H. Bartenschlager

A distinctive gene expression fingerprint in mentally retarded male patients reflects disease-causing defects in the histone demethylase KDM5C

BackgroundMental retardation is a genetically heterogeneous disorder, as more than 90 genes for this disorder has been found on the X chromosome alone. In addition the majority of patients are non-syndromic in that they do not present with clinically recognisable features. This makes it difficult to determine the molecular cause of this disorder on the basis of the phenotype alone. Mutations in KDM5C (previously named SMCX or JARID1C), a gene that encodes a transcriptional regulator with histone demethylase activity specific for dimethylated and trimethylated H3K4, are a comparatively frequent cause of non-syndromic X-linked mental retardation (NS-XLMR). Specific transcriptional targets of KDM5C, however, are still unknown and the effects of KDM5C deficiency on gene expression have not yet been investigated.ResultsBy whole-mount in situ hybridisation we showed that the mouse homologue of KDM5C is expressed in multiple tissues during mouse development.We present the results of gene expression profiling performed on lymphoblastoid cell lines as well as blood from patients with mutations in KDM5C. Using whole genome expression arrays and quantitative reverse transcriptase polymerase chain reaction (QRT-PCR) experiments, we identified several genes, including CMKOR1, KDM5B and KIAA0469 that were consistently deregulated in both tissues.ConclusionsOur findings shed light on the pathological mechanisms underlying mental retardation and have implications for future diagnostics of this heterogeneous disorder.

Rapid and precise genotyping of porcine microsatellites.

Microsatellites are useful markers for genetic mapping and linkage analysis because they are highly polymorphic, abundant in genomes and relatively easily scored with polymerase chain reaction (PCR). A rapid genotyping system for microsatellites was developed, which included multiplex PCRs, multiple use of Hydrolink™ gels, automated fluorescent detection of fragments on an A.L.F. DNA sequencer, automatic assignment of alleles to each locus and verification of genotypes with a self‐developed computer program “Fragtest”. Eight multiplex PCRs have been developed to genotype 29 microsatellites for genetic and quantitative trait loci (QTL) mapping on pig chromosomes 6, 7, 12 and 13. Three to six microsatellites could be amplified in one multiplex PCR. Each multiplex reaction required only different concentrations of each pair of primers and a low concentration of dNTP (100 μM). A dNTP concentration of 100 μM proved to be optimal for the coamplification of microsatellites under the concentration of 1.5 mM MgCl2. Using four internal size standards added in each sample, the 5% Hydrolink gel could subsequently be used up to five times (total running time of 500 min) on the A.L.F. automated sequencer without significant loss of resolution and precision of fragment length analysis. Automatic assignment of alleles on each locus using “Fragtest” significantly increased the efficiency and precision of the genotyping. This system is thus a rapid, cheap, and highly discriminating genotyping system.

Genome-wide mapping of quantitative trait loci for fatness, fat cell characteristics and fat metabolism in three porcine F2 crosses.

BackgroundQTL affecting fat deposition related performance traits have been considered in several studies and mapped on numerous porcine chromosomes. However, activity of specific enzymes, protein content and cell structure in fat tissue probably depend on a smaller number of genes than traits related to fat content in carcass. Thus, in this work traits related to metabolic and cytological features of back fat tissue and fat related performance traits were investigated in a genome-wide QTL analysis. QTL similarities and differences were examined between three F2 crosses, and between male and female animals.MethodsA total of 966 F2 animals originating from crosses between Meishan (M), Pietrain (P) and European wild boar (W) were analysed for traits related to fat performance (11), enzymatic activity (9) and number and volume of fat cells (20). Per cross, 216 (M × P), 169 (W × P) and 195 (W × M) genome-wide distributed marker loci were genotyped. QTL mapping was performed separately for each cross in steps of 1 cM and steps were reduced when the distance between loci was shorter. The additive and dominant components of QTL positions were detected stepwise by using a multiple position model.ResultsA total of 147 genome-wide significant QTL (76 at P < 0.05 and 71 at P < 0.01) were detected for the three crosses. Most of the QTL were identified on SSC1 (between 76-78 and 87-90 cM), SSC7 (predominantly in the MHC region) and SSCX (in the vicinity of the gene CAPN6). Additional genome-wide significant QTL were found on SSC8, 12, 13, 14, 16, and 18. In many cases, the QTL are mainly additive and differ between F2 crosses. Many of the QTL profiles possess multiple peaks especially in regions with a high marker density. Sex specific analyses, performed for example on SSC6, SSC7 and SSCX, show that for some traits the positions differ between male and female animals. For the selected traits, the additive and dominant components that were analysed for QTL positions on different chromosomes, explain in combination up to 23% of the total trait variance.ConclusionsOur results reveal specific and partly new QTL positions across genetically diverse pig crosses. For some of the traits associated with specific enzymes, protein content and cell structure in fat tissue, it is the first time that they are included in a QTL analysis. They provide large-scale information to analyse causative genes and useful data for the pig industry.

Association between polymorphism in the FTO gene and growth and carcass traits in pig crosses

BackgroundIndependent studies have shown that several single nucleotide polymorphisms (SNP) in the human FTO (fat mass and obesity associated) gene are associated with obesity. SNP have also been identified in the pig FTO gene, among which some are associated with selected fat-deposition traits in F2 crosses and commercial populations. In this study, using both commercial pig populations and an experimental Meishan × Pietrain F2 population, we have investigated the association between one FTO SNP and several growth and carcass traits. Association analyses were performed with the FTO polymorphism either alone or in combination with polymorphisms in flanking loci.MethodsSNP (FM244720:g.400C>G) in exon 3 of porcine FTO was genotyped by PCR-RFLP and tested for associations with some growth, carcass and fat-related traits. Proportions of genetic variance of four pig chromosome 6 genes (FTO, RYR1, LIPE and TGFB1) on selected traits were evaluated using single- and multi-locus models.ResultsLinkage analysis placed FTO on the p arm of pig chromosome 6, approximately 22 cM from RYR1. In the commercial populations, allele C of the FTO SNP was significantly associated with back fat depth and allele G with muscling traits. In the Meishan × Pietrain F2 pigs, heterozygotes with allele C from the Pietrain sows and allele G from the Meishan boar were more significantly associated with fat-related traits compared to homozygotes with allele G from the Pietrain and allele G from the Meishan breed. In single- and multi-locus models, genes RYR1, TGFB1 and FTO showed high associations. The contribution in genetic variance from the polymorphism in the FTO gene was highest for back fat depth, meat area on the musculus longissimus lumborum et thoracis tissues and metabolite glucose-6-phosphate dehydrogenase.ConclusionsOur results show that in pig, FTO influences back fat depth in the commercial populations, while in the Meishan × Pietrain F2 pigs with a CG genotype, heterosis occurs for several fat-related traits.

OLA-DRB1 microsatellite variants are associated with ovine growth and reproduction traits

The DRB1 intron 2 (GT)n (GA)m microsatellite was genotyped in experimental flocks of seven Merinoland rams and 249 ewes as well as their offspring (381 lambs) from consecutive lambings. A total of 16 DRB1 alleles were detected, ranging between 353 and 857 bp. In comparison with carriers of other alleles, the ewes carrying the predominant 411 bp allele had higher values of all the recorded fertility traits. For ewes carrying the 394 and 857 bp alleles, the birth weight of lambs was about 400 g higher as compared to the residual group of ewes. The observed associations could be due to differences in disease resistance, cell recognition or tissue differentiation between carriers of various MHC haplotypes which can in turn affect individual fertility and growth performance.

Calcium-release-channel genotypes in several pig populations-associations with halothane and CK reactions.

SUMMARY DNA of 2985 pigs from different sources were tested for variants of the calcium-release-channel (CRC) gene. Frequencies of the C allele, associated with stress resistance, were 0.0 for Belgian Landrace, 0.01 for Pietrain, 0.54 for German Landrace, 0.86 for German-Landrace sowline, 0.91 for Schwäbisch-Hällisches swine, 0.95 for European Wildboar, and 0.99 for Large White. All 50 Meishan individuals tested were C/C. In the two German Landrace populations more individuals with heterozygous genotypes were observed than had been expected. These results may indicate balanced allele frequencies caused by overdominance-type selection associated with meat quantity. 6.0 % of the halothane-positive pigs were C/C or C/T, and 3.6 % of the halothane-negative animals were T/T. As some of the pig groups were crossbreeds from extremely divergent sources (e.g. European Wildboar, Meishan, Pietrain), special gene effects may have influenced the phenotypic reaction to halothane. The average CK values vary between pigs of different CRC genotypes, e.g., the CK(80) values 2.64 ± 0.023, 2.83 ± 0.027, and 3.19 ± 0.036 were measured for individuals of C/C, C/T and T/T, respectively. For the German Landrace, culling according to a threshold of CK(80) ≥ 2.70 would eliminate 29.1 % of C/C, 63.0 % of C/T, and 90.4 % of T/T individuals. Whether CK-based selection may be used for further selection in populations with a fixed CRC C allele is discussed. ZUSAMMENFASSUNG: Genotypen des Kalziumfreisetzungskanals in verschiedenen Schweinepopulationen-Zusammenhänge mit Halothan- und CK-Reaktionen Auf die Genvariante des Calciumfreisetzungskanales (CRC), die als Ursache für das Maligne Hyperthermic Syndrom beim Schwein angesehen wird, wurden 2985 Schweine verschiedener Herkünfte untersucht. Dabei ergaben sich folgende Allelfrequenzen für das C-Allel, welches in Zusammenhang mit der Streßresistenz steht: 0,0 bei der Belgischen Landrasse, 0,01 bei der Rasse Pietrain, 0,54 bei der Deutschen Landrasse, 0,86 bei der Deutschen Landrasse Sauenlinie, 0,91 beim Schwäbisch-Hällischen Schwein, 0,95 beim europäischen Wildschweine und 0,99 bei der Rasse Large White. Alle 50 untersuchten Meishan-Tiere zeigten den Genotyp C/C. Für die beiden untersuchten Populationen der Deutschen Landrasse wurden mehr heterozygote Genotypen beobachtet als erwartet waren. Dieses Ergebnis mag auf balancierte Allelfrequenzen hinweisen, die auf Überdominanzeffekten beruhen können. Insgesamt 6 % der im Halothan-Test als positiv eingestuften Schweine zeigten die Genotypen C/C bzw. C/T, während 3,6 % der Nicht-Reagenten den Genotyp T/T aufwiesen. Da manche der untersuchten Schweine Kreuzungsprodukte genetisch extrem unterschiedlicher Herkünfte sind (europäisches Wildschein, Meishan und Pietrain), wird vermutet, daß bestimmte Geneffekte die phänotypische Reaktion auf Halothan ausgelöst haben. Der CK(80) Wert unterschied sich bei den Schweinen unterschiedlicher CRC-Genotypen: 2,64 ± 0,023, 2,83 ± 0,027 und 3,19 ± 0,036 für die Tiere mit den Genotypen C/C, C/T bzw. T/T. Bei einer Selektionsschranke für den CK(80) von ≥ 2,70 müßten 29,1 % der C/C-, 63,0 % der C/T- aber lediglich 90,4 % der T/T-Tiere ausgeschlossen werden. Es wird diskutiert, wie eine Selektion nach dem CK-Wert in Populationen, in denen das C-Allel fixiert ist, wirkt.

Porcine NAMPT gene: search for polymorphism, mapping and association studies

NAMPT encodes an enzyme catalysing the rate-limiting step in NAD biosynthesis. The extracellular form of the enzyme is known as adipokine visfatin. We detected SNP AM999341:g.669T>C (referred to as 669T>C) in intron 9 and SNP FN392209:g.358A>G (referred to as 358A>G) in the promoter of the gene. RH mapping linked the gene to microsatellite SW944. Linkage analysis placed the gene on the current USDA – USMARC linkage map at position 92 cM on SSC9. Association analyses were performed in a wild boar × Meishan F2 family (W × M), with 45 traits recorded (growth and fattening, fat deposition, muscling, meat quality, stress resistance and other traits), and in a commercial Landrace × Chinese-European (LCE) synthetic population with records for 15 traits (growth, fat deposition, muscling, intramuscular fat, meat colour and backfat fatty acid content). In the W × M, SNP 669T>C was associated with muscling, fat deposition, growth and fattening, meat quality and other traits and in the LCE with muscling, meat quality and backfat fatty acid composition. In the W × M, SNP 358A>G was associated with muscling, fat deposition, growth and other traits. After correction for multiple testing, the NAMPT haplotypes were associated in the W × M with, in descending order, muscling (q = 0.0056), growth (q = 0.0056), fat deposition (q = 0.0109), fat-to-meat ratio (q = 0.0135), cooling losses (q = 0.0568) and longissimus pHU (q = 0.0695). The SNPs are hypothesized to be in linkage disequilibrium with a causative mutation affecting energy metabolism as a whole rather than fat metabolism alone.

Association analyses of porcine SERPINE1 reveal sex-specific effects on muscling, growth, fat accretion and meat quality

The serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 (SERPINE1) gene encodes plasminogen activator inhibitor type 1 (PAI), which is the major physiological inhibitor of tissue-type and urokinase-type plasminogen activators and plays a role in obesity and insulin resistance in women but not in men. We detected SNP FN396538:g.566G>A in intron 3 and a non-synonymous substitution NM_213910:c.612A>G in exon 3 (p.Ile159Val) and mapped the gene to position 8.4 cM on the linkage map of chromosome 3. Association analyses were conducted on the 12th-15th generation of the Meishan × Large White (MLW) cross (n = 565), with records for weight at the end of test, lifetime daily gain, test time daily gain, loin depth and backfat depth, as well as on a European wild boar × Meishan (W × M) F(2) population (n = 333) with 47 traits recorded for carcass composition and meat quality. Analyses performed across the entire MLW population or in the male animals did not show any trait significantly associated with the loci studied. In female animals, both SNPs were associated with loin depth at nominal P < 0.05 with adjusted P values equal to 0.051 (g.566) and 0.057 (c.612). Differences between homozygotes were up to 0.65 SD. In the entire W × M population and female animals, SERPINE1 was significantly associated at adjusted P < 0.05 in descending order with muscling, growth and fat accretion and in male animals with meat quality (R-value). In the studied populations, allele effects were in opposite directions, which implies that the SNPs are markers that are in linkage disequilibrium with a causative mutation.

Polymorphism screening and mapping of nine meat performance-related genes in the pig

Supporting information Additional supporting information may be found in the online version of this article. Figure S1 Pedigree of German Spitz MRD cases. Table S1 BEST1 SNP genotypes observed in eight German Spitz Klein cases and in five-first degree relatives of cases, and in the parents of a German Spitz Mittle case. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer-reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors.

Partial genomic structure, mutation analysis and mapping of the porcine inhibitor of DNA binding genes ID1, ID2, ID3 and ID4

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