1
|
Kulesh B, Bozadjian R, Parisi RJ, Leong SA, Kautzman AG, Reese BE, Keeley PW. Quantitative trait loci on chromosomes 9 and 19 modulate AII amacrine cell number in the mouse retina. Front Neurosci 2023; 17:1078168. [PMID: 36816119 PMCID: PMC9932814 DOI: 10.3389/fnins.2023.1078168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/03/2023] [Indexed: 02/05/2023] Open
Abstract
Sequence variants modulating gene function or expression affect various heritable traits, including the number of neurons within a population. The present study employed a forward-genetic approach to identify candidate causal genes and their sequence variants controlling the number of one type of retinal neuron, the AII amacrine cell. Data from twenty-six recombinant inbred (RI) strains of mice derived from the parental C57BL/6J (B6/J) and A/J laboratory strains were used to identify genomic loci regulating cell number. Large variation in cell number is present across the RI strains, from a low of ∼57,000 cells to a high of ∼87,000 cells. Quantitative trait locus (QTL) analysis revealed three prospective controlling genomic loci, on Chromosomes (Chrs) 9, 11, and 19, each contributing additive effects that together approach the range of variation observed. Composite interval mapping validated two of these loci, and chromosome substitution strains, in which the A/J genome for Chr 9 or 19 was introgressed on a B6/J genetic background, showed increased numbers of AII amacrine cells as predicted by those two QTL effects. Analysis of the respective genomic loci identified candidate controlling genes defined by their retinal expression, their established biological functions, and by the presence of sequence variants expected to modulate gene function or expression. Two candidate genes, Dtx4 on Chr 19, being a regulator of Notch signaling, and Dixdc1 on Chr 9, a modulator of the WNT-β-catenin signaling pathway, were explored in further detail. Postnatal overexpression of Dtx4 was found to reduce the frequency of amacrine cells, while Dixdc1 knockout retinas contained an excess of AII amacrine cells. Sequence variants in each gene were identified, being the likely sources of variation in gene expression, ultimately contributing to the final number of AII amacrine cells.
Collapse
Affiliation(s)
- Bridget Kulesh
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Rachel Bozadjian
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Ryan J. Parisi
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Stephanie A. Leong
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Amanda G. Kautzman
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Benjamin E. Reese
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Patrick W. Keeley
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| |
Collapse
|
2
|
Takada T, Fukuta K, Usuda D, Kushida T, Kondo S, Kawamoto S, Yoshiki A, Obata Y, Fujiyama A, Toyoda A, Noguchi H, Shiroishi T, Masuya H. MoG+: a database of genomic variations across three mouse subspecies for biomedical research. Mamm Genome 2021; 33:31-43. [PMID: 34782917 PMCID: PMC8913468 DOI: 10.1007/s00335-021-09933-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/20/2021] [Indexed: 11/26/2022]
Abstract
Laboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains: Mus musculus musculus-derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms; M. m. domesticus-derived PGN2/Ms and BFM/Ms; M. m. castaneus-derived HMI/Ms; and JF1/Ms and MSM/Ms, which were derived from a hybrid between M. m. musculus and M. m. castaneus. These strains were established by Prof. Moriwaki in the 1980s and are collectively named the “Mishima Battery”. These strains show large phenotypic variations in body size and in many physiological traits. We resequenced the genomes of the Mishima Battery strains and performed a comparative genomic analysis with dbSNP data. More than 81 million nucleotide coordinates were identified as variant sites due to the large genetic distances among the mouse subspecies; 8,062,070 new SNP sites were detected in this study, and these may underlie the large phenotypic diversity observed in the Mishima Battery. The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. The data in MoG+ will be invaluable for research into phenotype-genotype links in diverse mouse strains.
Collapse
Affiliation(s)
- Toyoyuki Takada
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.
| | - Kentaro Fukuta
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 1111 Yata, Mishima, 411-8540, Japan
| | - Daiki Usuda
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Tatsuya Kushida
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Shinji Kondo
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 1111 Yata, Mishima, 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
| | - Shoko Kawamoto
- Genetic Informatics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yuichi Obata
- RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Asao Fujiyama
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 1111 Yata, Mishima, 411-8540, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
- Comparative Genomics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 1111 Yata, Mishima, 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
| | - Toshihiko Shiroishi
- RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.
| | - Hiroshi Masuya
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.
| |
Collapse
|
3
|
Meyers E, Werner Z, Wichman D, Mathews HL, Radcliffe RA, Nadeau JH, Stitzel JA. Genetic Modifiers of Oral Nicotine Consumption in Chrna5 Null Mutant Mice. Front Psychiatry 2021; 12:773400. [PMID: 34803779 PMCID: PMC8601376 DOI: 10.3389/fpsyt.2021.773400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Abstract
The gene CHRNA5 is strongly associated with the level of nicotine consumption in humans and manipulation of the expression or function of Chrna5 similarly alters nicotine consumption in rodents. In both humans and rodents, reduced or complete loss of function of Chrna5 leads to increased nicotine consumption. However, the mechanism through which decreased function of Chrna5 increases nicotine intake is not well-understood. Toward a better understanding of how loss of function of Chrna5 increases nicotine consumption, we have initiated efforts to identify genetic modifiers of Chrna5 deletion-dependent oral nicotine consumption in mice. For this, we introgressed the Chrna5 knockout (KO) mutation onto a panel of C57BL/6J-Chr#A/J/NAJ chromosome substitution strains (CSS) and measured oral nicotine consumption in 18 CSS and C57BL/6 (B6) mice homozygous for the Chrna5 KO allele as well as their Chrna5 wild type littermates. As expected, nicotine consumption was significantly increased in Chrna5 KO mice relative to Chrna5 wildtype mice on a B6 background. Among the CSS homozygous for the Chrna5 KO allele, several exhibited altered nicotine consumption relative to B6 Chrna5 KO mice. Sex-independent modifiers were detected in CSS possessing A/J chromosomes 5 and 11 and a male-specific modifier was found on chromosome 15. In all cases nicotine consumption was reduced in the CSS Chrna5 KO mice relative to B6 Chrna5 KO mice and consumption in the CSS KO mice was indistinguishable from their wild type littermates. Nicotine consumption was also reduced in both Chrna5 KO and wildtype CSS mice possessing A/J chromosome 1 and increased in both KO and wild type chromosome 17 CSS relative to KO and wild type B6 mice. These results demonstrate the presence of several genetic modifiers of nicotine consumption in Chrna5 KO mice as well as identify loci that may affect nicotine consumption independent of Chrna5 genotype. Identification of the genes that underlie the altered nicotine consumption may provide novel insight into the mechanism through which Chrna5 deletion increases nicotine consumption and, more generally, a better appreciation of the neurobiology of nicotine intake.
Collapse
Affiliation(s)
- Erin Meyers
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, United States
| | - Zachary Werner
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, United States
| | - David Wichman
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, United States
| | - Hunter L. Mathews
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, United States
| | - Richard A. Radcliffe
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Joseph H. Nadeau
- Maine Medical Center Research Institute, Scarborough, ME, United States
| | - Jerry A. Stitzel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, United States
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, United States
| |
Collapse
|
4
|
Özsoy ED, Yılmaz M, Patlar B, Emecen G, Durmaz E, Magwire MM, Zhou S, Huang W, Anholt RRH, Mackay TFC. Epistasis for head morphology in Drosophila melanogaster. G3 (BETHESDA, MD.) 2021; 11:jkab285. [PMID: 34568933 PMCID: PMC8473977 DOI: 10.1093/g3journal/jkab285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/28/2021] [Indexed: 11/12/2022]
Abstract
Epistasis-gene-gene interaction-is common for mutations with large phenotypic effects in humans and model organisms. Epistasis impacts quantitative genetic models of speciation, response to natural and artificial selection, genetic mapping, and personalized medicine. However, the existence and magnitude of epistasis between alleles with small quantitative phenotypic effects are controversial and difficult to assess. Here, we use the Drosophila melanogaster Genetic Reference Panel of sequenced inbred lines to evaluate the magnitude of naturally occurring epistasis modifying the effects of mutations in jing and inv, two transcription factors that have subtle quantitative effects on head morphology as homozygotes. We find significant epistasis for both mutations and performed single marker genome-wide association analyses to map candidate modifier variants and loci affecting head morphology. A subset of these loci was significantly enriched for a known genetic interaction network, and mutations of the candidate epistatic modifier loci also affect head morphology.
Collapse
Affiliation(s)
- Ergi D Özsoy
- Department of Biology, Functional and Evolutionary Genetics Laboratory (FEGL), Science Faculty, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Murat Yılmaz
- Department of Biology, Functional and Evolutionary Genetics Laboratory (FEGL), Science Faculty, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Bahar Patlar
- Department of Biology, Functional and Evolutionary Genetics Laboratory (FEGL), Science Faculty, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Güzin Emecen
- Department of Biology, Functional and Evolutionary Genetics Laboratory (FEGL), Science Faculty, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Esra Durmaz
- Department of Biology, Functional and Evolutionary Genetics Laboratory (FEGL), Science Faculty, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Michael M Magwire
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Shanshan Zhou
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Robert R H Anholt
- Department of Genetics, North Carolina State University, Raleigh, NC 27695-7614, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Trudy F C Mackay
- Department of Genetics, North Carolina State University, Raleigh, NC 27695-7614, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
- Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA
| |
Collapse
|
5
|
Mouse Systems Genetics as a Prelude to Precision Medicine. Trends Genet 2020; 36:259-272. [PMID: 32037011 DOI: 10.1016/j.tig.2020.01.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/17/2022]
Abstract
Mouse models have been instrumental in understanding human disease biology and proposing possible new treatments. The precise control of the environment and genetic composition of mice allows more rigorous observations, but limits the generalizability and translatability of the results into human applications. In the era of precision medicine, strategies using mouse models have to be revisited to effectively emulate human populations. Systems genetics is one promising paradigm that may promote the transition to novel precision medicine strategies. Here, we review the state-of-the-art resources and discuss how mouse systems genetics helps to understand human diseases and to advance the development of precision medicine, with an emphasis on the existing resources and strategies.
Collapse
|
6
|
Massett MP, Courtney SM, Kim SK, Avila JJ. Contribution of Chromosome 14 to Exercise Capacity and Training Responses in Mice. Front Physiol 2019; 10:1165. [PMID: 31572215 PMCID: PMC6753330 DOI: 10.3389/fphys.2019.01165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/28/2019] [Indexed: 11/22/2022] Open
Abstract
Quantitative trait loci for exercise capacity and training-induced changes in exercise capacity were identified previously on mouse Chromosome 14. The aim of this study was to further investigate the role of Chromosome 14 in exercise capacity and responses to training in mice. Exercise phenotypes were measured in chromosome substitution strain mice carrying Chromosome 14 from the PWD/PhJ donor strain on the genetic background of a host C57BL/6J (B6) strain (B6.PWD14). Eight week old female and male mice from both strains completed a graded exercise test to exhaustion to assess intrinsic or baseline exercise capacity. A separate group of 12-week old female and male mice, randomly assigned to sedentary control (SED) or exercise training (EX) groups, completed a graded exercise test before and after a 4-week exercise training period. EX mice completed a 4-week training program consisting of treadmill running 5 days/week, 60 min/day at a final intensity of approximately 65% of maximum. For intrinsic exercise capacity, exercise time and work were significantly greater in female and male B6.PWD14 than sex-matched B6 mice. In the training study, female B6.PWD14 mice had higher pre-training exercise capacity than B6 mice. In contrast, there were no significant differences for pre-training exercise capacity between male B6 and B6.PWD14 mice. There were no significant strain differences for responses to training. These data demonstrate that PWD/PhJ alleles on Chromosome 14 significantly affect intrinsic exercise capacity. Furthermore, these results support continued efforts to identify candidate genes on Chromosome 14 underlying variation in exercise capacity.
Collapse
|
7
|
Ebbers L, Weber M, Nothwang HG. Activity-dependent formation of a vesicular inhibitory amino acid transporter gradient in the superior olivary complex of NMRI mice. BMC Neurosci 2017; 18:75. [PMID: 29073893 PMCID: PMC5659004 DOI: 10.1186/s12868-017-0393-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/13/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the mammalian superior olivary complex (SOC), synaptic inhibition contributes to the processing of binaural sound cues important for sound localization. Previous analyses demonstrated a tonotopic gradient for postsynaptic proteins mediating inhibitory neurotransmission in the lateral superior olive (LSO), a major nucleus of the SOC. To probe, whether a presynaptic molecular gradient exists as well, we investigated immunoreactivity against the vesicular inhibitory amino acid transporter (VIAAT) in the mouse auditory brainstem. RESULTS Immunoreactivity against VIAAT revealed a gradient in the LSO and the superior paraolivary nucleus (SPN) of NMRI mice, with high expression in the lateral, low frequency processing limb and low expression in the medial, high frequency processing limb of both nuclei. This orientation is opposite to the previously reported gradient of glycine receptors in the LSO. Other nuclei of the SOC showed a uniform distribution of VIAAT-immunoreactivity. No gradient was observed for the glycine transporter GlyT2 and the neuronal protein NeuN. Formation of the VIAAT gradient was developmentally regulated and occurred around hearing-onset between postnatal days 8 and 16. Congenital deaf Claudin14 -/- mice bred on an NMRI background showed a uniform VIAAT-immunoreactivity in the LSO, whereas cochlear ablation in NMRI mice after hearing-onset did not affect the gradient. Additional analysis of C57Bl6/J, 129/SvJ and CBA/J mice revealed a strain-specific formation of the gradient. CONCLUSIONS Our results identify an activity-regulated gradient of VIAAT in the SOC of NRMI mice. Its absence in other mouse strains adds a novel layer of strain-specific features in the auditory system, i.e. tonotopic organization of molecular gradients. This calls for caution when comparing data from different mouse strains frequently used in studies involving transgenic animals. The presence of strain-specific differences offers the possibility of genetic mapping to identify molecular factors involved in activity-dependent developmental processes in the auditory system. This would provide an important step forward concerning improved auditory rehabilitation in cases of congenital deafness.
Collapse
Affiliation(s)
- Lena Ebbers
- Neurogenetics Group, Center of Excellence Hearing4All, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany
| | - Maren Weber
- Neurogenetics Group, Center of Excellence Hearing4All, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany
| | - Hans Gerd Nothwang
- Neurogenetics Group, Center of Excellence Hearing4All, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany
- Research Center for Neurosensory Science, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany
| |
Collapse
|
8
|
Abstract
Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#<A/J>, C57BL/6J-Chr#<PWD/Ph>, and C57BL/6J-Chr#<MSM/Ms>). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA.
Collapse
|
9
|
Chen A, Liu Y, Williams SM, Morris N, Buchner DA. Widespread epistasis regulates glucose homeostasis and gene expression. PLoS Genet 2017; 13:e1007025. [PMID: 28961251 PMCID: PMC5636166 DOI: 10.1371/journal.pgen.1007025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 10/11/2017] [Accepted: 09/17/2017] [Indexed: 02/07/2023] Open
Abstract
The relative contributions of additive versus non-additive interactions in the regulation of complex traits remains controversial. This may be in part because large-scale epistasis has traditionally been difficult to detect in complex, multi-cellular organisms. We hypothesized that it would be easier to detect interactions using mouse chromosome substitution strains that simultaneously incorporate allelic variation in many genes on a controlled genetic background. Analyzing metabolic traits and gene expression levels in the offspring of a series of crosses between mouse chromosome substitution strains demonstrated that inter-chromosomal epistasis was a dominant feature of these complex traits. Epistasis typically accounted for a larger proportion of the heritable effects than those due solely to additive effects. These epistatic interactions typically resulted in trait values returning to the levels of the parental CSS host strain. Due to the large epistatic effects, analyses that did not account for interactions consistently underestimated the true effect sizes due to allelic variation or failed to detect the loci controlling trait variation. These studies demonstrate that epistatic interactions are a common feature of complex traits and thus identifying these interactions is key to understanding their genetic regulation. Most complex traits and diseases are regulated by the combined influence of multiple genetic variants. However, it remains controversial whether these genetic variants independently influence complex traits, and therefore the impact of each variant could be simply added together (additivity), or whether the variants work together to influence trait variation, in which case the combined impact of multiple variants would differ from the summed impact of each individual variant (epistasis). In this study in mice, we discovered that the genetic regulation of blood sugar levels and gene expression in the liver were predominantly controlled by non-additive interactions, whereas body weight was predominantly controlled by additive interactions. Remarkably, the expression level of nearly 25% of all genes in the liver was controlled by non-additive interactions. The non-additive interactions typically acted to return trait values to the levels detected in control mice, thus contributing to a reduction in trait variation. We also demonstrated that not accounting for non-additive interactions significantly underestimated the phenotypic effect of a genetic variant on a particular genetic background, suggesting that many previously identified risk loci may have significantly larger effects on disease susceptibility in a subset of individuals. These studies highlight the importance of understanding interactions between genetic variants to better understand disease risk and personalize clinical care.
Collapse
Affiliation(s)
- Anlu Chen
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, United States of America
| | - Yang Liu
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, United States of America
| | - Scott M. Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Nathan Morris
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - David A. Buchner
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, United States of America
- * E-mail:
| |
Collapse
|
10
|
Genome Sequencing of Chromosome 1 Substitution Lines Derived from Chinese Wild Mice Revealed a Unique Resource for Genetic Studies of Complex Traits. G3-GENES GENOMES GENETICS 2016; 6:3571-3580. [PMID: 27605517 PMCID: PMC5100856 DOI: 10.1534/g3.116.033902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mouse resources such as Collaborative Cross, outbred stocks, Hybrid Mouse Diversity Panel, and chromosome substitution strains have been instrumental to many progresses in the studies of complex traits genetics. We have established a population of chromosome 1 (Chr 1) substitution lines (C1SLs) in which donor chromosomes were derived from Chinese wild mice. Genome sequencing of 18 lines of this population showed that Chr 1 had been replaced by the donor chromosome. About 4.5 million unique single nucleotide polymorphisms and indels were discovered on Chr 1, of which 1.3 million were novel. Compared with sequenced classical inbred strains, Chr 1 of each C1SL had fivefold more variants, and more loss of function and potentially regulatory variants. Further haplotype analysis showed that the donor chromosome accumulated more historical recombination events, with the largest haplotype block being only 100 kb, and about 57% of the blocks were <1 kb. Subspecies origin analysis showed that these chromosomes had a mosaic genome structure that dominantly originated from Mus musculus musculus and M. m. castaneus subspecies, except for the C57BL/6J-Chr1KM line from M. m. domesticus. In addition, phenotyping four of these lines on blood biochemistry suggested that there were substantial phenotypic variations among our lines, especially line C57BL/6J-Chr1HZ and donor strain C57BL/6J. Further gene ontology enrichment revealed that the differentially expressed genes among liver-expressed genes between C57BL/6J and C57BL/6J-Chr1HZ were enriched in lipid metabolism biological processes. All these characteristics enable C1SLs to be a unique resource for identifying and fine mapping quantitative trait loci on mouse Chr 1, and carrying out systems genetics studies of complex traits.
Collapse
|
11
|
Labots M, Laarakker MC, Ohl F, van Lith HA. Consomic mouse strain selection based on effect size measurement, statistical significance testing and integrated behavioral z-scoring: focus on anxiety-related behavior and locomotion. BMC Genet 2016; 17:95. [PMID: 27357390 PMCID: PMC4928255 DOI: 10.1186/s12863-016-0411-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 06/24/2016] [Indexed: 11/16/2022] Open
Abstract
Background Selecting chromosome substitution strains (CSSs, also called consomic strains/lines) used in the search for quantitative trait loci (QTLs) consistently requires the identification of the respective phenotypic trait of interest and is simply based on a significant difference between a consomic and host strain. However, statistical significance as represented by P values does not necessarily predicate practical importance. We therefore propose a method that pays attention to both the statistical significance and the actual size of the observed effect. The present paper extends on this approach and describes in more detail the use of effect size measures (Cohen’s d, partial eta squared - ηp2) together with the P value as statistical selection parameters for the chromosomal assignment of QTLs influencing anxiety-related behavior and locomotion in laboratory mice. Results The effect size measures were based on integrated behavioral z-scoring and were calculated in three experiments: (A) a complete consomic male mouse panel with A/J as the donor strain and C57BL/6J as the host strain. This panel, including host and donor strains, was analyzed in the modified Hole Board (mHB). The consomic line with chromosome 19 from A/J (CSS-19A) was selected since it showed increased anxiety-related behavior, but similar locomotion compared to its host. (B) Following experiment A, female CSS-19A mice were compared with their C57BL/6J counterparts; however no significant differences and effect sizes close to zero were found. (C) A different consomic mouse strain (CSS-19PWD), with chromosome 19 from PWD/PhJ transferred on the genetic background of C57BL/6J, was compared with its host strain. Here, in contrast with CSS-19A, there was a decreased overall anxiety in CSS-19PWD compared to C57BL/6J males, but not locomotion. Conclusions This new method shows an improved way to identify CSSs for QTL analysis for anxiety-related behavior using a combination of statistical significance testing and effect sizes. In addition, an intercross between CSS-19A and CSS-19PWD may be of interest for future studies on the genetic background of anxiety-related behavior. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0411-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- M Labots
- Division of Animal Welfare & Laboratory Animal Science, Department of Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, P.O. Box 80166, 3508 TD, Utrecht, The Netherlands. .,Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - M C Laarakker
- Division of Animal Welfare & Laboratory Animal Science, Department of Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, P.O. Box 80166, 3508 TD, Utrecht, The Netherlands.,Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands.,Present Address: Boston Scientific Nederland B.V., Nieuwegein, The Netherlands
| | - F Ohl
- Division of Animal Welfare & Laboratory Animal Science, Department of Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, P.O. Box 80166, 3508 TD, Utrecht, The Netherlands.,Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - H A van Lith
- Division of Animal Welfare & Laboratory Animal Science, Department of Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, P.O. Box 80166, 3508 TD, Utrecht, The Netherlands.,Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| |
Collapse
|
12
|
Lusis AJ, Seldin MM, Allayee H, Bennett BJ, Civelek M, Davis RC, Eskin E, Farber CR, Hui S, Mehrabian M, Norheim F, Pan C, Parks B, Rau CD, Smith DJ, Vallim T, Wang Y, Wang J. The Hybrid Mouse Diversity Panel: a resource for systems genetics analyses of metabolic and cardiovascular traits. J Lipid Res 2016; 57:925-42. [PMID: 27099397 PMCID: PMC4878195 DOI: 10.1194/jlr.r066944] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/12/2016] [Indexed: 02/07/2023] Open
Abstract
The Hybrid Mouse Diversity Panel (HMDP) is a collection of approximately 100 well-characterized inbred strains of mice that can be used to analyze the genetic and environmental factors underlying complex traits. While not nearly as powerful for mapping genetic loci contributing to the traits as human genome-wide association studies, it has some important advantages. First, environmental factors can be controlled. Second, relevant tissues are accessible for global molecular phenotyping. Finally, because inbred strains are renewable, results from separate studies can be integrated. Thus far, the HMDP has been studied for traits relevant to obesity, diabetes, atherosclerosis, osteoporosis, heart failure, immune regulation, fatty liver disease, and host-gut microbiota interactions. High-throughput technologies have been used to examine the genomes, epigenomes, transcriptomes, proteomes, metabolomes, and microbiomes of the mice under various environmental conditions. All of the published data are available and can be readily used to formulate hypotheses about genes, pathways and interactions.
Collapse
Affiliation(s)
- Aldons J Lusis
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA Microbiology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Marcus M Seldin
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Hooman Allayee
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA
| | - Brian J Bennett
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Mete Civelek
- Departments of Biomedical Engineering University of Virginia, Charlottesville, VA
| | - Richard C Davis
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Eleazar Eskin
- Departments of Computer Science, University of California-Los Angeles, Los Angeles, CA
| | - Charles R Farber
- Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Simon Hui
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Margarete Mehrabian
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Frode Norheim
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Calvin Pan
- Human Genetics, University of California-Los Angeles, Los Angeles, CA
| | - Brian Parks
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI
| | - Christoph D Rau
- Anesthesiology, University of California-Los Angeles, Los Angeles, CA
| | - Desmond J Smith
- Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Thomas Vallim
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Yibin Wang
- Anesthesiology, University of California-Los Angeles, Los Angeles, CA
| | - Jessica Wang
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| |
Collapse
|
13
|
Hybrid Sterility Locus on Chromosome X Controls Meiotic Recombination Rate in Mouse. PLoS Genet 2016; 12:e1005906. [PMID: 27104744 PMCID: PMC4841592 DOI: 10.1371/journal.pgen.1005906] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/08/2016] [Indexed: 11/28/2022] Open
Abstract
Meiotic recombination safeguards proper segregation of homologous chromosomes into gametes, affects genetic variation within species, and contributes to meiotic chromosome recognition, pairing and synapsis. The Prdm9 gene has a dual role, it controls meiotic recombination by determining the genomic position of crossover hotspots and, in infertile hybrids of house mouse subspecies Mus m. musculus (Mmm) and Mus m. domesticus (Mmd), it further functions as the major hybrid sterility gene. In the latter role Prdm9 interacts with the hybrid sterility X 2 (Hstx2) genomic locus on Chromosome X (Chr X) by a still unknown mechanism. Here we investigated the meiotic recombination rate at the genome-wide level and its possible relation to hybrid sterility. Using immunofluorescence microscopy we quantified the foci of MLH1 DNA mismatch repair protein, the cytological counterparts of reciprocal crossovers, in a panel of inter-subspecific chromosome substitution strains. Two autosomes, Chr 7 and Chr 11, significantly modified the meiotic recombination rate, yet the strongest modifier, designated meiotic recombination 1, Meir1, emerged in the 4.7 Mb Hstx2 genomic locus on Chr X. The male-limited transgressive effect of Meir1 on recombination rate parallels the male-limited transgressive role of Hstx2 in hybrid male sterility. Thus, both genetic factors, the Prdm9 gene and the Hstx2/Meir1 genomic locus, indicate a link between meiotic recombination and hybrid sterility. A strong female-specific modifier of meiotic recombination rate with the effect opposite to Meir1 was localized on Chr X, distally to Meir1. Mapping Meir1 to a narrow candidate interval on Chr X is an important first step towards positional cloning of the respective gene(s) responsible for variation in the global recombination rate between closely related mouse subspecies. During differentiation of germ cells into gametes, a maternal and a paternal copy of each chromosome have to find each other, pair, and synapse in order to ensure proper chromosome segregation into the gametes. Because of the unique ability to identify homologous DNA sequences between homologous chromosomes, meiotic recombination is an essential step in proper chromosome pairing and synapsis in the majority of species. However, when the paternal and maternal sets of chromosomes come from different (sub)species, the recognition of homologs can be disturbed and result in sterility of male hybrids. In this study we investigated the genetic control of variation in the global recombination rate between two closely related mouse subspecies with regard to the known infertility of their F1 hybrids. We show that the variation in the global recombination rate between both subspecies is under the control of three genomic loci. The strongest one appeared within the hybrid sterility X2 genomic locus on Chromosome X. Our findings will allow positional cloning of the gene and will shed new light on the role of meiotic recombination in reproductive isolation between closely related species.
Collapse
|
14
|
Sinasac DS, Riordan JD, Spiezio SH, Yandell BS, Croniger CM, Nadeau JH. Genetic control of obesity, glucose homeostasis, dyslipidemia and fatty liver in a mouse model of diet-induced metabolic syndrome. Int J Obes (Lond) 2015; 40:346-55. [PMID: 26381349 DOI: 10.1038/ijo.2015.184] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/24/2015] [Accepted: 08/19/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND/OBJECTIVES Both genetic and dietary factors contribute to the metabolic syndrome (MetS) in humans and animal models. Characterizing their individual roles as well as relationships among these factors is critical for understanding MetS pathogenesis and developing effective therapies. By studying phenotypic responsiveness to high-risk versus control diet in two inbred mouse strains and their derivatives, we estimated the relative contributions of diet and genetic background to MetS, characterized strain-specific combinations of MetS conditions, and tested genetic and phenotypic complexity on a single substituted chromosome. METHODS Ten measures of metabolic health were assessed in susceptible C57BL/6 J and resistant A/J male mice fed either a control or a high-fat, high-sucrose (HFHS) diet, permitting estimates of the relative influences of strain, diet and strain-diet interactions for each trait. The same traits were measured in a panel of C57BL/6 J (B6)-Chr(A/J) chromosome substitution strains (CSSs) fed the HFHS diet, followed by characterization of interstrain relationships, covariation among metabolic traits and quantitative trait loci (QTLs) on Chromosome 10. RESULTS We identified significant genetic contributions to nine of ten metabolic traits and significant dietary influence on eight. Significant strain-diet interaction effects were detected for four traits. Although a range of HFHS-induced phenotypes were observed among the CSSs, significant associations were detected among all traits but one. Strains were grouped into three clusters based on overall phenotype and specific CSSs were identified with distinct and reproducible trait combinations. Finally, several Chr10 regions were shown to control the severity of MetS conditions. CONCLUSIONS Generally strong genetic and dietary effects validate these CSSs as a multifactorial model of MetS. Although traits tended to segregate together, considerable phenotypic heterogeneity suggests that underlying genetic factors influence their co-occurrence and severity. Identification of multiple QTLs within and among strains highlights both the complexity of genetically regulated, diet-induced MetS and the ability of CSSs to prioritize candidate loci for mechanistic studies.
Collapse
Affiliation(s)
- D S Sinasac
- Department of Genetics, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
| | - J D Riordan
- Pacific Northwest Diabetes Research Institute, Seattle, WA, USA
| | - S H Spiezio
- Department of Genetics, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
| | - B S Yandell
- Department of Statistics, University of Wisconsin, Madison, WI, USA
| | - C M Croniger
- Department of Nutrition, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
| | - J H Nadeau
- Department of Genetics, Case Western Reserve University, School of Medicine, Cleveland, OH, USA.,Pacific Northwest Diabetes Research Institute, Seattle, WA, USA
| |
Collapse
|
15
|
Goto T, Okayama T, Toyoda A. Strain differences in temporal changes of nesting behaviors in C57BL/6N, DBA/2N, and their F1 hybrid mice assessed by a three-dimensional monitoring system. Behav Processes 2015. [PMID: 26220275 DOI: 10.1016/j.beproc.2015.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nest building is one of the innate behaviors that are widely observed throughout the animal kingdom. Previous studies have reported specific brain regions and genetic loci associated with nest building in mice. These studies mainly evaluated the nest structure, without observing the nesting process. In this study, we evaluated the effects of strain and learning on the nesting process of mice using a 3D depth camera. To determine the quality of the nest structure, a conventional scoring method, Deacon scores 1-5, was applied to the recorded depth images. The final score of the nest, latency to start nesting behavior, and latencies to reach Deacon scores 3-5, were determined using three genetically different mouse strains-C57BL/6NCrl (B6), DBA/2NCrlCrlj (DBA), and B6D2F1/Crl (B6D2F1). The final score of the DBA nest was significantly lower than that of the B6D2F1 nest, and DBA mice showed significantly longer latency to start nest building than the other two strains in the first trial. By observing the time course of nest building, we confirmed that DBA mice took significantly longer to build their nests than B6 and B6D2F1 mice. Although we did not find any significant differences between DBA and B6 mice in the final assessment of the nest based on the Deacon method, overnight monitoring of the nesting behavior using a 3D depth camera could elucidate the clear differences in the amount of time spent nesting between DBA and B6 mice. In addition, the learning effect was more evident in DBA mice than it was in B6 in terms of latencies to reach Deacon score 3-5 in five repeated trials. DBA mice showed a gradual decrease in latency to build, whereas nesting behaviors of B6 mice were relatively consistent throughout the five trials. Therefore, our 3D depth image method gives higher resolution and structural information regarding the nesting process in mice. Future genetic analyses using the 3D assessment system will provide novel insights into the complex genetic basis for nesting and other behaviors in animals.
Collapse
Affiliation(s)
- Tatsuhiko Goto
- College of Agriculture, Ibaraki University, Ami, Ibaraki 300-0393, Japan; Ibaraki University Cooperation between Agriculture and Medical Science (IUCAM), Ami, Ibaraki 300-0393, Japan
| | - Tsuyoshi Okayama
- College of Agriculture, Ibaraki University, Ami, Ibaraki 300-0393, Japan; Ibaraki University Cooperation between Agriculture and Medical Science (IUCAM), Ami, Ibaraki 300-0393, Japan; United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu-city, Tokyo 183-8509, Japan
| | - Atsushi Toyoda
- College of Agriculture, Ibaraki University, Ami, Ibaraki 300-0393, Japan; Ibaraki University Cooperation between Agriculture and Medical Science (IUCAM), Ami, Ibaraki 300-0393, Japan; United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu-city, Tokyo 183-8509, Japan.
| |
Collapse
|
16
|
Buchner DA, Nadeau JH. Contrasting genetic architectures in different mouse reference populations used for studying complex traits. Genome Res 2015; 25:775-91. [PMID: 25953951 PMCID: PMC4448675 DOI: 10.1101/gr.187450.114] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/31/2015] [Indexed: 01/14/2023]
Abstract
Quantitative trait loci (QTLs) are being used to study genetic networks, protein functions, and systems properties that underlie phenotypic variation and disease risk in humans, model organisms, agricultural species, and natural populations. The challenges are many, beginning with the seemingly simple tasks of mapping QTLs and identifying their underlying genetic determinants. Various specialized resources have been developed to study complex traits in many model organisms. In the mouse, remarkably different pictures of genetic architectures are emerging. Chromosome Substitution Strains (CSSs) reveal many QTLs, large phenotypic effects, pervasive epistasis, and readily identified genetic variants. In contrast, other resources as well as genome-wide association studies (GWAS) in humans and other species reveal genetic architectures dominated with a relatively modest number of QTLs that have small individual and combined phenotypic effects. These contrasting architectures are the result of intrinsic differences in the study designs underlying different resources. The CSSs examine context-dependent phenotypic effects independently among individual genotypes, whereas with GWAS and other mouse resources, the average effect of each QTL is assessed among many individuals with heterogeneous genetic backgrounds. We argue that variation of genetic architectures among individuals is as important as population averages. Each of these important resources has particular merits and specific applications for these individual and population perspectives. Collectively, these resources together with high-throughput genotyping, sequencing and genetic engineering technologies, and information repositories highlight the power of the mouse for genetic, functional, and systems studies of complex traits and disease models.
Collapse
Affiliation(s)
- David A Buchner
- Department of Genetics and Genome Sciences, Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Joseph H Nadeau
- Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122, USA
| |
Collapse
|
17
|
Case LK, Teuscher C. Y genetic variation and phenotypic diversity in health and disease. Biol Sex Differ 2015; 6:6. [PMID: 25866616 PMCID: PMC4392626 DOI: 10.1186/s13293-015-0024-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/22/2015] [Indexed: 11/10/2022] Open
Abstract
Sexually dimorphic traits arise through the combined effects of sex hormones and sex chromosomes on sex-biased gene expression, and experimental mouse models have been instrumental in determining their relative contribution in modulating sex differences. A role for the Y chromosome (ChrY) in mediating sex differences outside of development and reproduction has historically been overlooked due to its unusual genetic composition and the predominant testes-specific expression of ChrY-encoded genes. However, ample evidence now exists supporting ChrY as a mediator of other physiological traits in males, and genetic variation in ChrY has been linked to several diseases, including heart disease, cancer, and autoimmune diseases in experimental animal models, as well as humans. The genetic and molecular mechanisms by which ChrY modulates phenotypic variation in males remain unknown but may be a function of copy number variation between homologous X-Y multicopy genes driving differential gene expression. Here, we review the literature identifying an association between ChrY polymorphism and phenotypic variation and present the current evidence depicting the mammalian ChrY as a member of the regulatory genome in males and as a factor influencing paternal parent-of-origin effects in female offspring.
Collapse
Affiliation(s)
- Laure K Case
- Department of Medicine, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405 USA
| | - Cory Teuscher
- Department of Medicine, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405 USA ; Department of Pathology, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405 USA ; University of Vermont, Given Medical Building C317, Burlington, VT 05405 USA
| |
Collapse
|
18
|
Case LK, Wall EH, Osmanski EE, Dragon JA, Saligrama N, Zachary JF, Lemos B, Blankenhorn EP, Teuscher C. Copy number variation in Y chromosome multicopy genes is linked to a paternal parent-of-origin effect on CNS autoimmune disease in female offspring. Genome Biol 2015; 16:28. [PMID: 25886764 PMCID: PMC4396973 DOI: 10.1186/s13059-015-0591-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/20/2015] [Indexed: 12/11/2022] Open
Abstract
Background The prevalence of some autoimmune diseases is greater in females compared with males, although disease severity is often greater in males. The reason for this sexual dimorphism is unknown, but it may reflect negative selection of Y chromosome-bearing sperm during spermatogenesis or male fetuses early in the course of conception/pregnancy. Previously, we showed that the sexual dimorphism in experimental autoimmune encephalomyelitis (EAE) is associated with copy number variation (CNV) in Y chromosome multicopy genes. Here, we test the hypothesis that CNV in Y chromosome multicopy genes influences the paternal parent-of-origin effect on EAE susceptibility in female mice. Results We show that C57BL/6 J consomic strains of mice possessing an identical X chromosome and CNV in Y chromosome multicopy genes exhibit sperm head abnormalities and female-biased sex ratio. This is consistent with X-Y intragenomic conflict arising from an imbalance in CNV between homologous X:Y chromosome multicopy genes. These males also display paternal transmission of EAE to female offspring and differential loading of microRNAs within the sperm nucleus. Furthermore, in humans, families of probands with multiple sclerosis similarly exhibit a female-biased sex ratio, whereas families of probands affected with non-sexually dimorphic autoimmune diseases exhibit unbiased sex ratios. Conclusions These findings provide evidence for a mechanism at the level of the male gamete that contributes to the sexual dimorphism in EAE and paternal parent-of-origin effects in female mice, raising the possibility that a similar mechanism may contribute to the sexual dimorphism in multiple sclerosis. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0591-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Laure K Case
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA.
| | - Emma H Wall
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA.
| | - Erin E Osmanski
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA.
| | - Julie A Dragon
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA.
| | - Naresha Saligrama
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA. .,Current address: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - James F Zachary
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA.
| | - Bernardo Lemos
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, 02115, USA.
| | - Elizabeth P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19129, USA.
| | - Cory Teuscher
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA. .,Department of Pathology, University of Vermont, Burlington, VT, 05405, USA.
| |
Collapse
|
19
|
Kebede MA, Attie AD. Insights into obesity and diabetes at the intersection of mouse and human genetics. Trends Endocrinol Metab 2014; 25:493-501. [PMID: 25034129 PMCID: PMC4177963 DOI: 10.1016/j.tem.2014.06.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/06/2014] [Accepted: 06/06/2014] [Indexed: 11/25/2022]
Abstract
Many of our insights into obesity and diabetes come from studies in mice carrying natural or induced mutations. In parallel, genome-wide association studies (GWAS) in humans have identified numerous genes that are causally associated with obesity and diabetes, but discovering the underlying mechanisms required in-depth studies in mice. We discuss the advantages of studying natural variation in mice and summarize several examples where the combination of human and mouse genetics opened windows into fundamental physiological pathways. A noteworthy example is the melanocortin-4 receptor (MC4R) and its role in energy balance. The pathway was delineated by discovering the gene responsible for the Agouti mutation in mice. With more targeted phenotyping, we predict that additional pathways relevant to human pathophysiology will be discovered.
Collapse
Affiliation(s)
- Melkam A Kebede
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| |
Collapse
|
20
|
Spiezio SH, Amon LM, McMillen TS, Vick CM, Houston BA, Caldwell M, Ogimoto K, Morton GJ, Kirk EA, Schwartz MW, Nadeau JH, LeBoeuf RC. Genetic determinants of atherosclerosis, obesity, and energy balance in consomic mice. Mamm Genome 2014; 25:549-63. [PMID: 25001233 DOI: 10.1007/s00335-014-9530-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/11/2014] [Indexed: 12/18/2022]
Abstract
Metabolic diseases such as obesity and atherosclerosis result from complex interactions between environmental factors and genetic variants. A panel of chromosome substitution strains (CSSs) was developed to characterize genetic and dietary factors contributing to metabolic diseases and other biological traits and biomedical conditions. Our goal here was to identify quantitative trait loci (QTLs) contributing to obesity, energy expenditure, and atherosclerosis. Parental strains C57BL/6 and A/J together with a panel of 21 CSSs derived from these progenitors were subjected to chronic feeding of rodent chow and atherosclerotic (females) or diabetogenic (males) test diets, and evaluated for a variety of metabolic phenotypes including several traits unique to this report, namely fat pad weights, energy balance, and atherosclerosis. A total of 297 QTLs across 35 traits were discovered, two of which provided significant protection from atherosclerosis, and several dozen QTLs modulated body weight, body composition, and circulating lipid levels in females and males. While several QTLs confirmed previous reports, most QTLs were novel. Finally, we applied the CSS quantitative genetic approach to energy balance, and identified three novel QTLs controlling energy expenditure and one QTL modulating food intake. Overall, we identified many new QTLs and phenotyped several novel traits in this mouse model of diet-induced metabolic diseases.
Collapse
Affiliation(s)
- Sabrina H Spiezio
- Institute for Systems Biology, 401 North Terry Ave, Seattle, WA, 98109, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
FMRI and fcMRI phenotypes map the genomic effect of chromosome 13 in Brown Norway and Dahl salt-sensitive rats. Neuroimage 2014; 90:403-12. [DOI: 10.1016/j.neuroimage.2013.09.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 09/16/2013] [Accepted: 09/19/2013] [Indexed: 01/13/2023] Open
|
22
|
Case LK, Wall EH, Dragon JA, Saligrama N, Krementsov DN, Moussawi M, Zachary JF, Huber SA, Blankenhorn EP, Teuscher C. The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease. Genome Res 2013; 23:1474-85. [PMID: 23800453 PMCID: PMC3759723 DOI: 10.1101/gr.156703.113] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 06/19/2013] [Indexed: 11/25/2022]
Abstract
Understanding the DNA elements that constitute and control the regulatory genome is critical for the appropriate therapeutic management of complex diseases. Here, using chromosome Y (ChrY) consomic mouse strains on the C57BL/6J (B6) background, we show that susceptibility to two diverse animal models of autoimmune disease, experimental allergic encephalomyelitis (EAE) and experimental myocarditis, correlates with the natural variation in copy number of Sly and Rbmy multicopy ChrY genes. On the B6 background, ChrY possesses gene regulatory properties that impact genome-wide gene expression in pathogenic CD4(+) T cells. Using a ChrY consomic strain on the SJL background, we discovered a preference for ChrY-mediated gene regulation in macrophages, the immune cell subset underlying the EAE sexual dimorphism in SJL mice, rather than CD4(+) T cells. Importantly, in both genetic backgrounds, an inverse correlation exists between the number of Sly and Rbmy ChrY gene copies and the number of significantly up-regulated genes in immune cells, thereby supporting a link between copy number variation of Sly and Rbmy with the ChrY genetic element exerting regulatory properties. Additionally, we show that ChrY polymorphism can determine the sexual dimorphism in EAE and myocarditis. In humans, an analysis of the CD4(+) T cell transcriptome from male multiple sclerosis patients versus healthy controls provides further evidence for an evolutionarily conserved mechanism of gene regulation by ChrY. Thus, as in Drosophila, these data establish the mammalian ChrY as a member of the regulatory genome due to its ability to epigenetically regulate genome-wide gene expression in immune cells.
Collapse
Affiliation(s)
| | | | | | | | | | - Mohamad Moussawi
- Department of Pathology, University of Vermont, Burlington, Vermont 05405, USA
| | - James F. Zachary
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61802, USA
| | - Sally A. Huber
- Department of Pathology, University of Vermont, Burlington, Vermont 05405, USA
| | - Elizabeth P. Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19129, USA
| | - Cory Teuscher
- Department of Medicine
- Department of Pathology, University of Vermont, Burlington, Vermont 05405, USA
| |
Collapse
|
23
|
Wang Y, Chen X, Tsai S, Thomas A, Shizuru JA, Cao TM. Fine mapping of the Bmgr5 quantitative trait locus for allogeneic bone marrow engraftment in mice. Immunogenetics 2013; 65:585-96. [PMID: 23666360 PMCID: PMC3713196 DOI: 10.1007/s00251-013-0709-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/26/2013] [Indexed: 01/04/2023]
Abstract
To identify novel mechanisms regulating allogeneic hematopoietic cell engraftment, we used forward genetics and previously described identification, in mice, of a bone marrow (BM) engraftment quantitative trait locus (QTL), termed Bmgr5. This QTL confers dominant and large allele effects for engraftment susceptibility. It was localized to chromosome 16 by quantitative genetic techniques in a segregating backcross bred from susceptible BALB.K and resistant B10.BR mice. We now report verification of the Bmgr5 QTL using reciprocal chromosome 16 consomic strains. The BM engraftment phenotype in these consomic mice shows that Bmgr5 susceptibility alleles are not only sufficient but also indispensable for conferring permissiveness for allogeneic BM engraftment. Using panels of congenic mice, we resolved the Bmgr5 QTL into two separate subloci, termed Bmgr5a (Chr16:14.6-15.8 Mb) and Bmgr5b (Chr16:15.8-17.6 Mb), each conferring permissiveness for the engraftment phenotype and both fine mapped to an interval amenable to positional cloning. Candidate Bmgr5 genes were then prioritized using whole exome DNA sequencing and microarray gene expression data. Further studies are warranted to elucidate the genetic interaction between the Bmgr5a and Bmgr5b QTL and identify causative genes and underlying gene variants. This may lead to new approaches for overcoming the problem of graft rejection in clinical hematopoietic cell transplantation.
Collapse
Affiliation(s)
- Yuanyuan Wang
- Blood and Marrow Transplantation Program, Department of Medicine, University of Utah, Salt Lake City, UT
| | - Xinjian Chen
- Department of Pathology, University of Utah, Salt Lake City, UT
| | - Schickwann Tsai
- Blood and Marrow Transplantation Program, Department of Medicine, University of Utah, Salt Lake City, UT
| | - Alun Thomas
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Judith A. Shizuru
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Thai M. Cao
- Blood and Marrow Transplantation Program, Department of Medicine, University of Utah, Salt Lake City, UT
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| |
Collapse
|
24
|
Meeting report of the European mouse complex genetics network SYSGENET. Mamm Genome 2013; 24:190-7. [PMID: 23673683 DOI: 10.1007/s00335-013-9458-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 04/26/2013] [Indexed: 10/26/2022]
Abstract
The second scientific meeting of the European systems genetics network for the study of complex genetic human disease using genetic reference populations (SYSGENET) took place at the Center for Cooperative Research in Biosciences in Bilbao, Spain, December 10-12, 2012. SYSGENET is funded by the European Cooperation in the Field of Scientific and Technological Research (COST) and represents a network of scientists in Europe that use mouse genetic reference populations (GRPs) to identify complex genetic factors influencing disease phenotypes (Schughart, Mamm Genome 21:331-336, 2010). About 50 researchers working in the field of systems genetics attended the meeting, which consisted of 27 oral presentations, a poster session, and a management committee meeting. Participants exchanged results, set up future collaborations, and shared phenotyping and data analysis methodologies. This meeting was particularly instrumental for conveying the current status of the US, Israeli, and Australian Collaborative Cross (CC) mouse GRP. The CC is an open source project initiated nearly a decade ago by members of the Complex Trait Consortium to aid the mapping of multigenetic traits (Threadgill, Mamm Genome 13:175-178, 2002). In addition, representatives of the International Mouse Phenotyping Consortium were invited to exchange ongoing activities between the knockout and complex genetics communities and to discuss and explore potential fields for future interactions.
Collapse
|
25
|
Abstract
According to the Dobzhansky-Muller model, hybrid sterility is a consequence of the independent evolution of related taxa resulting in incompatible genomic interactions of their hybrids. The model implies that the incompatibilities evolve randomly, unless a particular gene or nongenic sequence diverges much faster than the rest of the genome. Here we propose that asynapsis of heterospecific chromosomes in meiotic prophase provides a recurrently evolving trigger for the meiotic arrest of interspecific F1 hybrids. We observed extensive asynapsis of chromosomes and disturbance of the sex body in >95% of pachynemas of Mus m. musculus × Mus m. domesticus sterile F1 males. Asynapsis was not preceded by a failure of double-strand break induction, and the rate of meiotic crossing over was not affected in synapsed chromosomes. DNA double-strand break repair was delayed or failed in unsynapsed autosomes, and misexpression of chromosome X and chromosome Y genes was detected in single pachynemas and by genome-wide expression profiling. Oocytes of F1 hybrid females showed the same kind of synaptic problems but with the incidence reduced to half. Most of the oocytes with pachytene asynapsis were eliminated before birth. We propose the heterospecific pairing of homologous chromosomes as a preexisting condition of asynapsis in interspecific hybrids. The asynapsis may represent a universal mechanistic basis of F1 hybrid sterility manifested by pachytene arrest. It is tempting to speculate that a fast-evolving subset of the noncoding genomic sequence important for chromosome pairing and synapsis may be the culprit.
Collapse
|