1
|
Teixeira SK, Pontes R, Zuleta LFG, Wang J, Xu D, Hildebrand S, Russell J, Zhan X, Choi M, Tang M, Li X, Ludwig S, Beutler B, Krieger JE. Genetic determinants of blood pressure and heart rate identified through ENU-induced mutagenesis with automated meiotic mapping. SCIENCE ADVANCES 2024; 10:eadj9797. [PMID: 38427739 PMCID: PMC10906923 DOI: 10.1126/sciadv.adj9797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/29/2024] [Indexed: 03/03/2024]
Abstract
We used N-ethyl-N-nitrosurea-induced germline mutagenesis combined with automated meiotic mapping to identify specific systolic blood pressure (SBP) and heart rate (HR) determinant loci. We analyzed 43,627 third-generation (G3) mice from 841 pedigrees to assess the effects of 45,378 variant alleles within 15,760 genes, in both heterozygous and homozygous states. We comprehensively tested 23% of all protein-encoding autosomal genes and found 87 SBP and 144 HR (with 7 affecting both) candidates exhibiting detectable hypomorphic characteristics. Unexpectedly, only 18 of the 87 SBP genes were previously known, while 26 of the 144 genes linked to HR were previously identified. Furthermore, we confirmed the influence of two genes on SBP regulation and three genes on HR control through reverse genetics. This underscores the importance of our research in uncovering genes associated with these critical cardiovascular risk factors and illustrate the effectiveness of germline mutagenesis for defining key determinants of polygenic phenotypes that must be studied in an intact organism.
Collapse
Affiliation(s)
- Samantha K. Teixeira
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Roberto Pontes
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Luiz Fernando G. Zuleta
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Darui Xu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mihwa Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jose E. Krieger
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
2
|
Miura I, Kikkawa Y, Yasuda SP, Shinogi A, Usuda D, Kumar V, Takahashi JS, Tamura M, Masuya H, Wakana S. Characterization of single nucleotide polymorphisms for a forward genetics approach using genetic crosses in C57BL/6 and BALB/c substrains of mice. Exp Anim 2021; 71:240-251. [PMID: 34980769 PMCID: PMC9130033 DOI: 10.1538/expanim.21-0181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Forward genetics is a powerful approach based on chromosomal mapping of phenotypes and has successfully led to the discovery of many mouse mutations in genes responsible for various
phenotypes. Although crossing between genetically remote strains can produce F2 and backcross mice for chromosomal mapping, the phenotypes are often affected by background effects
from the partner strains in genetic crosses. Genetic crosses between substrains might be useful in genetic mapping to avoid genetic background effects. In this study, we investigated single
nucleotide polymorphisms (SNPs) available for genetic mapping using substrains of C57BL/6 and BALB/c mice. In C57BL/6 mice, 114 SNP markers were developed and assigned to locations on all
chromosomes for full utilization for genetic mapping using genetic crosses between the C57BL/6J and C57BL/6N substrains. Moreover, genetic differences were identified in the 114 SNP markers
among the seven C57BL/6 substrains from five production breeders. In addition, 106 SNPs were detected on all chromosomes of BALB/cAJcl and BALB/cByJJcl substrains. These SNPs could be used
for genotyping in BALB/cJ, BALB/cAJcl, BALB/cAnNCrlCrlj, and BALB/cCrSlc mice, and they are particularly useful for genetic mapping using crosses between BALB/cByJJcl and other BALB/c
substrains. The SNPs characterized in this study can be utilized for genetic mapping to identify the causative mutations of the phenotypes induced by N-ethyl-N-nitrosourea mutagenesis and
the SNPs responsible for phenotypic differences between the substrains of C57BL/6 and BALB/c mice.
Collapse
Affiliation(s)
- Ikuo Miura
- Division of Molecular Genetics, Department of Cooperative Graduate School, School of Medicine, Faculty of Medicine, Graduate School of Medical and Dental Sciences (Medicine), Niigata University.,Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, RIKEN BioResource Research Center.,Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science
| | - Yoshiaki Kikkawa
- Division of Molecular Genetics, Department of Cooperative Graduate School, School of Medicine, Faculty of Medicine, Graduate School of Medical and Dental Sciences (Medicine), Niigata University.,Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science
| | - Shumpei P Yasuda
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science
| | - Akiko Shinogi
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, RIKEN BioResource Research Center
| | - Daiki Usuda
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, RIKEN BioResource Research Center.,Integrated Bioresource Information Division, RIKEN BioResource Research Center
| | | | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, RIKEN BioResource Research Center
| | - Hiroshi Masuya
- Integrated Bioresource Information Division, RIKEN BioResource Research Center
| | - Shigeharu Wakana
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, RIKEN BioResource Research Center.,Department of Animal Experimentation, Foundation for Biomedical Research and Innovation at Kobe, Creative Lab for Innovation in Kobe
| |
Collapse
|
3
|
Facilitating Complex Trait Analysis via Reduced Complexity Crosses. Trends Genet 2020; 36:549-562. [PMID: 32482413 DOI: 10.1016/j.tig.2020.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 05/05/2020] [Accepted: 05/12/2020] [Indexed: 01/02/2023]
Abstract
Genetically diverse inbred strains are frequently used in quantitative trait mapping to identify sequence variants underlying trait variation. Poor locus resolution and high genetic complexity impede variant discovery. As a solution, we explore reduced complexity crosses (RCCs) between phenotypically divergent, yet genetically similar, rodent substrains. RCCs accelerate functional variant discovery via decreasing the number of segregating variants by orders of magnitude. The simplified genetic architecture of RCCs often permit immediate identification of causal variants or rapid fine-mapping of broad loci to smaller intervals. Whole-genome sequences of substrains make RCCs possible by supporting the development of array- and targeted sequencing-based genotyping platforms, coupled with rapid genome editing for variant validation. In summary, RCCs enhance discovery-based genetics of complex traits.
Collapse
|
4
|
Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice. Proc Natl Acad Sci U S A 2020; 117:12931-12942. [PMID: 32457148 DOI: 10.1073/pnas.1921224117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Retinal disease and loss of vision can result from any disruption of the complex pathways controlling retinal development and homeostasis. Forward genetics provides an excellent tool to find, in an unbiased manner, genes that are essential to these processes. Using N-ethyl-N-nitrosourea mutagenesis in mice in combination with a screening protocol using optical coherence tomography (OCT) and automated meiotic mapping, we identified 11 mutations presumably causative of retinal phenotypes in genes previously known to be essential for retinal integrity. In addition, we found multiple statistically significant gene-phenotype associations that have not been reported previously and decided to target one of these genes, Sfxn3 (encoding sideroflexin-3), using CRISPR/Cas9 technology. We demonstrate, using OCT, light microscopy, and electroretinography, that two Sfxn3 -/- mouse lines developed progressive and severe outer retinal degeneration. Electron microscopy showed thinning of the retinal pigment epithelium and disruption of the external limiting membrane. Using single-cell RNA sequencing of retinal cells isolated from C57BL/6J mice, we demonstrate that Sfxn3 is expressed in several bipolar cell subtypes, retinal ganglion cells, and some amacrine cell subtypes but not significantly in Müller cells or photoreceptors. In situ hybridization confirmed these findings. Furthermore, pathway analysis suggests that Sfxn3 may be associated with synaptic homeostasis. Importantly, electron microscopy analysis showed disruption of synapses and synaptic ribbons in the outer plexiform layer of Sfxn3 -/- mice. Our work describes a previously unknown requirement for Sfxn3 in retinal function.
Collapse
|
5
|
Williams JA, Powell G, Mallon AM, Simon MM. Genomic Mutation Identification in Mice Using Illumina Sequencing and Linux-Based Computational Methods. ACTA ACUST UNITED AC 2019; 9:e64. [PMID: 31532925 DOI: 10.1002/cpmo.64] [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: 11/10/2022]
Abstract
Genetically modified mice are an essential tool for modeling disease-causing mechanisms and discovering gene function. SNP genotyping was traditionally used to associate candidate regions with traits in the mouse, but failed to reveal novel variants without further targeted sequencing. Using a robust set of computational protocols, we present a platform to enable scientists to detect variants arising from whole-genome and exome sequencing experiments. This article guides researchers on aligning reads to the mouse genome, quality-assurance strategies, mutation discovery, comparing mutations to previously discovered mouse SNPs, and the annotation of novel variants, in order to predict mutation consequences on the protein level. Challenges unique to the mouse are discussed, and two protocols use self-contained containers to maintain version control and allow users to adapt our approach to new techniques by upgrading container versions. Our protocols are suited for servers or office workstations and are usable by non-bioinformatics specialists. © 2019 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- John A Williams
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom.,Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom.,Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - George Powell
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ann-Marie Mallon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Michelle M Simon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| |
Collapse
|
6
|
Zhang W, Jia P, Liu W, Jia K, Yi M. Screening for Antiviral Medaka Haploid Embryonic Stem Cells by Genome Wide Mutagenesis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:186-195. [PMID: 30617926 DOI: 10.1007/s10126-018-09870-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
Nervous necrosis virus (NNV), one of the most prevalent fish pathogens, has caused significant losses in both yield and economy to the aquaculture. Host factors involved in NNV infection remain to be identified due to the lack of ideal model for the study of NNV and host interaction. Haploid stem cells have proven to be ideal materials in genetic screens. Here, we generated a cell line HX1G1 (simply named G1) with the activity against red-spotted grouper nervous necrosis virus (RGNNV) by N-ethyl-N-nitrosourea (ENU)-mediated whole genome random mutagenesis from the haploid embryonic stem cell HX1a, a cell clone from haploid cell line HX1 that we previously derived from the medaka fish. G1 cells retained the characteristics of haploidy and pluripotency as indicated by the EBs differentiation ability after genetic mutagenesis. Compared with HX1a cells, no typical cytopathic effects were observed, and the expression of RNA-dependent RNA polymerase (RDRP) was significantly reduced in G1 cells post RGNNV infection, indicating the enhanced anti-RGNNV activity of G1. Furthermore, we demonstrated that RGNNV entry into G1 cells was partially inhibited, and this inhibition might be relevant to the induced mutation of heat shock cognate protein 70 (HSC70) which was decisive for NNV entry. Interestingly, G1 cells were to some extent permissive to RGNNV infection, but RGNNV was spontaneously cleared in G1 cells during serial passage. In addition, we also found that the expression levels of interferon (IFN)-related genes were higher in G1 cells than those in HX1a cells, suggesting that viral clearance might be associated with the elevated expression of IFN-related genes in G1 cells.
Collapse
Affiliation(s)
- Wanwan Zhang
- School of Marine Sciences, Sun Yat-sen University, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
- Zhuhai Key Laboratory of Marine Bioresources and Environment, Guangdong, China
| | - Peng Jia
- School of Marine Sciences, Sun Yat-sen University, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
- Zhuhai Key Laboratory of Marine Bioresources and Environment, Guangdong, China
| | - Wei Liu
- School of Marine Sciences, Sun Yat-sen University, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
- Zhuhai Key Laboratory of Marine Bioresources and Environment, Guangdong, China
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-sen University, Guangdong, China.
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China.
- Zhuhai Key Laboratory of Marine Bioresources and Environment, Guangdong, China.
| | - Meisheng Yi
- School of Marine Sciences, Sun Yat-sen University, Guangdong, China.
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China.
- Zhuhai Key Laboratory of Marine Bioresources and Environment, Guangdong, China.
| |
Collapse
|
7
|
Tomberg K, Westrick RJ, Kotnik EN, Cleuren AC, Siemieniak DR, Zhu G, Saunders TL, Ginsburg D. Whole exome sequencing of ENU-induced thrombosis modifier mutations in the mouse. PLoS Genet 2018; 14:e1007658. [PMID: 30188893 PMCID: PMC6143275 DOI: 10.1371/journal.pgen.1007658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/18/2018] [Accepted: 08/27/2018] [Indexed: 12/30/2022] Open
Abstract
Although the Factor V Leiden (FVL) gene variant is the most prevalent genetic risk factor for venous thrombosis, only 10% of FVL carriers will experience such an event in their lifetime. To identify potential FVL modifier genes contributing to this incomplete penetrance, we took advantage of a perinatal synthetic lethal thrombosis phenotype in mice homozygous for FVL (F5L/L) and haploinsufficient for tissue factor pathway inhibitor (Tfpi+/-) to perform a sensitized dominant ENU mutagenesis screen. Linkage analysis conducted in the 3 largest pedigrees generated from the surviving F5L/L Tfpi+/- mice ('rescues') using ENU-induced coding variants as genetic markers was unsuccessful in identifying major suppressor loci. Whole exome sequencing was applied to DNA from 107 rescue mice to identify candidate genes enriched for ENU mutations. A total of 3,481 potentially deleterious candidate ENU variants were identified in 2,984 genes. After correcting for gene size and multiple testing, Arl6ip5 was identified as the most enriched gene, though not reaching genome-wide significance. Evaluation of CRISPR/Cas9 induced loss of function in the top 6 genes failed to demonstrate a clear rescue phenotype. However, a maternally inherited (not ENU-induced) de novo mutation (Plcb4R335Q) exhibited significant co-segregation with the rescue phenotype (p = 0.003) in the corresponding pedigree. Thrombosis suppression by heterozygous Plcb4 loss of function was confirmed through analysis of an independent, CRISPR/Cas9-induced Plcb4 mutation (p = 0.01).
Collapse
Affiliation(s)
- Kärt Tomberg
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Randal J. Westrick
- Department of Biological Sciences and Center for Data Science and Big Data Analysis, Oakland University, Rochester, Michigan, United States of America
| | - Emilee N. Kotnik
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Audrey C. Cleuren
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David R Siemieniak
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Guojing Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Thomas L. Saunders
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Transgenic Animal Model Core Laboratory, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David Ginsburg
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
| |
Collapse
|
8
|
Unpackaging the genetics of mammalian fertility: strategies to identify the “reproductive genome”†. Biol Reprod 2018; 99:1119-1128. [DOI: 10.1093/biolre/ioy133] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 06/05/2018] [Indexed: 12/18/2022] Open
|
9
|
Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice. G3-GENES GENOMES GENETICS 2018; 8:401-409. [PMID: 29208648 PMCID: PMC5919724 DOI: 10.1534/g3.117.300292] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Positional cloning of ENU-induced mutations has traditionally relied on analysis of polymorphic variation between two strains. In contrast, the application of whole-genome sequencing (WGS) has enabled gene discovery in mutant lines maintained on an inbred genetic background. This approach utilizes genetic variation derived from ENU-induced variants for mapping and reduces the likelihood of phenotypic variation, making it an ideal method for genetic modifier screening. Here, we describe the results of such a screen, wherein we determined the minimal number of mutant genomic DNA samples to include in our analyses and improved the sensitivity of our screen by individually barcoding each genomic DNA library. We present several unique cases to illustrate this approach's efficacy, including the discovery of two distinct mutations that generate essentially identical mutant phenotypes, the ascertainment of a non-ENU-induced candidate variant through homozygosity mapping, and an approach for the identification of putative dominant genetic modifiers.
Collapse
|
10
|
Westrick RJ, Tomberg K, Siebert AE, Zhu G, Winn ME, Dobies SL, Manning SL, Brake MA, Cleuren AC, Hobbs LM, Mishack LM, Johnston AJ, Kotnik E, Siemieniak DR, Xu J, Li JZ, Saunders TL, Ginsburg D. Sensitized mutagenesis screen in Factor V Leiden mice identifies thrombosis suppressor loci. Proc Natl Acad Sci U S A 2017; 114:9659-9664. [PMID: 28827327 PMCID: PMC5594664 DOI: 10.1073/pnas.1705762114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Factor V Leiden (F5L ) is a common genetic risk factor for venous thromboembolism in humans. We conducted a sensitized N-ethyl-N-nitrosourea (ENU) mutagenesis screen for dominant thrombosuppressor genes based on perinatal lethal thrombosis in mice homozygous for F5L (F5L/L ) and haploinsufficient for tissue factor pathway inhibitor (Tfpi+/- ). F8 deficiency enhanced the survival of F5L/LTfpi+/- mice, demonstrating that F5L/LTfpi+/- lethality is genetically suppressible. ENU-mutagenized F5L/L males and F5L/+Tfpi+/- females were crossed to generate 6,729 progeny, with 98 F5L/LTfpi+/- offspring surviving until weaning. Sixteen lines, referred to as "modifier of Factor 5 Leiden (MF5L1-16)," exhibited transmission of a putative thrombosuppressor to subsequent generations. Linkage analysis in MF5L6 identified a chromosome 3 locus containing the tissue factor gene (F3). Although no ENU-induced F3 mutation was identified, haploinsufficiency for F3 (F3+/- ) suppressed F5L/LTfpi+/- lethality. Whole-exome sequencing in MF5L12 identified an Actr2 gene point mutation (p.R258G) as the sole candidate. Inheritance of this variant is associated with suppression of F5L/LTfpi+/- lethality (P = 1.7 × 10-6), suggesting that Actr2p.R258G is thrombosuppressive. CRISPR/Cas9 experiments to generate an independent Actr2 knockin/knockout demonstrated that Actr2 haploinsufficiency is lethal, supporting a hypomorphic or gain-of-function mechanism of action for Actr2p.R258G Our findings identify F8 and the Tfpi/F3 axis as key regulators in determining thrombosis balance in the setting of F5L and also suggest a role for Actr2 in this process.
Collapse
Affiliation(s)
- Randal J Westrick
- Department of Biological Sciences, Oakland University, Rochester, MI 48309;
- Center for Data Science and Big Data Analysis, Oakland University, Rochester, MI 48309
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Kärt Tomberg
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Amy E Siebert
- Department of Biological Sciences, Oakland University, Rochester, MI 48309
| | - Guojing Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Mary E Winn
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, MI 49503
| | - Sarah L Dobies
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Sara L Manning
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Marisa A Brake
- Department of Biological Sciences, Oakland University, Rochester, MI 48309
| | - Audrey C Cleuren
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Linzi M Hobbs
- Department of Biological Sciences, Oakland University, Rochester, MI 48309
| | - Lena M Mishack
- Department of Biological Sciences, Oakland University, Rochester, MI 48309
| | | | - Emilee Kotnik
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - David R Siemieniak
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109
| | - Jishu Xu
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Thomas L Saunders
- Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109
| | - David Ginsburg
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109;
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Internal Medicine, Ann Arbor, MI 48109
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109
| |
Collapse
|
11
|
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: 61] [Impact Index Per Article: 7.6] [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.
Collapse
Affiliation(s)
- Janan T. Eppig
- Janan T. Eppig, PhD, is Professor Emeritus at The Jackson Laboratory in Bar Harbor, Maine
| |
Collapse
|
12
|
Hai T, Cao C, Shang H, Guo W, Mu Y, Yang S, Zhang Y, Zheng Q, Zhang T, Wang X, Liu Y, Kong Q, Li K, Wang D, Qi M, Hong Q, Zhang R, Wang X, Jia Q, Wang X, Qin G, Li Y, Luo A, Jin W, Yao J, Huang J, Zhang H, Li M, Xie X, Zheng X, Guo K, Wang Q, Zhang S, Li L, Xie F, Zhang Y, Weng X, Yin Z, Hu K, Cong Y, Zheng P, Zou H, Xin L, Xia J, Ruan J, Li H, Zhao W, Yuan J, Liu Z, Gu W, Li M, Wang Y, Wang H, Yang S, Liu Z, Wei H, Zhao J, Zhou Q, Meng A. Pilot study of large-scale production of mutant pigs by ENU mutagenesis. eLife 2017. [PMID: 28639938 PMCID: PMC5505698 DOI: 10.7554/elife.26248] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
N-ethyl-N-nitrosourea (ENU) mutagenesis is a powerful tool to generate mutants on a large scale efficiently, and to discover genes with novel functions at the whole-genome level in Caenorhabditis elegans, flies, zebrafish and mice, but it has never been tried in large model animals. We describe a successful systematic three-generation ENU mutagenesis screening in pigs with the establishment of the Chinese Swine Mutagenesis Consortium. A total of 6,770 G1 and 6,800 G3 pigs were screened, 36 dominant and 91 recessive novel pig families with various phenotypes were established. The causative mutations in 10 mutant families were further mapped. As examples, the mutation of SOX10 (R109W) in pig causes inner ear malfunctions and mimics human Mondini dysplasia, and upregulated expression of FBXO32 is associated with congenital splay legs. This study demonstrates the feasibility of artificial random mutagenesis in pigs and opens an avenue for generating a reservoir of mutants for agricultural production and biomedical research. DOI:http://dx.doi.org/10.7554/eLife.26248.001
Collapse
Affiliation(s)
- Tang Hai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Chunwei Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Haitao Shang
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Weiwei Guo
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Yanshuang Mu
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Shulin Yang
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qiantao Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Tao Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xianlong Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Yu Liu
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Qingran Kong
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Kui Li
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dayu Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Meng Qi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qianlong Hong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Rui Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xiupeng Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qitao Jia
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Guosong Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Yongshun Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Ailing Luo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Weiwu Jin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Jing Yao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Jiaojiao Huang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Hongyong Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Menghua Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xiangmo Xie
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xuejuan Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Kenan Guo
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Qinghua Wang
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Shibin Zhang
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Liang Li
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Fei Xie
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Yu Zhang
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Xiaogang Weng
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Zhi Yin
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Kui Hu
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Yimei Cong
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Peng Zheng
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Hailong Zou
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Leilei Xin
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jihan Xia
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinxue Ruan
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hegang Li
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiming Zhao
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Yuan
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zizhan Liu
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiwang Gu
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Pearl Laboratory Animal Sci. & Tech. Co. Ltd, Guangzhou, China
| | - Ming Li
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Pearl Laboratory Animal Sci. & Tech. Co. Ltd, Guangzhou, China
| | - Yong Wang
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Shiming Yang
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China.,Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Zhonghua Liu
- College of Life Science, Northeast Agricultural University of China, Harbin, China.,Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China.,Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Jianguo Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Anming Meng
- Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| |
Collapse
|
13
|
Abstract
In order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of ethyl methanesulfonate (EMS)-mutagenized Sorghum bicolor, including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error-prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequences in wild-type siblings and heterozygous in segregating families. This region contained a single nonsynonymous change that cosegregated with dwarfism in a validation population and caused a premature stop codon in the Sorghum ortholog encoding the gibberellic acid (GA) biosynthetic enzyme ent-kaurene oxidase. Application of exogenous GA rescued the mutant phenotype. Our method for mapping did not require outcrossing and introduced no segregation variance. This enables work when line crossing is complicated by life history, permitting gene discovery outside of genetic models. This inverts the historical approach of first using recombination to define a locus and then sequencing genes. Our formally identical approach first sequences all the genes and then seeks cosegregation with the trait. Mutagenized lines lacking obvious phenotypic alterations are available for an extension of this approach: mapping with a known marker set in a line that is phenotypically identical to starting material for EMS mutant generation.
Collapse
|
14
|
Potter PK, Bowl MR, Jeyarajan P, Wisby L, Blease A, Goldsworthy ME, Simon MM, Greenaway S, Michel V, Barnard A, Aguilar C, Agnew T, Banks G, Blake A, Chessum L, Dorning J, Falcone S, Goosey L, Harris S, Haynes A, Heise I, Hillier R, Hough T, Hoslin A, Hutchison M, King R, Kumar S, Lad HV, Law G, MacLaren RE, Morse S, Nicol T, Parker A, Pickford K, Sethi S, Starbuck B, Stelma F, Cheeseman M, Cross SH, Foster RG, Jackson IJ, Peirson SN, Thakker RV, Vincent T, Scudamore C, Wells S, El-Amraoui A, Petit C, Acevedo-Arozena A, Nolan PM, Cox R, Mallon AM, Brown SDM. Novel gene function revealed by mouse mutagenesis screens for models of age-related disease. Nat Commun 2016; 7:12444. [PMID: 27534441 PMCID: PMC4992138 DOI: 10.1038/ncomms12444] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/01/2016] [Indexed: 12/19/2022] Open
Abstract
Determining the genetic bases of age-related disease remains a major challenge requiring a spectrum of approaches from human and clinical genetics to the utilization of model organism studies. Here we report a large-scale genetic screen in mice employing a phenotype-driven discovery platform to identify mutations resulting in age-related disease, both late-onset and progressive. We have utilized N-ethyl-N-nitrosourea mutagenesis to generate pedigrees of mutagenized mice that were subject to recurrent screens for mutant phenotypes as the mice aged. In total, we identify 105 distinct mutant lines from 157 pedigrees analysed, out of which 27 are late-onset phenotypes across a range of physiological systems. Using whole-genome sequencing we uncover the underlying genes for 44 of these mutant phenotypes, including 12 late-onset phenotypes. These genes reveal a number of novel pathways involved with age-related disease. We illustrate our findings by the recovery and characterization of a novel mouse model of age-related hearing loss.
Collapse
Affiliation(s)
- Paul K. Potter
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Michael R. Bowl
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Prashanthini Jeyarajan
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Laura Wisby
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Andrew Blease
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | | | - Michelle M. Simon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Simon Greenaway
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Vincent Michel
- Génétique et Physiologie de l'Audition, Institut Pasteur, INSERM UMR-S 1120, Sorbonne Universités, UPMC Univ Paris 06, Collège de France, 25 rue Dr Roux, Paris 75015, France
| | - Alun Barnard
- The Nuffield Laboratory of Ophthalmology & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK
| | - Carlos Aguilar
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Thomas Agnew
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Gareth Banks
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Andrew Blake
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Lauren Chessum
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Joanne Dorning
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Sara Falcone
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Laurence Goosey
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Shelley Harris
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Andy Haynes
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Ines Heise
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Rosie Hillier
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Tertius Hough
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Angela Hoslin
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Marie Hutchison
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Ruairidh King
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Saumya Kumar
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Heena V. Lad
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Gemma Law
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Robert E. MacLaren
- The Nuffield Laboratory of Ophthalmology & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK
| | - Susan Morse
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Thomas Nicol
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Andrew Parker
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Karen Pickford
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Siddharth Sethi
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Becky Starbuck
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Femke Stelma
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Michael Cheeseman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Sally H. Cross
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Russell G. Foster
- Nuffield Department of Clinical Neurosciences (Nuffield Laboratory of Ophthalmology), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Ian J. Jackson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Stuart N. Peirson
- Nuffield Department of Clinical Neurosciences (Nuffield Laboratory of Ophthalmology), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Rajesh V. Thakker
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Tonia Vincent
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, UK
| | - Cheryl Scudamore
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Sara Wells
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Aziz El-Amraoui
- Génétique et Physiologie de l'Audition, Institut Pasteur, INSERM UMR-S 1120, Sorbonne Universités, UPMC Univ Paris 06, Collège de France, 25 rue Dr Roux, Paris 75015, France
| | - Christine Petit
- Génétique et Physiologie de l'Audition, Institut Pasteur, INSERM UMR-S 1120, Sorbonne Universités, UPMC Univ Paris 06, Collège de France, 25 rue Dr Roux, Paris 75015, France
| | | | - Patrick M. Nolan
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Roger Cox
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Anne-Marie Mallon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Steve D. M. Brown
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| |
Collapse
|
15
|
Schneider C, Nobs SP, Heer AK, Hirsch E, Penninger J, Siggs OM, Kopf M. Frontline Science: Coincidental null mutation of Csf2rα in a colony of PI3Kγ-/- mice causes alveolar macrophage deficiency and fatal respiratory viral infection. J Leukoc Biol 2016; 101:367-376. [PMID: 27468760 DOI: 10.1189/jlb.4hi0316-157r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/05/2016] [Accepted: 06/12/2016] [Indexed: 12/25/2022] Open
Abstract
PI3Ks have been identified as key signaling proteins involved in many basic biologic processes in health and disease. Transgenic animals have been essential tools to study the underlying molecular mechanisms in this context and therefore, have been widely used to elucidate the role of these factors in many different settings. More specifically, PI3Kγ, a subunit highly expressed in the hematopoietic system, has been implicated to play an important role in many inflammatory diseases as well as cancer. Here, we report identification of multiple, additional, previously unknown mutations in the genome of a widely used PI3Kγ-deficient (PI3Kγ-/-) mouse colony. These include a STOP mutation in the GM-CSFRα chain, leading to a complete and specific deficiency in GM-CSF signaling. PI3Kγ-/- animals consequently lacked alveolar macrophages (AMs) and succumbed rapidly to influenza virus infection. Furthermore, PI3Kγ-/- mice carried an additional mutation that affects mucin 2 (Muc2) transcripts. This protein is strongly involved in the regulation of colorectal cancer, and indeed, conflicting reports have indicated that PI3Kγ-/- animals spontaneously develop colorectal tumors. Thus, we uncover previously unknown, confounding factors present in a strain of PI3Kγ-/- mice, leading to additional deficiencies in important signaling pathways with potentially wide-ranging implications for the interpretation of previous studies. By separating the mutations, we established a unique Csf2ra-/- mouse model that allows us to study the role of cell intrinsic GM-CSFR signaling in vivo without confounding variables introduced by defective IL-5R and IL-3R signaling in mice lacking the common β chain (Csf2rb).
Collapse
Affiliation(s)
- Christoph Schneider
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Samuel P Nobs
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Alex K Heer
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Emilio Hirsch
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | | | - Owen M Siggs
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Manfred Kopf
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland;
| |
Collapse
|
16
|
Mutation of Fnip1 is associated with B-cell deficiency, cardiomyopathy, and elevated AMPK activity. Proc Natl Acad Sci U S A 2016; 113:E3706-15. [PMID: 27303042 DOI: 10.1073/pnas.1607592113] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Folliculin (FLCN) is a tumor-suppressor protein mutated in the Birt-Hogg-Dubé (BHD) syndrome, which associates with two paralogous proteins, folliculin-interacting protein (FNIP)1 and FNIP2, forming a complex that interacts with the AMP-activated protein kinase (AMPK). Although it is clear that this complex influences AMPK and other metabolic regulators, reports of its effects have been inconsistent. To address this issue, we created a recessive loss-of-function variant of Fnip1 Homozygous FNIP1 deficiency resulted in profound B-cell deficiency, partially restored by overexpression of the antiapoptotic protein BCL2, whereas heterozygous deficiency caused a loss of marginal zone B cells. FNIP1-deficient mice developed cardiomyopathy characterized by left ventricular hypertrophy and glycogen accumulation, with close parallels to mice and humans bearing gain-of-function mutations in the γ2 subunit of AMPK. Concordantly, γ2-specific AMPK activity was elevated in neonatal FNIP1-deficient myocardium, whereas AMPK-dependent unc-51-like autophagy activating kinase 1 (ULK1) phosphorylation and autophagy were increased in FNIP1-deficient B-cell progenitors. These data support a role for FNIP1 as a negative regulator of AMPK.
Collapse
|
17
|
Abstract
Full evaluation of the interactions between a virus and host during infection and clearance requires a living organism. A live animal is also necessary for development of vaccines requiring evaluation of immunogenicity and an immune response that protects from challenge. Study of the natural host for the virus is ideal, but often not possible. Mice have emerged over the last 60 years as the most popular animal model for studying viral pathogenesis due to extensive genetic and immunologic characterization, wide availability of reagents, inbred and transgenic strains, and small size. However, responses in mice are not always predictive of those in the natural host. Other species commonly used include guinea pigs, ferrets, chickens, and nonhuman primates. When choosing an animal model for a study, factors to be considered include host susceptibility to the infection, animal size, cost, availability of housing and reagents, potential confounding coinfections, and ethical restrictions.
Collapse
|
18
|
What Lies Ahead? VIRAL PATHOGENESIS 2016. [PMCID: PMC7149599 DOI: 10.1016/b978-0-12-800964-2.00022-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Viral pathogenesis is a field in rapid evolution, reflecting the dynamic development of systems biology and the continuing introduction of new or improved methodologies. Therefore, this final chapter is dedicated to “futurism,” a look at what lies ahead for this field. We have recruited a number of scientists to write short pieces where they are free to speculate on future developments in their respective areas of expertise.
Collapse
|
19
|
Sustaining large-scale infrastructure to promote pre-competitive biomedical research: lessons from mouse genomics. N Biotechnol 2015; 33:280-94. [PMID: 26563511 DOI: 10.1016/j.nbt.2015.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 08/07/2015] [Accepted: 10/12/2015] [Indexed: 01/25/2023]
Abstract
Bio-repositories and databases for biomedical research enable the efficient community-wide sharing of reagents and data. These archives play an increasingly prominent role in the generation and dissemination of bioresources and data essential for fundamental and translational research. Evidence suggests, however, that current funding and governance models, generally short-term and nationally focused, do not adequately support the role of archives in long-term, transnational endeavours to make and share high-impact resources. Our qualitative case study of the International Knockout Mouse Consortium and the International Mouse Phenotyping Consortium examines new governance mechanisms for archive sustainability. Funders and archive managers highlight in interviews that archives need stable public funding and new revenue-generation models to be sustainable. Sustainability also requires archives, journal publishers, and funders to implement appropriate incentives, associated metrics, and enforcement mechanisms to ensure that researchers use archives to deposit reagents and data to make them publicly accessible for academia and industry alike.
Collapse
|
20
|
Gallego-Llamas J, Timms AE, Geister KA, Lindsay A, Beier DR. Variant mapping and mutation discovery in inbred mice using next-generation sequencing. BMC Genomics 2015; 16:913. [PMID: 26552429 PMCID: PMC4640199 DOI: 10.1186/s12864-015-2173-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 10/31/2015] [Indexed: 12/04/2022] Open
Abstract
Background The development of powerful new methods for DNA sequencing enable the discovery of sequence variants, their utilization for the mapping of mutant loci, and the identification of causal variants in a single step. We have applied this approach for the analysis of ENU-mutagenized mice maintained on an inbred background. Results We ascertained ENU-induced variants in four different phenotypically mutant lines. These were then used as informative markers for positional cloning of the mutated genes. We tested both whole genome (WGS) and whole exome (WES) datasets. Conclusion Both approaches were successful as a means to localize a region of homozygosity, as well as identifying mutations of candidate genes, which could be individually assessed. As expected, the WGS strategy was more reliable, since many more ENU-induced variants were ascertained. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2173-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jabier Gallego-Llamas
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA. .,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| | - Andrew E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| | - Krista A Geister
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| | - Anna Lindsay
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| | - David R Beier
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA. .,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| |
Collapse
|
21
|
Simon MM, Moresco EMY, Bull KR, Kumar S, Mallon AM, Beutler B, Potter PK. Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing. Mamm Genome 2015; 26:486-500. [PMID: 26449678 PMCID: PMC4602060 DOI: 10.1007/s00335-015-9603-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/01/2015] [Indexed: 02/07/2023]
Abstract
Mutagenesis-based screens in mice are a powerful discovery platform to identify novel genes or gene functions associated with disease phenotypes. An N-ethyl-N-nitrosourea (ENU) mutagenesis screen induces single nucleotide variants randomly in the mouse genome. Subsequent phenotyping of mutant and wildtype mice enables the identification of mutated pathways resulting in phenotypes associated with a particular ENU lesion. This unbiased approach to gene discovery conducts the phenotyping with no prior knowledge of the functional mutations. Before the advent of affordable next generation sequencing (NGS), ENU variant identification was a limiting step in gene characterization, akin to ‘finding a needle in a haystack’. The emergence of a reliable reference genome alongside advances in NGS has propelled ENU mutation discovery from an arduous, time-consuming exercise to an effective and rapid form of mutation discovery. This has permitted large mouse facilities worldwide to use ENU for novel mutation discovery in a high-throughput manner, helping to accelerate basic science at the mechanistic level. Here, we describe three different strategies used to identify ENU variants from NGS data and some of the subsequent steps for mutation characterisation.
Collapse
Affiliation(s)
- Michelle M Simon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK.
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Katherine R Bull
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Saumya Kumar
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Paul K Potter
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| |
Collapse
|
22
|
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: 30] [Impact Index Per Article: 3.0] [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.
Collapse
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
| |
Collapse
|
23
|
Abstract
With the wide availability of massively parallel sequencing technologies, genetic mapping has become the rate limiting step in mammalian forward genetics. Here we introduce a method for real-time identification of N-ethyl-N-nitrosourea-induced mutations that cause phenotypes in mice. All mutations are identified by whole exome G1 progenitor sequencing and their zygosity is established in G2/G3 mice before phenotypic assessment. Quantitative and qualitative traits, including lethal effects, in single or multiple combined pedigrees are then analyzed with Linkage Analyzer, a software program that detects significant linkage between individual mutations and aberrant phenotypic scores and presents processed data as Manhattan plots. As multiple alleles of genes are acquired through mutagenesis, pooled "superpedigrees" are created to analyze the effects. Our method is distinguished from conventional forward genetic methods because it permits (1) unbiased declaration of mappable phenotypes, including those that are incompletely penetrant (2), automated identification of causative mutations concurrent with phenotypic screening, without the need to outcross mutant mice to another strain and backcross them, and (3) exclusion of genes not involved in phenotypes of interest. We validated our approach and Linkage Analyzer for the identification of 47 mutations in 45 previously known genes causative for adaptive immune phenotypes; our analysis also implicated 474 genes not previously associated with immune function. The method described here permits forward genetic analysis in mice, limited only by the rates of mutant production and screening.
Collapse
|
24
|
Tokunaga M, Kokubu C, Maeda Y, Sese J, Horie K, Sugimoto N, Kinoshita T, Yusa K, Takeda J. Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells. BMC Genomics 2014; 15:1016. [PMID: 25418962 PMCID: PMC4301880 DOI: 10.1186/1471-2164-15-1016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 11/12/2014] [Indexed: 12/04/2022] Open
Abstract
Background Genome-wide saturation mutagenesis and subsequent phenotype-driven screening has been central to a comprehensive understanding of complex biological processes in classical model organisms such as flies, nematodes, and plants. The degree of “saturation” (i.e., the fraction of possible target genes identified) has been shown to be a critical parameter in determining all relevant genes involved in a biological function, without prior knowledge of their products. In mammalian model systems, however, the relatively large scale and labor intensity of experiments have hampered the achievement of actual saturation mutagenesis, especially for recessive traits that require biallelic mutations to manifest detectable phenotypes. Results By exploiting the recently established haploid mouse embryonic stem cells (ESCs), we present an implementation of almost complete saturation mutagenesis in a mammalian system. The haploid ESCs were mutagenized with the chemical mutagen N-ethyl-N-nitrosourea (ENU) and processed for the screening of mutants defective in various steps of the glycosylphosphatidylinositol-anchor biosynthetic pathway. The resulting 114 independent mutant clones were characterized by a functional complementation assay, and were shown to be defective in any of 20 genes among all 22 known genes essential for this well-characterized pathway. Ten mutants were further validated by whole-exome sequencing. The predominant generation of single-nucleotide substitutions by ENU resulted in a gene mutation rate proportional to the length of the coding sequence, which facilitated the experimental design of saturation mutagenesis screening with the aid of computational simulation. Conclusions Our study enables mammalian saturation mutagenesis to become a realistic proposition. Computational simulation, combined with a pilot mutagenesis experiment, could serve as a tool for the estimation of the number of genes essential for biological processes such as drug target pathways when a positive selection of mutants is available. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1016) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Kosuke Yusa
- Department of Social and Environmental Medicine, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan.
| | | |
Collapse
|
25
|
Siggs OM, Grieve A, Xu H, Bambrough P, Christova Y, Freeman M. Genetic interaction implicates iRhom2 in the regulation of EGF receptor signalling in mice. Biol Open 2014; 3:1151-7. [PMID: 25395669 PMCID: PMC4265752 DOI: 10.1242/bio.201410116] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 10/15/2014] [Indexed: 01/18/2023] Open
Abstract
iRhoms are closely related to rhomboid intramembrane proteases but lack catalytic activity. In mammals iRhoms are known to regulate the trafficking of TACE, the protease that cleaves the membrane bound inflammatory cytokine TNF. We have mapped a spontaneously occurring mouse mutation with a loss of hair phenotype, curly bare (cub), to the Rhbdf2 locus, which encodes the iRhom2 protein. The cub deletion removes the first 268 amino acids of the iRhom2 protein but is not a loss of function. We have also identified a previously reported suppressor of cub, called Mcub (modifier of curly bare), and find it to be a loss of function allele of the amphiregulin gene (Areg). Amphiregulin is an activating ligand of the epidermal growth factor receptor (EGFR) that, like TNF, is released by TACE. Our results therefore imply a regulatory link between iRhoms and EGFR signalling in mammals. We have tested the model that the cub mutation leads to iRhom2 hyperactivity and consequently excess TACE processing of amphiregulin and elevated EGFR signalling. Our results do not support this hypothesis: we find that, compared to wild-type cells, cub mutant embryonic fibroblasts release less amphiregulin, and that the cub mutant form of iRhom2 is less able than wild type to bind to TACE and promote its maturation.
Collapse
Affiliation(s)
- Owen M Siggs
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Adam Grieve
- Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Hongmei Xu
- Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Paul Bambrough
- Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Yonka Christova
- Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Matthew Freeman
- Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| |
Collapse
|
26
|
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: 26.6] [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.
Collapse
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
| | | | | |
Collapse
|
27
|
Haelterman NA, Jiang L, Li Y, Bayat V, Sandoval H, Ugur B, Tan KL, Zhang K, Bei D, Xiong B, Charng WL, Busby T, Jawaid A, David G, Jaiswal M, Venken KJT, Yamamoto S, Chen R, Bellen HJ. Large-scale identification of chemically induced mutations in Drosophila melanogaster. Genome Res 2014; 24:1707-1718. [PMID: 25258387 PMCID: PMC4199363 DOI: 10.1101/gr.174615.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 07/08/2014] [Indexed: 02/06/2023]
Abstract
Forward genetic screens using chemical mutagens have been successful in defining the function of thousands of genes in eukaryotic model organisms. The main drawback of this strategy is the time-consuming identification of the molecular lesions causative of the phenotypes of interest. With whole-genome sequencing (WGS), it is now possible to sequence hundreds of strains, but determining which mutations are causative among thousands of polymorphisms remains challenging. We have sequenced 394 mutant strains, generated in a chemical mutagenesis screen, for essential genes on the Drosophila X chromosome and describe strategies to reduce the number of candidate mutations from an average of -3500 to 35 single-nucleotide variants per chromosome. By combining WGS with a rough mapping method based on large duplications, we were able to map 274 (-70%) mutations. We show that these mutations are causative, using small 80-kb duplications that rescue lethality. Hence, our findings demonstrate that combining rough mapping with WGS dramatically expands the toolkit necessary for assigning function to genes.
Collapse
Affiliation(s)
- Nele A Haelterman
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lichun Jiang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Vafa Bayat
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hector Sandoval
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Berrak Ugur
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kai Li Tan
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ke Zhang
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Danqing Bei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bo Xiong
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wu-Lin Charng
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Theodore Busby
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Adeel Jawaid
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gabriela David
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Manish Jaiswal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Koen J T Venken
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Verna and Mars Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA
| | - Rui Chen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA; Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
28
|
Mouse ENU Mutagenesis to Understand Immunity to Infection: Methods, Selected Examples, and Perspectives. Genes (Basel) 2014; 5:887-925. [PMID: 25268389 PMCID: PMC4276919 DOI: 10.3390/genes5040887] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/19/2014] [Accepted: 08/21/2014] [Indexed: 12/30/2022] Open
Abstract
Infectious diseases are responsible for over 25% of deaths globally, but many more individuals are exposed to deadly pathogens. The outcome of infection results from a set of diverse factors including pathogen virulence factors, the environment, and the genetic make-up of the host. The completion of the human reference genome sequence in 2004 along with technological advances have tremendously accelerated and renovated the tools to study the genetic etiology of infectious diseases in humans and its best characterized mammalian model, the mouse. Advancements in mouse genomic resources have accelerated genome-wide functional approaches, such as gene-driven and phenotype-driven mutagenesis, bringing to the fore the use of mouse models that reproduce accurately many aspects of the pathogenesis of human infectious diseases. Treatment with the mutagen N-ethyl-N-nitrosourea (ENU) has become the most popular phenotype-driven approach. Our team and others have employed mouse ENU mutagenesis to identify host genes that directly impact susceptibility to pathogens of global significance. In this review, we first describe the strategies and tools used in mouse genetics to understand immunity to infection with special emphasis on chemical mutagenesis of the mouse germ-line together with current strategies to efficiently identify functional mutations using next generation sequencing. Then, we highlight illustrative examples of genes, proteins, and cellular signatures that have been revealed by ENU screens and have been shown to be involved in susceptibility or resistance to infectious diseases caused by parasites, bacteria, and viruses.
Collapse
|
29
|
Sittig LJ, Jeong C, Tixier E, Davis J, Barrios-Camacho CM, Palmer AA. Phenotypic instability between the near isogenic substrains BALB/cJ and BALB/cByJ. Mamm Genome 2014; 25:564-72. [PMID: 24997021 DOI: 10.1007/s00335-014-9531-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/11/2014] [Indexed: 12/29/2022]
Abstract
Closely related substrains of inbred mice often show phenotypic differences that are presumed to be caused by recent mutations. The substrains BALB/cJ and BALB/cByJ, which were separated in 1935, have been reported to show numerous highly significant behavioral and morphological differences. In an effort to identify some of the causal mutations, we phenotyped BALB/cJ and BALB/cByJ mice as well as their F1, F2, and N2 progeny for behavioral and morphological phenotypes. We also generated whole-genome sequence data for both inbred strains (~3.5× coverage) with the intention of identifying polymorphic markers to be used for linkage analysis. We observed significant differences in body weight, the weight of the heart, liver, spleen and brain, and corpus callosum length between the two substrains. We also observed that BALB/cJ animals showed greater anxiety-like behavior in the open field test, less depression-like behavior in the tail suspension test, and reduced aggression compared to BALB/cByJ mice. Some but not all of these physiological and behavioral results were inconsistent with prior publications. These inconsistencies led us to suspect that the differences were due to, or modified by, non-genetic factors. Thus, we did not perform linkage analysis. We provide a comprehensive summary of the prior literature about phenotypic differences between these substrains as well as our current findings. We conclude that many differences between these strains are unstable and therefore ill-suited to linkage analysis; the source of this instability is unclear. We discuss the broader implications of these observations for the design of future studies.
Collapse
Affiliation(s)
- Laura J Sittig
- Department of Human Genetics, University of Chicago, 920 E 58th St. CLSC-501, Chicago, IL, 60637, USA,
| | | | | | | | | | | |
Collapse
|
30
|
Siggs OM. Dissecting mammalian immunity through mutation. Immunol Cell Biol 2014; 92:392-9. [PMID: 24518983 PMCID: PMC4038135 DOI: 10.1038/icb.2014.8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/15/2014] [Accepted: 01/15/2014] [Indexed: 12/27/2022]
Abstract
Although mutation and natural selection have given rise to our immune system, a well-placed mutation can also cripple it, and within an expanding population we are recognizing more and more cases of single-gene mutations that compromise immunity. These mutations are an ideal tool for understanding human immunology, and there are more ways than ever to measure their physiological effects. There are also more ways to create mutations in the laboratory, and to use these resources to systematically define the function of every gene in our genome. This review focuses on the discovery and creation of mutations in the context of mammalian immunity, with an emphasis on the use of genome-wide chemical and CRISPR/Cas9 mutagenesis to reveal gene function.
Collapse
Affiliation(s)
- Owen M Siggs
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| |
Collapse
|
31
|
Bull KR, Mason T, Rimmer AJ, Crockford TL, Silver KL, Bouriez-Jones T, Hough TA, Chaudhry S, Roberts ISD, Goodnow CC, Cornall RJ. Next-generation sequencing to dissect hereditary nephrotic syndrome in mice identifies a hypomorphic mutation in Lamb2 and models Pierson's syndrome. J Pathol 2014; 233:18-26. [PMID: 24293254 PMCID: PMC4241031 DOI: 10.1002/path.4308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/15/2013] [Accepted: 11/21/2013] [Indexed: 01/11/2023]
Abstract
The study of mutations causing the steroid-resistant nephrotic syndrome in children has greatly advanced our understanding of the kidney filtration barrier. In particular, these genetic variants have illuminated the roles of the podocyte, glomerular basement membrane and endothelial cell in glomerular filtration. However, in a significant number of familial and early onset cases, an underlying mutation cannot be identified, indicating that there are likely to be multiple unknown genes with roles in glomerular permeability. We now show how the combination of N-ethyl-N-nitrosourea mutagenesis and next-generation sequencing could be used to identify the range of mutations affecting these pathways. Using this approach, we isolated a novel mouse strain with a viable nephrotic phenotype and used whole-genome sequencing to isolate a causative hypomorphic mutation in Lamb2. This discovery generated a model for one part of the spectrum of human Pierson's syndrome and provides a powerful proof of principle for accelerating gene discovery and improving our understanding of inherited forms of renal disease.
Collapse
Affiliation(s)
- Katherine R Bull
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford UniversityUK
| | - Thomas Mason
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford UniversityUK
| | - Andrew J Rimmer
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford UniversityUK
| | - Tanya L Crockford
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford UniversityUK
- MRC Human Immunology Unit, Weatherall Institute for Molecular Medicine, Oxford UniversityUK
| | - Karlee L Silver
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford UniversityUK
| | - Tiphaine Bouriez-Jones
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford UniversityUK
| | - Tertius A Hough
- MRC Harwell, Harwell Science and Innovation CampusOxfordshire, UK
| | - Shirine Chaudhry
- Australian Phenomics Facility, Australian National UniversityCanberra, Australia
| | - Ian SD Roberts
- Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Headington, OxfordUK
| | - Christopher C Goodnow
- Department of Immunology, John Curtin School of Medical Research, Australian National UniversityCanberra, Australia
| | - Richard J Cornall
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford UniversityUK
- MRC Human Immunology Unit, Weatherall Institute for Molecular Medicine, Oxford UniversityUK
| |
Collapse
|
32
|
Carré GA, Greenfield A. Characterising Novel Pathways in Testis Determination Using Mouse Genetics. Sex Dev 2014; 8:199-207. [DOI: 10.1159/000358402] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
33
|
Damerla RR, Chatterjee B, Li Y, Francis RJB, Fatakia SN, Lo CW. Ion Torrent sequencing for conducting genome-wide scans for mutation mapping analysis. Mamm Genome 2013; 25:120-8. [PMID: 24306492 DOI: 10.1007/s00335-013-9494-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/08/2013] [Indexed: 01/08/2023]
Abstract
Mutation mapping in mice can be readily accomplished by genome wide segregation analysis of polymorphic DNA markers. In this study, we showed the efficacy of Ion Torrent next generation sequencing for conducting genome-wide scans to map and identify a mutation causing congenital heart disease in a mouse mutant, Bishu, recovered from a mouse mutagenesis screen. The Bishu mutant line generated in a C57BL/6J (B6) background was intercrossed with another inbred strain, C57BL/10J (B10), and the resulting B6/B10 hybrid offspring were intercrossed to generate mutants used for the mapping analysis. For each mutant sample, a panel of 123 B6/B10 polymorphic SNPs distributed throughout the mouse genome was PCR amplified, bar coded, and then pooled to generate a single library used for Ion Torrent sequencing. Sequencing carried out using the 314 chip yielded >600,000 usable reads. These were aligned and mapped using a custom bioinformatics pipeline. Each SNP was sequenced to a depth >500×, allowing accurate automated calling of the B6/B10 genotypes. This analysis mapped the mutation in Bishu to an interval on the proximal region of mouse chromosome 4. This was confirmed by parallel capillary sequencing of the 123 polymorphic SNPs. Further analysis of genes in the map interval identified a splicing mutation in Dnaic1(c.204+1G>A), an intermediate chain dynein, as the disease causing mutation in Bishu. Overall, our experience shows Ion Torrent amplicon sequencing is high throughput and cost effective for conducting genome-wide mapping analysis and is easily scalable for other high volume genotyping analyses.
Collapse
Affiliation(s)
- Rama Rao Damerla
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Rangos Research Center Rm 8120, 530 45 St., Pittsburgh, PA, 15201, USA,
| | | | | | | | | | | |
Collapse
|
34
|
Zuryn S, Jarriault S. Deep sequencing strategies for mapping and identifying mutations from genetic screens. WORM 2013; 2:e25081. [PMID: 24778934 PMCID: PMC3875646 DOI: 10.4161/worm.25081] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/16/2013] [Accepted: 05/17/2013] [Indexed: 11/23/2022]
Abstract
The development of next-generation sequencing technologies has enabled rapid and cost effective whole genome sequencing. This technology has allowed researchers to shortcut time-consuming and laborious methods used to identify nucleotide mutations in forward genetic screens in model organisms. However, causal mutations must still be mapped to a region of the genome so as to aid in their identification. This can be achieved simultaneously with deep sequencing through various methods. Here we discuss alternative deep sequencing strategies for simultaneously mapping and identifying causal mutations in Caenorhabditis elegans from mutagenesis screens. Focusing on practical considerations, such as the particular mutant phenotype obtained, this review aims to aid the reader in choosing which strategy to adopt to successfully clone their mutant.
Collapse
Affiliation(s)
- Steven Zuryn
- Institut de GA(c)nA(c)tique et de Biologie MolA(c)culaire et Cellulaire (IGBMC); Institut National de la SantA(c) et de la Recherche MA(c)dicale (INSERM) U964/Centre National de la Recherche Scientifique (CNRS) UMR 1704/UniversitA(c) de Strasbourg; Strasbourg, France
| | - Sophie Jarriault
- Institut de GA(c)nA(c)tique et de Biologie MolA(c)culaire et Cellulaire (IGBMC); Institut National de la SantA(c) et de la Recherche MA(c)dicale (INSERM) U964/Centre National de la Recherche Scientifique (CNRS) UMR 1704/UniversitA(c) de Strasbourg; Strasbourg, France
| |
Collapse
|