in C57BL/6 mice and, as part of the IMPC initiative, the Origins of Bone and Cartilage Disease project identifies mutants with significant outlier skeletal phenotypes. This initiative will add value to data from large human cohorts and provide a new understanding of bone and cartilage pathophysiology, ultimately leading to the identification of novel drug targets for the treatment of skeletal disease.
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Affiliation(s)
- Bernard Freudenthal
- Molecular Endocrinology LaboratoryDepartment of Medicine, Imperial College London, London, UK
| | - John Logan
- Molecular Endocrinology LaboratoryDepartment of Medicine, Imperial College London, London, UK
| | - Peter I Croucher
- Garvan Institute of Medical ResearchSydney, New South Wales, Australia
| | - Graham R Williams
- Molecular Endocrinology LaboratoryDepartment of Medicine, Imperial College London, London, UK
| | - J H Duncan Bassett
- Molecular Endocrinology LaboratoryDepartment of Medicine, Imperial College London, London, UK
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30
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Ren Q, Awasaki T, Huang YF, Liu Z, Lee T. Cell Class-Lineage Analysis Reveals Sexually Dimorphic Lineage Compositions in the Drosophila Brain. Curr Biol 2016; 26:2583-2593. [PMID: 27618265 DOI: 10.1016/j.cub.2016.07.086] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 12/16/2022]
Abstract
The morphology and physiology of neurons are directed by developmental decisions made within their lines of descent from single stem cells. Distinct stem cells may produce neurons having shared properties that define their cell class, such as the type of secreted neurotransmitter. The relationship between cell class and lineage is complex. Here we developed the transgenic cell class-lineage intersection (CLIn) system to assign cells of a particular class to specific lineages within the Drosophila brain. CLIn also enables birth-order analysis and genetic manipulation of particular cell classes arising from particular lineages. We demonstrated the power of CLIn in the context of the eight central brain type II lineages, which produce highly diverse progeny through intermediate neural progenitors. We mapped 18 dopaminergic neurons from three distinct clusters to six type II lineages that show lineage-characteristic neurite trajectories. In addition, morphologically distinct dopaminergic neurons are produced within a given lineage, and they arise in an invariant sequence. We also identified type II lineages that produce doublesex- and fruitless-expressing neurons and examined whether female-specific apoptosis in these lineages accounts for the lower number of these neurons in the female brain. Blocking apoptosis in these lineages resulted in more cells in both sexes with males still carrying more cells than females. This argues that sex-specific stem cell fate together with differential progeny apoptosis contribute to the final sexual dimorphism.
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Affiliation(s)
- Qingzhong Ren
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Takeshi Awasaki
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Yu-Fen Huang
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Zhiyong Liu
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Tzumin Lee
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.
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31
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de Leeuw CN, Korecki AJ, Berry GE, Hickmott JW, Lam SL, Lengyell TC, Bonaguro RJ, Borretta LJ, Chopra V, Chou AY, D'Souza CA, Kaspieva O, Laprise S, McInerny SC, Portales-Casamar E, Swanson-Newman MI, Wong K, Yang GS, Zhou M, Jones SJM, Holt RA, Asokan A, Goldowitz D, Wasserman WW, Simpson EM. rAAV-compatible MiniPromoters for restricted expression in the brain and eye. Mol Brain 2016; 9:52. [PMID: 27164903 PMCID: PMC4862195 DOI: 10.1186/s13041-016-0232-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/30/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Small promoters that recapitulate endogenous gene expression patterns are important for basic, preclinical, and now clinical research. Recently, there has been a promising revival of gene therapy for diseases with unmet therapeutic needs. To date, most gene therapies have used viral-based ubiquitous promoters-however, promoters that restrict expression to target cells will minimize off-target side effects, broaden the palette of deliverable therapeutics, and thereby improve safety and efficacy. Here, we take steps towards filling the need for such promoters by developing a high-throughput pipeline that goes from genome-based bioinformatic design to rapid testing in vivo. METHODS For much of this work, therapeutically interesting Pleiades MiniPromoters (MiniPs; ~4 kb human DNA regulatory elements), previously tested in knock-in mice, were "cut down" to ~2.5 kb and tested in recombinant adeno-associated virus (rAAV), the virus of choice for gene therapy of the central nervous system. To evaluate our methods, we generated 29 experimental rAAV2/9 viruses carrying 19 different MiniPs, which were injected intravenously into neonatal mice to allow broad unbiased distribution, and characterized in neural tissues by X-gal immunohistochemistry for icre, or immunofluorescent detection of GFP. RESULTS The data showed that 16 of the 19 (84 %) MiniPs recapitulated the expression pattern of their design source. This included expression of: Ple67 in brain raphe nuclei; Ple155 in Purkinje cells of the cerebellum, and retinal bipolar ON cells; Ple261 in endothelial cells of brain blood vessels; and Ple264 in retinal Müller glia. CONCLUSIONS Overall, the methodology and MiniPs presented here represent important advances for basic and preclinical research, and may enable a paradigm shift in gene therapy.
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Affiliation(s)
- Charles N de Leeuw
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Garrett E Berry
- Gene Therapy Centre, University of North Carolina, Chapel Hill, NC, 27599, U.S.A
| | - Jack W Hickmott
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Siu Ling Lam
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Tess C Lengyell
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Russell J Bonaguro
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Lisa J Borretta
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Vikramjit Chopra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Alice Y Chou
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Cletus A D'Souza
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Olga Kaspieva
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Stéphanie Laprise
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Simone C McInerny
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Elodie Portales-Casamar
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Magdalena I Swanson-Newman
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Kaelan Wong
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - George S Yang
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Michelle Zhou
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Steven J M Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Robert A Holt
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,Department of Psychiatry, University of British Columbia, Vancouver, BC, V6T 2A1, Canada
| | - Aravind Asokan
- Gene Therapy Centre, University of North Carolina, Chapel Hill, NC, 27599, U.S.A
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada. .,Department of Psychiatry, University of British Columbia, Vancouver, BC, V6T 2A1, Canada.
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Meinke G, Bohm A, Hauber J, Pisabarro MT, Buchholz F. Cre Recombinase and Other Tyrosine Recombinases. Chem Rev 2016; 116:12785-12820. [PMID: 27163859 DOI: 10.1021/acs.chemrev.6b00077] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tyrosine-type site-specific recombinases (T-SSRs) have opened new avenues for the predictable modification of genomes as they enable precise genome editing in heterologous hosts. These enzymes are ubiquitous in eubacteria, prevalent in archaea and temperate phages, present in certain yeast strains, but barely found in higher eukaryotes. As tools they find increasing use for the generation and systematic modification of genomes in a plethora of organisms. If applied in host organisms, they enable precise DNA cleavage and ligation without the gain or loss of nucleotides. Criteria directing the choice of the most appropriate T-SSR system for genetic engineering include that, whenever possible, the recombinase should act independent of cofactors and that the target sequences should be long enough to be unique in a given genome. This review is focused on recent advancements in our mechanistic understanding of simple T-SSRs and their application in developmental and synthetic biology, as well as in biomedical research.
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Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Andrew Bohm
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Joachim Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , 20251 Hamburg, Germany
| | | | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
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33
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Condie BG. The untapped potential of the GENSAT mice-A valuable resource for developmental biology. Genesis 2016; 54:245-56. [PMID: 27074373 DOI: 10.1002/dvg.22942] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 12/13/2022]
Abstract
Gene Expression Nervous System Atlas (GENSAT) transgenic mice express EGFP, tdTomato, or Cre recombinase in a wide range of cell types. The mice and the bacterial artificial chromosome transgenes are available from repositories (MMRRC or CHORI), thereby making these resources readily available to the research community. This resource of 1,386 transgenic lines was developed and validated for neuroscience research. However, GENSAT mice have many potential applications in other contexts including studies of development outside of the CNS. The cell type-specific expression of fluorescent proteins in these mice has been used to identify cells in living embryos, in living embryo explants, and in stem or progenitor cell populations in postnatal tissues. The large number of fluorescent protein driver lines generated by GENSAT greatly expands the range of cell type markers that can be used for live cell sorting. In addition, the GENSAT project has generated 278 new Cre driver lines. This review provides an overview of the GENSAT lines and information for identifying lines that may be useful for a particular application. I also provide a review of the few published cases in which GENSAT mice have been used for studies of embryonic development or analysis of stem/progenitor cells in nonneural tissues. genesis 54:245-256, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Brian G Condie
- Department of Genetics, Developmental Biology Alliance, University of Georgia, Athens, Georgia
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34
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Abstract
The use of Cre recombinase to carry out conditional mutagenesis of transgenes and insert DNA cassettes into eukaryotic chromosomes is widespread. In addition to the numerous in vivo and in vitro applications that have been reported since Cre was first shown to function in yeast and mammalian cells nearly 30 years ago, the Cre-loxP system has also played an important role in understanding the mechanism of recombination by the tyrosine recombinase family of site-specific recombinases. The simplicity of this system, requiring only a single recombinase enzyme and short recombination sequences for robust activity in a variety of contexts, has been an important factor in both cases. This review discusses advances in the Cre recombinase field that have occurred over the past 12 years since the publication of Mobile DNA II. The focus is on those recent contributions that have provided new mechanistic insights into the reaction. Also discussed are modifications of Cre and/or the loxP sequence that have led to improvements in genome engineering applications.
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35
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van Amerongen R. Lineage Tracing in the Mammary Gland Using Cre/lox Technology and Fluorescent Reporter Alleles. Methods Mol Biol 2016; 1293:187-211. [PMID: 26040689 DOI: 10.1007/978-1-4939-2519-3_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lineage tracing using Cre/lox technology has become a well-established technique to study the contribution of different (stem) cell populations to organ development and function. When used in the mammary gland, it forms a valuable addition to the already existing experimental toolbox and an important alternative to other readouts measuring stem cell potential, such as the fat pad transplantation assay.Here I describe how to set up and analyze an in vivo lineage tracing experiment using tamoxifen-inducible Cre/lox technology, highlighting the specific challenges that the investigator faces when employing this method and interpreting the results in the mammary gland.
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Affiliation(s)
- Renée van Amerongen
- Section of Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands,
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36
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Kaloff C, Anastassiadis K, Ayadi A, Baldock R, Beig J, Birling MC, Bradley A, Brown S, Bürger A, Bushell W, Chiani F, Collins F, Doe B, Eppig J, Finnell R, Fletcher C, Flicek P, Fray M, Friedel R, Gambadoro A, Gates H, Hansen J, Herault Y, Hicks G, Hörlein A, Hrabé de Angelis M, Iyer V, de Jong P, Koscielny G, Kühn R, Liu P, Lloyd K, Lopez R, Marschall S, Martínez S, McKerlie C, Meehan T, von Melchner H, Moore M, Murray S, Nagy A, Nutter L, Pavlovic G, Pombero A, Prosser H, Ramirez-Solis R, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Skarnes W, Schick J, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Smedley D, Simpson E, Stewart A, Teboul L, Tocchini Valentini G, Valenzuela D, West A, Wurst W. Genome wide conditional mouse knockout resources. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.ddmod.2017.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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37
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Moving epithelia: Tracking the fate of mammalian limbal epithelial stem cells. Prog Retin Eye Res 2015; 48:203-25. [DOI: 10.1016/j.preteyeres.2015.04.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/10/2015] [Accepted: 04/16/2015] [Indexed: 12/13/2022]
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38
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Eppig JT, Richardson JE, Kadin JA, Ringwald M, Blake JA, Bult CJ. Mouse Genome Informatics (MGI): reflecting on 25 years. Mamm Genome 2015; 26:272-84. [PMID: 26238262 PMCID: PMC4534491 DOI: 10.1007/s00335-015-9589-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 12/02/2022]
Abstract
From its inception in 1989, the mission of the Mouse Genome Informatics (MGI) resource remains to integrate genetic, genomic, and biological data about the laboratory mouse to facilitate the study of human health and disease. This mission is ever more feasible as the revolution in genetics knowledge, the ability to sequence genomes, and the ability to specifically manipulate mammalian genomes are now at our fingertips. Through major paradigm shifts in biological research and computer technologies, MGI has adapted and evolved to become an integral part of the larger global bioinformatics infrastructure and honed its ability to provide authoritative reference datasets used and incorporated by many other established bioinformatics resources. Here, we review some of the major changes in research approaches over that last quarter century, how these changes are reflected in the MGI resource you use today, and what may be around the next corner.
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Affiliation(s)
- Janan T. Eppig
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Joel E. Richardson
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - James A. Kadin
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Martin Ringwald
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Judith A. Blake
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Carol J. Bult
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA
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39
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Eppig JT, Richardson JE, Kadin JA, Smith CL, Blake JA, Bult CJ. Mouse Genome Database: From sequence to phenotypes and disease models. Genesis 2015; 53:458-73. [PMID: 26150326 PMCID: PMC4545690 DOI: 10.1002/dvg.22874] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 12/19/2022]
Abstract
The Mouse Genome Database (MGD, www.informatics.jax.org) is the international scientific database for genetic, genomic, and biological data on the laboratory mouse to support the research requirements of the biomedical community. To accomplish this goal, MGD provides broad data coverage, serves as the authoritative standard for mouse nomenclature for genes, mutants, and strains, and curates and integrates many types of data from literature and electronic sources. Among the key data sets MGD supports are: the complete catalog of mouse genes and genome features, comparative homology data for mouse and vertebrate genes, the authoritative set of Gene Ontology (GO) annotations for mouse gene functions, a comprehensive catalog of mouse mutations and their phenotypes, and a curated compendium of mouse models of human diseases. Here, we describe the data acquisition process, specifics about MGD's key data areas, methods to access and query MGD data, and outreach and user help facilities. genesis 53:458–473, 2015. © 2015 The Authors. Genesis Published by Wiley Periodicals, Inc.
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40
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Vanden Berghe T, Hulpiau P, Martens L, Vandenbroucke RE, Van Wonterghem E, Perry SW, Bruggeman I, Divert T, Choi SM, Vuylsteke M, Shestopalov VI, Libert C, Vandenabeele P. Passenger Mutations Confound Interpretation of All Genetically Modified Congenic Mice. Immunity 2015; 43:200-9. [PMID: 26163370 DOI: 10.1016/j.immuni.2015.06.011] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/09/2015] [Accepted: 06/11/2015] [Indexed: 12/13/2022]
Abstract
Targeted mutagenesis in mice is a powerful tool for functional analysis of genes. However, genetic variation between embryonic stem cells (ESCs) used for targeting (previously almost exclusively 129-derived) and recipient strains (often C57BL/6J) typically results in congenic mice in which the targeted gene is flanked by ESC-derived passenger DNA potentially containing mutations. Comparative genomic analysis of 129 and C57BL/6J mouse strains revealed indels and single nucleotide polymorphisms resulting in alternative or aberrant amino acid sequences in 1,084 genes in the 129-strain genome. Annotating these passenger mutations to the reported genetically modified congenic mice that were generated using 129-strain ESCs revealed that nearly all these mice possess multiple passenger mutations potentially influencing the phenotypic outcome. We illustrated this phenotypic interference of 129-derived passenger mutations with several case studies and developed a Me-PaMuFind-It web tool to estimate the number and possible effect of passenger mutations in transgenic mice of interest.
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Affiliation(s)
- Tom Vanden Berghe
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.
| | - Paco Hulpiau
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Liesbet Martens
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Roosmarijn E Vandenbroucke
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Elien Van Wonterghem
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Seth W Perry
- Department of Biomedical Engineering, University of Rochester, Rochester NY 14627, USA
| | - Inge Bruggeman
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Tatyana Divert
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Sze Men Choi
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | | | - Valery I Shestopalov
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, FL 33136, USA; Department of Cell Biology and Anatomy, University of Miami School of Medicine, Miami, FL 33136, USA; Department of Cell Biology and Anatomy, Vavilov Institute for General Genetics, Moscow 119333, Russia
| | - Claude Libert
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
| | - Peter Vandenabeele
- Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium; Methusalem Program, Ghent University, 9000 Ghent.
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41
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Generation and Imaging of Transgenic Mice that Express G-CaMP7 under a Tetracycline Response Element. PLoS One 2015; 10:e0125354. [PMID: 25946002 PMCID: PMC4422725 DOI: 10.1371/journal.pone.0125354] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 03/11/2015] [Indexed: 11/19/2022] Open
Abstract
The spatiotemporally controlled expression of G-CaMP fluorescent calcium indicator proteins can facilitate reliable imaging of brain circuit activity. Here, we generated a transgenic mouse line that expresses G-CaMP7 under a tetracycline response element. When crossed with a forebrain-specific tetracycline-controlled transactivator driver line, the mice expressed G-CaMP7 in defined cell populations in a tetracycline-controlled manner, notably in pyramidal neurons in layer 2/3 of the cortex and in the CA1 area of the hippocampus; this expression allowed for imaging of the in vivo activity of these circuits. This mouse line thus provides a useful genetic tool for controlled G-CaMP expression in vivo.
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42
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Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE. The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Res 2014; 43:D726-36. [PMID: 25348401 PMCID: PMC4384027 DOI: 10.1093/nar/gku967] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Mouse Genome Database (MGD, http://www.informatics.jax.org) serves the international biomedical research community as the central resource for integrated genomic, genetic and biological data on the laboratory mouse. To facilitate use of mouse as a model in translational studies, MGD maintains a core of high-quality curated data and integrates experimentally and computationally generated data sets. MGD maintains a unified catalog of genes and genome features, including functional RNAs, QTL and phenotypic loci. MGD curates and provides functional and phenotype annotations for mouse genes using the Gene Ontology and Mammalian Phenotype Ontology. MGD integrates phenotype data and associates mouse genotypes to human diseases, providing critical mouse–human relationships and access to repositories holding mouse models. MGD is the authoritative source of nomenclature for genes, genome features, alleles and strains following guidelines of the International Committee on Standardized Genetic Nomenclature for Mice. A new addition to MGD, the Human–Mouse: Disease Connection, allows users to explore gene–phenotype–disease relationships between human and mouse. MGD has also updated search paradigms for phenotypic allele attributes, incorporated incidental mutation data, added a module for display and exploration of genes and microRNA interactions and adopted the JBrowse genome browser. MGD resources are freely available to the scientific community.
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Affiliation(s)
- Janan T Eppig
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Judith A Blake
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Carol J Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - James A Kadin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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43
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Humphreys BD, DiRocco DP. Lineage-tracing methods and the kidney. Kidney Int 2014; 86:481-8. [PMID: 24088959 PMCID: PMC3975825 DOI: 10.1038/ki.2013.368] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/16/2013] [Accepted: 05/23/2013] [Indexed: 12/17/2022]
Abstract
The kidney is a complex organ with over 30 different cell types, and understanding the lineage relationships between these cells is challenging. During nephrogenesis, a central question is how the coordinated morphogenesis, growth, and differentiation of distinct cell types leads to development of a functional organ. In mature kidney, understanding cell division and fate during injury, regeneration and aging are critical topics for understanding disease. Genetic lineage tracing offers a powerful tool to decipher cellular hierarchies in both development and disease because it allows the progeny of a single cell, or group of cells, to be tracked unambiguously. Recent advances in this field include the use of inducible recombinases, multicolor reporters, and mosaic analysis. In this review, we discuss lineage-tracing methods focusing on the mouse model system and consider the impact of these methods on our understanding of kidney biology and prospects for future application.
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Affiliation(s)
- Benjamin D Humphreys
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Derek P DiRocco
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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44
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Peters J. The role of genomic imprinting in biology and disease: an expanding view. Nat Rev Genet 2014; 15:517-30. [PMID: 24958438 DOI: 10.1038/nrg3766] [Citation(s) in RCA: 288] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon that results in monoallelic gene expression according to parental origin. It has long been established that imprinted genes have major effects on development and placental biology before birth. More recently, it has become evident that imprinted genes also have important roles after birth. In this Review, I bring together studies of the effects of imprinted genes from the prenatal period onwards. Recent work on postnatal stages shows that imprinted genes influence an extraordinarily wide-ranging array of biological processes, the effects of which extend into adulthood, and play important parts in common diseases that range from obesity to psychiatric disorders.
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Affiliation(s)
- Jo Peters
- Medical Research Council Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
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45
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Comparative analysis of the efficiency and specificity of myeloid-Cre deleting strains using ROSA-EYFP reporter mice. J Immunol Methods 2014; 408:89-100. [PMID: 24857755 DOI: 10.1016/j.jim.2014.05.009] [Citation(s) in RCA: 348] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/06/2014] [Accepted: 05/07/2014] [Indexed: 12/22/2022]
Abstract
Since the first example of conditional gene targeting in mice in 1994, the use of Cre recombinase and loxP flanked sequences has become an invaluable technique to generate tissue and temporal specific gene knockouts. The number of mouse strains expressing floxed-gene sequences, and tissue-specific or temporal-specific Cre-recombinase that have been reported in the literature has grown exponentially. However, increased use of this technology has highlighted several problems that can impact the interpretation of any phenotype observed in these mouse models. In particular, accurate knowledge of the specificity of Cre expression in each strain is critical in order to make conclusions about the role of specific cell types in the phenotypes observed. Cre-mediated deletion specificity and efficiency have been described in many different ways in the literature, making direct comparisons between these Cre strains impossible. Here we report crossing thirteen different myeloid-Cre mouse strains to ROSA-EYFP reporter mice and assaying YFP expression in a variety of naïve unstimulated hematopoietic cells, in parallel. By focusing on myeloid subsets, we directly compare the relative efficiency and specificity of myeloid deletion in these strains under steady-state conditions.
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46
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Abstract
The endolysosomal system and autophagy are essential components of macromolecular turnover in eukaryotic cells. The low-abundance signaling lipid PI(3,5)P2 is a key regulator of this pathway. Analysis of mouse models with defects in PI(3,5)P2 biosynthesis has revealed the unique dependence of the mammalian nervous system on this signaling pathway. This insight led to the discovery of the molecular basis for several human neurological disorders, including Charcot-Marie-Tooth disease and Yunis-Varon syndrome. Spontaneous mutants, conditional knockouts, transgenic lines, and gene-trap alleles of Fig4, Vac14, and Pikfyve (Fab1) in the mouse have provided novel information regarding the role of PI(3,5)P2in vivo. This review summarizes what has been learned from mouse models and highlights the utility of manipulating complex signaling pathways in vivo.
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Affiliation(s)
- Guy M Lenk
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Miriam H Meisler
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA.
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47
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Gridley T, Groves AK. Overview of genetic tools and techniques to study Notch signaling in mice. Methods Mol Biol 2014; 1187:47-61. [PMID: 25053480 DOI: 10.1007/978-1-4939-1139-4_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aberrations of Notch signaling in humans cause both congenital and acquired defects and cancers. Genetically engineered mice provide the most efficient and cost-effective models to study Notch signaling in a mammalian system. Here, we review the various types of genetic models, tools, and strategies to study Notch signaling in mice, and provide examples of their use. We also provide advice on breeding strategies for conditional mutant mice, and a protocol for tamoxifen administration to mouse strains expressing inducible Cre recombinase-estrogen receptor fusion proteins.
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Affiliation(s)
- Thomas Gridley
- Center for Molecular Medicine, Maine Medical Center Research Institute, 81 Research Drive, Scarborough, ME, 04074, USA,
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48
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Abstract
Lineage tracing involves labeling cells to track their subsequent behavior within the normal tissue environment. The advent of genetic lineage tracing and cell proliferation assays, together with high resolution three-dimensional (3D) imaging and quantitative methods to infer cell behavior from lineage-tracing data, has transformed our understanding of murine epidermal stem and progenitor cells. Here, we review recent insights that reveal how a progenitor cell population maintains interfollicular epidermis, whereas stem cells, quiescent under homeostatic conditions, are mobilized in response to wounding. We discuss progress in understanding how the various stem cell populations of the hair follicle sustain this complex and highly dynamic structure, and recent analysis of stem cells in sweat and sebaceous glands. The extent to which insights from mouse studies can be applied to human epidermis is also considered.
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Affiliation(s)
- Maria P Alcolea
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, United Kingdom
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49
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Abstract
The kidney is a complex organ with over 30 different cell types, and understanding the lineage relationships between these cells is challenging. During nephrogenesis, a central question is how the coordinated morphogenesis, growth, and differentiation of distinct cell types leads to development of a functional organ. In mature kidney, understanding cell division and fate during injury, regeneration and aging are critical topics for understanding disease. Genetic lineage tracing offers a powerful tool to decipher cellular hierarchies in both development and disease because it allows the progeny of a single cell, or group of cells, to be tracked unambiguously. Recent advances in this field include the use of inducible recombinases, multicolor reporters, and mosaic analysis. In this review, we discuss lineage-tracing methods focusing on the mouse model system and consider the impact of these methods on our understanding of kidney biology and prospects for future application.
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50
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Deussing JM. Targeted mutagenesis tools for modelling psychiatric disorders. Cell Tissue Res 2013; 354:9-25. [PMID: 24078022 DOI: 10.1007/s00441-013-1708-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/16/2013] [Indexed: 12/15/2022]
Abstract
In the 1980s, the basic principles of gene targeting were discovered and forged into sharp tools for efficient and precise engineering of the mouse genome. Since then, genetic mouse models have substantially contributed to our understanding of major neurobiological concepts and are of utmost importance for our comprehension of neuropsychiatric disorders. The "domestication" of site-specific recombinases and the continuous creative technological developments involving the implementation of previously identified biological principles such as transcriptional and posttranslational control now enable conditional mutagenesis with high spatial and temporal resolution. The initiation and successful accomplishment of large-scale efforts to annotate functionally the entire mouse genome and to build strategic resources for the research community have significantly accelerated the rapid proliferation and broad propagation of mouse genetic tools. Addressing neurobiological processes with the assistance of genetic mouse models is a routine procedure in psychiatric research and will be further extended in order to improve our understanding of disease mechanisms. In light of the highly complex nature of psychiatric disorders and the current lack of strong causal genetic variants, a major future challenge is to model of psychiatric disorders more appropriately. Humanized mice, and the recently developed toolbox of site-specific nucleases for more efficient and simplified tailoring of the genome, offer the perspective of significantly improved models. Ultimately, these tools will push the limits of gene targeting beyond the mouse to allow genome engineering in any model organism of interest.
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Affiliation(s)
- Jan M Deussing
- Max Planck Institute of Psychiatry, Molecular Neurogenetics, Kraepelinstrasse 2-10, 80804, Munich, Germany,
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