Distributions of single nucleotide polymorphisms in differential chromosome segments of congenic resistant strains that define minor histocompatibility antigens

Minor histocompatibility antigens (MiHAs) stimulate the rejection of allografts when donors and recipients are matched at the major histocompatibility complex (MHC). The majority of identified autosomal MiHAs were generated by non-synonymous (NS) substitutions that alter MHC class I-binding peptides. The mosaic distribution of single nucleotide polymorphisms (SNPs) that distinguish inbred mouse strains led us to hypothesize that MiHA genes defined by congenic strains on C57BL/6 and C57BL/10 backgrounds map to chromosomal regions with relatively high numbers of NS SNPs that distinguish C57 strains from other common inbred strains. To test this hypothesis, we mapped the ends of differential chromosome segments of congenic strains, which define 12 MiHAs, relative to microsatellites and SNPs. The lengths of differential segments ranged from 9.7 to 105.9 Mbp in congenic strains where no attempts were made to select recombinants within these segments. There was no apparent correlation between differential segment length and number of backcrosses, suggesting that factors other than the number of opportunities for recombination affected the differential segment lengths in these congenics. These differential segments included higher numbers of NS SNPs that distinguish C57BL/6J from A/J, DBA/2J, and 129S1/J than would be predicted if these SNPs were uniformly distributed along the chromosomes. The most extreme case was the H8 congenic that included 74% of the SNPs on chromosome 14 within its 9.7-11.1 Mbp differential segment. These results point toward a direct relationship between the level of genomic divergence, as indicated by numbers of NS SNPs, and numbers of MiHAs that collectively determine the magnitude of allograft rejection.     

Factors involved in ethanol narcosis: analysis in mice of three inbred strains

We have studied the effects of genotype and dose on the time of onset of ethanol-induced sleep, as measured by fall time, and on the length of sleep. We have also investigated the relationships among genotype, dose and the blood ethanol levels at time of fall and time of awakening in three inbred mouse strains (C57BL/6J, DBA/2J and BALB/cJ). The sleep-time dose response curves are linear for the dose range tested in all three strains. There was no significant linear correlation between dose and blood ethanol level at awakening in any of the three strains. Between-strain comparisons showed significant differences in rate of ethanol clearance from the blood, and differences in tissue sensitivity to ethanol among the strains were demonstrated. Our data suggest that the major factor influencing sleep time is blood alcohol clearance, reflecting differences in alcohol metabolic rates.Between-strain comparisons of fall time showed significant differences, over the dosage range tested, in nervous system tissue sensitivity (as inferred from blood alcohol level at time of fall) between the BALB/cJ strain and the C57BL/6J and DBA/2J strains. Differences between C57BL/6J and DBA/2J strains were significant only at the lowest dose tested. The rank-ordering of the strains with respect to tissue sensitivity to ethanol is identical for all three tissue sensitivity measures obtained in these experiments.     

Integrative strategies to identify candidate genes in rodent models of human alcoholism.

The search for genes underlying alcohol-related behaviours in rodent models of human alcoholism has been ongoing for many years with only limited success. Recently, new strategies that integrate several of the traditional approaches have provided new insights into the molecular mechanisms underlying ethanol's actions in the brain. We have used alcohol-preferring C57BL/6J (B6) and alcohol-avoiding DBA/2J (D2) genetic strains of mice in an integrative strategy combining high-throughput gene expression screening, genetic segregation analysis, and mapping to previously published quantitative trait loci to uncover candidate genes for the ethanol-preference phenotype. In our study, 2 genes, retinaldehyde binding protein 1 (Rlbp1) and syntaxin 12 (Stx12), were found to be strong candidates for ethanol preference. Such experimental approaches have the power and the potential to greatly speed up the laborious process of identifying candidate genes for the animal models of human alcoholism.     

Liver cytosolic aldehyde dehydrogenases from "alcohol-drinking" and "alcohol-avoiding" mouse strains: purification and molecular properties

Liver cytosolic aldehyde dehydrogenases (AHD-2) have been isolated in a highly purified state from "alcohol-drinking" (C57BL/6J) and "alcohol-avoiding" (DBA/2J) strains of mice. The purified enzymes were resolved into three major and one minor form of activity by isoelectric focusing (IEF) techniques and showed similar zymogram patterns. The enzymes had identical subunit sizes on SDS-polyacrylamide gels: 53,000. Gel exclusion chromatography, using Ultrogel AcA34, indicated that the enzymes were dimers. The enzymes exhibited biphasic kinetic characteristics and were readily distinguished from each other. The purified forms of AHD-2 from C57BL/6J and DBA/2J mice exhibited two apparent Km values in each case: 10 microM/100 microM and 30 microM/330 microM respectively. AHD-2 exhibited a broad pH optimum in the range 7.0-9.0 and was very sensitive towards disulphuram inhibition, with 50% inhibition occurring at 0.17 microM. The kinetic results support proposals that AHD-2 may be the primary enzyme for oxidizing acetaldehyde during ethanol oxidation in vivo.     

Identification of novel mouse genes conferring posthypoxic pauses

Although central to the susceptibility of adult diseases characterized by abnormal rhythmogenesis, characterizing the genes involved is a challenge. We took advantage of the C57BL/6J (B6) trait of hypoxia-induced periodic breathing and its absence in the C57BL/6J-Chr 1(A/J)/NaJ chromosome substitution strain to test the feasibility of gene discovery for this abnormality. Beginning with a genetic and phenotypic analysis of an intercross study between these strains, we discovered three quantitative trait loci (QTLs) on mouse chromosome 1, with phenotypic effects. Fine-mapping reduced the genomic intervals and gene content, and the introgression of one QTL region back onto the C57BL/6J-Chr 1(A/J)/NaJ restored the trait. mRNA expression of non-synonymous genes in the introgressed region in the medulla and pons found evidence for differential expression of three genes, the highest of which was apolipoprotein A2, a lipase regulator; the apo a2 peptide fragment (THEQLTPLVR), highly expressed in the liver, was expressed in low amounts in the medulla but did not correlate with trait expression. This work directly demonstrates the impact of elements on mouse chromosome 1 in respiratory rhythmogenesis.     

Identification of 129S6/SvEvTac-specific polymorphisms on mouse chromosome 11

Polymorphisms such as single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) can be associated with phenotypic traits and be used as markers for disease diagnosis. Identification of these genetic variations within laboratory mice is crucial to improve our understanding of the genetic background of the mice used for research. As part of a positional cloning project, we sequenced six genes (Mettl16, Evi2a, Psmd11, Cct6d, Rffl, and Ap2b1) within a 6.8-Mb domain of mmu chr 11 in the C57BL/6J and 129S6/SvEvTac inbred strains. Although 129S6/SvEvTac is widely used in the mouse community, there is very little current (or projected future) sequence information available for this strain. We identified 6 Indels and 21 novel SNPs and confirmed genotype information for 114 additional SNPs in these 6 genes. Mettl16 and Ap2b1 contained the largest numbers of variants between the C57BL/6J and 129S6/SvEvTac strains. In addition, we found five new SNPs between 129S6/SvEvTac and 129S1/SvImJ within the Ap2b1 locus. Although we did not detect differences between C57BL/6J and 129S6/SvEvTac within Evi2a, this locus contains a relatively high SNP density compared with the surrounding sequence. Our study highlights the genetic differences among three inbred mouse strains (C57BL/6J, 129S6/SvEvTac, and 129S1/SvImJ) and provides valuable sequence information that can be used to track alleles in genomics-based studies.     

Antidepressant-like responses to lithium in genetically diverse mouse strains

A mood stabilizing and antidepressant response to lithium is only found in a subgroup of patients with bipolar disorder and depression. Identifying strains of mice that manifest differential behavioral responses to lithium may assist in the identification of genomic and other biologic factors that play a role in lithium responsiveness. Mouse strains were tested in the forced swim test (FST), tail suspension test (TST) and open-field test after acute and chronic systemic and intracerebroventricular (ICV) lithium treatments. Serum and brain lithium levels were measured. Three (129S6/SvEvTac, C3H/HeNHsd and C57BL/6J) of the eight inbred strains tested, and one (CD-1) of the three outbred strains, showed an antidepressant-like response in the FST following acute systemic administration of lithium. The three responsive inbred strains, as well as the DBA/2J strain, displayed antidepressant-like responses to lithium in the FST after chronic administration of lithium. However, in the TST, acute lithium resulted in an antidepressant-like effect only in C3H/HeNHsd mice. Only C57BL/6J and DBA/2J showed an antidepressant-like response to lithium in the TST after chronic administration. ICV lithium administration resulted in a similar response profile in BALB/cJ (non-responsive) and C57BL/6J (responsive) strains. Serum and brain lithium concentrations showed that behavioral results were not because of differential pharmacokinetics of lithium in individual strains, suggesting that genetic factors likely regulate these behavioral responses to lithium. Our results indicate that antidepressant-like responses to lithium in tests of antidepressant efficacy varies among genetically diverse mouse strains. These results will assist in identifying genomic factors associated with lithium responsiveness and the mechanisms of lithium action.     

A strain-specific alteration of proteomic expression in mouse liver fructose 1,6-bisphosphatase isoforms by alcohol

To study alcohol-related metabolism across inbred mouse strains, liver tissues from C57BL/6J (B6, an alcohol-preferring mouse) and DBA/2J (D2, an alcohol-avoiding strain) mice were analyzed for proteomic expression patterns over time after a single-dose of alcohol (1.5 g/kg ingestion). Despite no significant difference in the elimination rate of blood ethanol, two-dimensional electrophoresis gel images of liver proteins showed that proteins in B6 mice exhibited faster response and more quantitative (spot numbers) and qualitative (spot densities) changes than in D2 mice. Among the differentially expressed metabolic enzymes, four variants (alpha, beta, gamma and delta) of fructose 1,6-bisphosphatase (FBPase), a key regulatory gluconeogenic enzyme, showed remarkable changes in expression with time across the strains. The degree of spot alteration in alpha- and gamma-variants of FBPase in B6 mice was much higher than in D2 mice, while the beta- and delta-forms were not changed as much. Mass spectrometry (MS) analysis showed that the 1714.9 +/- 1 mass peak from the alpha- and gamma-variants of FBPase was much stronger than that of the beta- and delta-variants in both strains regardless of spot density. This MS peak contains 2-ANHAPFETDISTLTR-16, located at the N-terminal of FBPase, where the N-terminal alanine was found to be trimethylated. Thus, we propose this N-terminal fragment as a potential site for enzyme modification in response to ethanol, allowing for differences in two-dimensional gel spot intensity of variants of FBPase in the two mouse strains.     

Cannabinoid-serotonin interactions in alcohol-preferring vs. alcohol-avoiding mice

Because cannabinoid and serotonin (5-HT) systems have been proposed to play an important role in drug craving, we investigated whether cannabinoid 1 (CB1) and 5-HT(1A) receptor ligands could affect voluntary alcohol intake in two mouse strains, C57BL/6 J and DBA/2 J, with marked differences in native alcohol preference. When offered progressively (3-10% ethanol) in drinking water, in a free-choice procedure, alcohol intake was markedly lower (approximately 70%) in DBA/2 J than in C57BL/6 J mice. In DBA/2 J mice, chronic treatment with the cannabinoid receptor agonist WIN 55,212-2 increased alcohol intake. WIN 55,212-2 effect was prevented by concomitant, chronic CB1 receptor blockade by rimonabant or chronic 5-HT(1A) receptor stimulation by 8-hydroxy-2-(di-n-propylamino)-tetralin, which, on their own, did not affect alcohol intake. In C57BL/6 J mice, chronic treatment with WIN 55,212-2 had no effect but chronic CB1 receptor blockade or chronic 5-HT(1A) receptor stimulation significantly decreased alcohol intake. Parallel autoradiographic investigations showed that chronic treatment with WIN 55,212-2 significantly decreased 5-HT(1A)-mediated [35S]guanosine triphosphate-gamma-S binding in the hippocampus of both mouse strains. Conversely, chronic rimonabant increased this binding in C57BL/6 J mice. These results show that cannabinoid neurotransmission can exert a permissive control on alcohol intake, possibly through CB1-5-HT(1A) interactions. However, the differences between C57BL/6 J and DBA/2 J mice indicate that such modulations of alcohol intake are under genetic control.     

A simple pattern classification method for alcohol-responsive proteins that are differentially expressed in mouse brain

Proteomic analysis of brain tissues obtained from two inbred mice, C57BL/6J (B6, an alcohol-preferring strain) and DBA/2J (D2, an alcohol-avoiding strain), that were orally administered 1.5 g/kg ethanol, was performed to investigate alcohol-responsive proteins. To analyze relationships of alcohol-responsive protein spots between B6 and D2 mice, we have developed a simple spot classification method (SCM) for the fully matched spot data sets produced by the Melanie 4 analysis software using the paired two-dimensional (2-D) gels of two strains over time. By applying SCM, 55 protein spots that were differentially expressed in brain tissue were classified into 16 patterns as mirror images (2x8 patterns), and additionally in an ordered fashion such as 'fast turn over' and 'slow turn over' forms, depending on the frequency of repetition and rate of changed expression profile in 2-D gels over time. Searching for any interaction proteins through databases of interacting proteins using the classified data set has led to the construction of a linkage map, which reveals the interrelationship of the alcohol-responsive proteins between different species. Thus, it is suggested that the different responses for alcohol between B6 and D2 may come from differences of the response rates and interactions of different variants of the alcohol-responsive protein family.     

Examination of ethanol responsive liver and brain specific gene expression,in the mouse strains with variable ethanol preferences,using cDNA expression arrays

Strains of mice that differ in voluntary alcohol consumption (VAC) are valuable models for the identification of genes involved in the complex etiology of alcohol effects and alcoholism. These mice offer a novel approach to the identification of strain-specific ethanol responsive (SSER) genes in tissues directly involved in alcohol metabolism and preference. We assessed mRNA from the liver and brain from male mice representing C57BL/6J, BALB/c, A/J, and DBA/2J strains following ethanol treatment (chronic ethanol fed liquid diet for 14 days or acute i.p. injection at two doses; 4 g/kg or 8 g/kg), using an expression array containing 588 genes (Clontech #7741-1). The results have identified NADPH cytochrome P450 oxidoreductase, insulin-like growth factor binding protein-1, glutathione S-transferase Mu 1, and cathepsin L as ethanol responsive genes in the liver. Further, we have established that IkB-alpha and clusterin genes in the brain are ethanol responsive, but only at the lower dose of the ethanol challenge. Although a number of other genes showing subtle (<2X) differences across strains and treatment combinations were reproducible in repeated blots, they were not confirmed by still evolving independent technologies of gene specific mRNA quantitation. The results demonstrate that comparative expression studies are an efficient approach to discover interacting gene networks that underlie the etiology of complex phenotypes including response to alcohols.     

Development of SNP markers for C57BL/6N-derived mouse inbred strains

C57BL/6N inbred mice are used as the genetic background for producing knockout mice in large-scale projects worldwide; however, the genetic divergence among C57BL/6N-derived substrains has not been verified. Here, we identified novel single nucleotide polymorphisms (SNPs) specific to the C57BL/6NJ strain and selected useful SNPs for the genetic monitoring of C57BL/6N-derived substrains. Informative SNPs were selected from the public SNP database at the Wellcome Trust Sanger Institute by comparing sequence data from C57BL/6NJ and C57BL/6J mice. A total of 1,361 candidate SNPs from the SNP database could distinguish the C57BL/6NJ strain from 12 other inbred strains. We confirmed 277 C57BL/6NJ-specific SNPs including 10 nonsynonymous SNPs by direct sequencing, and selected 100 useful SNPs that cover all of the chromosomes except Y. Genotyping of 11 C57BL/6N-derived substrains at these 100 SNP loci demonstrated genetic differences among the substrains. This information will be useful for accurate genetic monitoring of mouse strains with a C57BL/6N-derived background.     

Enzyme activities and ethanol preference in mice

Alcohol dehydrogenase and aldehyde dehydrogenase, the two principal enzymes of alcohol metabolism, were assayed in the livers of the inbred mouse strains C57BL/6J and DBA/2J. Previous work has shown that animals of various C57BL substrains prefer a 10% ethanol solution to water in a two-bottle preference test, and that animals of various DBA/2 substrains avoid alcohol. In the present study, C57BL/6J mice were found to have 300% more aldehyde dehydrogenase activity than DBA/2J mice and 30% more alcohol dehydrogenase activity. The F₁ generation is intermediate to the parents in preference for the 10% alcohol solution and is also found to possess intermediate levels of alcohol and aldehyde dehydrogenase activity. These experiments suggest a systematic relationship between the behavioral trait of ethanol preference and the activity of aldehyde dehydrogenase and a similar but much less pronounced relationship with alcohol dehydrogenase.This research was supported by grant GM14547 from the National Institute of General Medical Sciences.     

A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains

Background

The mouse inbred line C57BL/6J is widely used in mouse genetics and its genome has been incorporated into many genetic reference populations. More recently large initiatives such as the International Knockout Mouse Consortium (IKMC) are using the C57BL/6N mouse strain to generate null alleles for all mouse genes. Hence both strains are now widely used in mouse genetics studies. Here we perform a comprehensive genomic and phenotypic analysis of the two strains to identify differences that may influence their underlying genetic mechanisms.

Results

We undertake genome sequence comparisons of C57BL/6J and C57BL/6N to identify SNPs, indels and structural variants, with a focus on identifying all coding variants. We annotate 34 SNPs and 2 indels that distinguish C57BL/6J and C57BL/6N coding sequences, as well as 15 structural variants that overlap a gene. In parallel we assess the comparative phenotypes of the two inbred lines utilizing the EMPReSSslim phenotyping pipeline, a broad based assessment encompassing diverse biological systems. We perform additional secondary phenotyping assessments to explore other phenotype domains and to elaborate phenotype differences identified in the primary assessment. We uncover significant phenotypic differences between the two lines, replicated across multiple centers, in a number of physiological, biochemical and behavioral systems.

Conclusions

Comparison of C57BL/6J and C57BL/6N demonstrates a range of phenotypic differences that have the potential to impact upon penetrance and expressivity of mutational effects in these strains. Moreover, the sequence variants we identify provide a set of candidate genes for the phenotypic differences observed between the two strains.     

Mouse inbred strain differences in ethanol drinking to intoxication

Recently, we described a simple procedure, Drinking in the Dark (DID), in which C57BL/6J mice self-administer ethanol to a blood ethanol concentration (BEC) above 1 mg/ml. The test consists of replacing the water with 20% ethanol in the home cage for 4 h early during the dark phase of the light/dark cycle. Three experiments were conducted to explore this high ethanol drinking model further. In experiment 1, a microanalysis of C57BL/6J behavior showed that the pattern of ethanol drinking was different from routine water intake. In experiment 2, drinking impaired performance of C57BL/6J on the accelerating rotarod and balance beam. In experiment 3, 12 inbred strains were screened to estimate genetic influences on DID and correlations with other traits. Large, reliable differences in intake and BEC were detected among the strains, with C57BL/6J showing the highest values. Strain means were positively correlated with intake and BEC in the standard (24 h) and a limited (4 h) two-bottle ethanol vs. water test, but BECs reached higher levels for DID. Strain mean correlations with other traits in the Mouse Phenome Project database supported previously reported genetic relationships of high ethanol drinking with low chronic ethanol withdrawal severity and low ethanol-conditioned taste aversion. We extend these findings by showing that the correlation estimates remain relatively unchanged even after correcting for phylogenetic relatedness among the strains, thus relaxing the assumption that the strain means are statistically independent. We discuss applications of the model for finding genes that predispose pharmacologically significant drinking in mice.     

Characterization of single nucleotide polymorphisms for a forward genetics approach using genetic crosses in C57BL/6 and BALB/c substrains of mice

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.     

Variation in Galr1 expression determines susceptibility to exocitotoxin-induced cell death in mice

Inbred strains of mice differ in their susceptibility to excitotoxin-induced cell death, but the genetic basis of individual variation in differential susceptibility is unknown. Previously, we identified a highly significant quantitative trait locus (QTL) on chromosome 18 that influenced susceptibility to kainic acid-induced cell death ( Sicd1 ). Comparison of susceptibility to seizure-induced cell death between reciprocal congenic lines for Sicd1 and parental background mice indicates that genes influencing this trait were captured in both strains. Two positional gene candidates, Galr1 and Mbp , map to 55 cM, where the Sicd1 QTL had been previously mapped. Thus, this study was undertaken to determine if Galr1 and/or Mbp could be considered as candidate genes. Genomic sequence comparison of these two functional candidate genes from the C57BL/6J (resistant at Sicd1 ) and the FVB/NJ (susceptible at Sicd1 ) strains showed no single-nucleotide polymorphisms. However, expression studies confirmed that Galr1 shows significant differential expression in the congenic and parental inbred strains. Galr1 expression was downregulated in the hippocampus of C57BL/6J mice and FVB.B6- Sicd1 congenic mice when compared with FVB/NJ or B6.FVB- Sicd1 congenic mice. A survey of Galr1 expression among other inbred strains showed a significant effect such that 'susceptible' strains showed a reduction in Galr1 expression as compared with 'resistant' strains. In contrast, no differences in Mbp expression were observed. In summary, these results suggest that differential expression of Galr1 may contribute to the differences in susceptibility to seizure-induced cell death between cell death-resistant and cell death-susceptible strains.