TY  - JOUR
AB  - There has been a growing interest in the role of the subchondral bone and its resident osteoclasts in the progression of osteoarthritis (OA). A recent genome-wide association study (GWAS) identified 100 independent association signals for OA traits. Most of these signals are led by noncoding variants, suggesting that genetic regulatory effects may drive many of the associations. We have generated a unique human osteoclast-like cell-specific expression quantitative trait locus (eQTL) resource for studying the genetics of bone disease. Considering the potential role of osteoclasts in the pathogenesis of OA, we performed an integrative analysis of this dataset with the recently published OA GWAS results. Summary data-based Mendelian randomization (SMR) and colocalization analyses identified 38 genes with a potential role in OA, including some that have been implicated in Mendelian diseases with joint/skeletal abnormalities, such as BICRA, EIF6, CHST3, and FBN2. Several OA GWAS signals demonstrated colocalization with more than one eQTL peak, including at 19q13.32 (hip OA with BCAM, PRKD2, and BICRA eQTL). We also identified a number of eQTL signals colocalizing with more than one OA trait, including FAM53A, GCAT, HMGN1, MGAT4A, RRP7BP, and TRIOBP. An SMR analysis identified 3 loci with evidence of pleiotropic effects on OA-risk and gene expression: LINC01481, CPNE1, and EIF6. Both CPNE1 and EIF6 are located at 20q11.22, a locus harboring 2 other strong OA candidate genes, GDF5 and UQCC1, suggesting the presence of an OA-risk gene cluster. In summary, we have used our osteoclast-specific eQTL dataset to identify genes potentially involved with the pathogenesis of OA.
AU  - Mullin, B.H.*
AU  - Zhu, K.*
AU  - Brown, S.J.*
AU  - Mullin, S.*
AU  - Dudbridge, F.*
AU  - Pavlos, N.J.*
AU  - Richards, J.B.*
AU  - Grundberg, E.*
AU  - Bell, J.T.*
AU  - Zeggini, E.
AU  - Walsh, J.P.*
AU  - Xu, J.*
AU  - Wilson, S.G.*
C1  - 67999
C2  - 54477
CY  - 9650 Rockville Ave, Bethesda, Md 20814 Usa
TI  - Leveraging osteoclast genetic regulatory data to identify genes with a role in osteoarthritis.
JO  - Genetics
VL  - 225
IS  - 2
PB  - Genetics Society America
PY  - 2023
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - In humans, most genome-wide association studies have been conducted using data from Caucasians and many of the reported findings have not replicated in other populations. This lack of replication may be due to statistical issues (small sample sizes or confounding) or perhaps more fundamentally to differences in the genetic architecture of traits between ethnically diverse subpopulations. What aspects of the genetic architecture of traits vary between subpopulations and how can this be quantified? We consider studying effect heterogeneity using Bayesian random effect interaction models. The proposed methodology can be applied using shrinkage and variable selection methods, and produces useful information about effect heterogeneity in the form of whole-genome summaries (e.g., the proportions of variance of a complex trait explained by a set of SNPs and the average correlation of effects) as well as SNP-specific attributes. Using simulations, we show that the proposed methodology yields (nearly) unbiased estimates when the sample size is not too small relative to the number of SNPs used. Subsequently, we used the methodology for the analyses of four complex human traits (standing height, high-density lipoprotein, low-density lipoprotein, and serum urate levels) in European-Americans (EAs) and African-Americans (AAs). The estimated correlations of effects between the two subpopulations were well below unity for all the traits, ranging from 0.73 to 0.50. The extent of effect heterogeneity varied between traits and SNP sets. Height showed less differences in SNP effects between AAs and EAs whereas HDL, a trait highly influenced by lifestyle, exhibited a greater extent of effect heterogeneity. For all the traits, we observed substantial variability in effect heterogeneity across SNPs, suggesting that effect heterogeneity varies between regions of the genome.
AU  - Veturi, Y.*
AU  - de Los Campos, G.*
AU  - Yi, N.*
AU  - Huang, W.*
AU  - Vazquez, A.I.*
AU  - Kühnel, B.
C1  - 55568
C2  - 46399
CY  - 9650 Rockville Ave, Bethesda, Md 20814 Usa
SP  - 1395–1407
TI  - Modeling heterogeneity in the genetic architecture of ethnically diverse groups using random effect interaction models.
JO  - Genetics
VL  - 211
IS  - 3
PB  - Genetics Society America
PY  - 2019
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - In this work, we present a comprehensive analysis of the H3K36 histone methyltransferases Set2 and Ash1 in the filamentous ascomycete Fusarium fujikuroi In Saccharomyces cerevisiae, one single methyltransferase, Set2, confers all H3K36 methylation, while there are two members of the Set2 family in filamentous fungi, and even more H3K36 methyltransferases in higher eukaryotes. Whereas the yeast Set2 homolog has been analyzed in fungi previously, the second member of the Set2 family, designated Ash1, has not been described for any filamentous fungus. Western blot and ChIP-Seq analyses confirmed that F. fujikuroi Set2 and Ash1 are H3K36-specific histone methyltransferases that deposit H3K36me3 at specific loci: Set2 is most likely responsible for H3K36 methylation of euchromatic regions of the genome, while Ash1 methylates H3K36 at the subtelomeric regions (facultative heterochromatin) of all chromosomes including the accessory chromosome XII. Our data indicate that H3K36me3 cannot be considered a hallmark of euchromatin in F. fujikuroi, and likely also other filamentous fungi, making them different to what is known about nuclear characteristics in yeast and higher eukaryotes. We suggest that the H3K36 methylation mark exerts specific functions when deposited at euchromatic or subtelomeric regions by Set2 or Ash1, respectively. We found an enhanced level of H3K27me3, an increased instability of subtelomeric regions and losses of the accessory chromosome XII over time in Δash1 mutants, indicating an involvement of Ash1 in DNA repair processes. Further phenotypic analyses revealed a role of H3K36 methylation in vegetative growth, sporulation, secondary metabolite biosynthesis and virulence in F. fujikuroi.
AU  - Janevska, S.*
AU  - Baumann, L.*
AU  - Sieber, C.M.K.*
AU  - Münsterkötter, M.
AU  - Ulrich, J.*
AU  - Kämper, J.*
AU  - Güldener, U.*
AU  - Tudzynski, B.*
C1  - 52366
C2  - 43934
SP  - 153-171
TI  - Elucidation of the two H3K36me3 histone methyltransferases Set2 and Ash1 in Fusarium fujikuroi unravels their different chromosomal targets and a major impact of Ash1 on genome stability.
JO  - Genetics
VL  - 208
IS  - 1
PY  - 2018
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - Testing for the existence of variance components in linear mixed models is a fundamental task in many applicative fields. In statistical genetics, the score test has recently become instrumental in the task of testing an association between a set of genetic markers and a phenotype. With few markers, this amounts to set-based variance component tests, which attempt to increase power in association studies by aggregating weak individual effects. When the entire genome is considered, it allows testing for the heritability of a phenotype, defined as the proportion of phenotypic variance explained by genetics. In the popular score-based Sequence Kernel Association Test (SKAT) method, the assumed distribution of the score test statistic is uncalibrated in small samples, with a correction being computationally expensive. This may cause severe inflation or deflation of p-values, even when the null hypothesis is true. Here, we characterize the conditions under which this discrepancy holds, and show it may occur also in large real datasets, such as a dataset from the Wellcome Trust Case Control Consortium 2 (n=13,950) study, and in particular when the individuals in the sample are unrelated. In these cases the SKAT approximation tends to be highly over-conservative and therefore underpowered. To address this limitation, we suggest an efficient method to calculate exact p-values for the score test in the case of a single variance component and a continuous response vector, which can speed up the analysis by orders of magnitude. Our results enable fast and accurate application of the score test in heritability and in set-based association tests. Our method is available in http://github.com/cozygene/RL-SKAT.
AU  - Schweiger, R.*
AU  - Weissbrod, O.*
AU  - Rahmani, E.*
AU  - Müller-Nurasyid, M.
AU  - Kunze, S.
AU  - Gieger, C.
AU  - Waldenberger, M.
AU  - Rosset, S.*
AU  - Halperin, E.*
C1  - 52113
C2  - 43724
CY  - Bethesda
SP  - 1275-1283
TI  - RL-SKAT: An exact and efficient score Test for heritability and set tests.
JO  - Genetics
VL  - 207
IS  - 4
PB  - Genetics Society America
PY  - 2017
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - Extensive work has been dedicated to study mechanisms of microRNA-mediated gene regulation. However, the transcriptional regulation of microRNAs themselves is far less well understood, due to difficulties determining the transcription start sites of transient primary transcripts. This challenge can be addressed using expression quantitative trait loci (eQTLs) whose regulatory effects represent a natural source of perturbation of cis-regulatory elements. Here we used previously published cis-microRNA-eQTL data for the human GM12878 cell line, promoter predictions and other functional annotations to determine the relationship between functional elements and microRNA regulation. We built a logistic regression model which classifies microRNA/SNP pairs into eQTLs or non-eQTLs with 85% accuracy and shows microRNA-eQTL enrichment for microRNA precursors, promoters, enhancers and transcription factor binding sites and depletion for repressed chromatin. Interestingly, although there is a large overlap between microRNA-eQTLs and mRNA-eQTLs of host genes, 74% of these shared eQTLs affect microRNA and host expression independently. Considering microRNA-only eQTLs we find a significant enrichment for intronic promoters, validating the existence of alternative promoters for intragenic microRNAs. Finally, in line with the GM12878 cell line being derived from B-cells, we find genome-wide association (GWA) variants associated to blood-related traits more likely to be miRNA-eQTLs than random GWA and non-GWA variants, aiding the interpretation of GWA results.
AU  - Budach, S.*
AU  - Heinig, M.
AU  - Marsico, A.*
C1  - 48738
C2  - 41286
CY  - Bethesda
SP  - 1629-1640
TI  - Principles of microRNA regulation revealed through modeling microRNA expression quantitative trait loci.
JO  - Genetics
VL  - 203
IS  - 4
PB  - Genetics Society America
PY  - 2016
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - Inflorescences of the tribe Triticeae, which includes wheat (Triticum sp. L.) and barley (Hordeum vulgare L.) are characterized by sessile spikelets directly borne on the main axis, thus forming a branchless spike. "Compositum-Barley" and tetraploid "Miracle-Wheat" (T. turgidum convar. compositum (L.f.) Filat.) display non-canonical spike-branching in which spikelets are replaced by lateral branch-like structures resembling small-sized secondary spikes. As a result of this branch formation "Miracle-Wheat" produces significantly more grains per spike, leading to higher spike yield. In this study, we first isolated the gene underlying spike-branching in "Compositum-Barley", i.e. compositum 2 (com2). Moreover, we found that COM2 is orthologous to the branched head(t) (bh(t)) locus regulating spike-branching in tetraploid "Miracle-Wheat". Both genes possess orthologs with similar functions in maize BRANCHED SILKLESS 1 (BD1) and rice FRIZZY PANICLE/BRANCHED FLORETLESS 1 (FZP/BFL1) encoding AP2/ERF transcription factors. Sequence analysis of the bh(t) locus in a collection of mutant and wild type tetraploid wheat accessions revealed that a single amino acid substitution in the DNA-binding domain gave rise to the domestication of "Miracle-Wheat". mRNA in situ hybridization, microarray experiments, and independent qRT-PCR validation analyses revealed that the branch repression pathway in barley is governed through the spike architecture gene Six-rowed spike 4 regulating COM2 expression, while HvIDS1 (barley ortholog of maize INDETERMINATE SPIKELET 1) is a putative down-stream target of COM2. These findings presented here provide new insights into the genetic basis of spike architecture in Triticeae, and have disclosed new targets for genetic manipulations aiming at boosting wheat's yield potential.
AU  - Poursarebani, N.*
AU  - Seidensticker, T.*
AU  - Koppolu, R.*
AU  - Trautewig, C.*
AU  - Gawroński, P.*
AU  - Bini, F.*
AU  - Govind, G.*
AU  - Rutten, T.*
AU  - Sakuma, S.*
AU  - Tagiri, A.*
AU  - Wolde, G.M.*
AU  - Youssef, H.M.*
AU  - Battal, A.*
AU  - Ciannamea, S.*
AU  - Fusca, T.*
AU  - Youssef, H.M.*
AU  - Nussbaumer, T.
AU  - Pozzi, C.*
AU  - Börner, A.*
AU  - Lundqvist, U.*
AU  - Komatsuda, T.*
AU  - Salvi, S.*
AU  - Tuberosa, R.*
AU  - Uauy, C.*
AU  - Sreenivasulu, N.*
AU  - Rossini, L.*
AU  - Schnurbusch, T.*
C1  - 46305
C2  - 37487
SP  - 155-165
TI  - The genetic basis of composite spike form in barley and "Miracle-Wheat".
JO  - Genetics
VL  - 201
IS  - 1
PY  - 2015
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - Genome-wide association studies (GWAS) are widely applied to analyze the genetic effects on phenotypes. With the availability of high-throughput technologies for metabolite measurements, GWAS successfully identified loci that affect metabolite concentrations and underlying pathways. In most GWAS the effect of each SNP on the phenotype is assumed to be additive. Other genetic models such as recessive, dominant or over-dominant were considered only by very few studies. In contrast to that, there are theories that emphasize the relevance of non-additive effects as a consequence of physiological mechanisms. This might be especially important for metabolites as these intermediate phenotypes are closer to the underlying pathways than other traits or diseases. In this study we analyzed systematically non-additive effects on a large panel of serum metabolites and all possible ratios (22,801 in total) in a population based study (KORA F4, N=1,785). We applied four different 1 df tests corresponding to an additive, dominant, recessive and over-dominant trait model and additionally a genotypic model with 2 df that allows a more general consideration of genetic effects. Twenty three loci were found to be genome-wide significantly associated (Bonferroni corrected p-value ≤2.19x10(-12)) with at least one metabolite or ratio. For five of them we show the evidence of non-additive effects. We replicated seventeen loci including three loci with non-additive effects in an independent study (TwinsUK, N=846). In conclusion, we found that most genetic effects on metabolite concentrations and ratios were indeed additive, which verifies the practice of using the additive model for analyzing SNP effects on metabolites.
AU  - Tsepilov, Y.A.
AU  - Shin, S.Y.*
AU  - Soranzo, N.*
AU  - Spector, T.D.*
AU  - Prehn, C.
AU  - Adamski, J.
AU  - Kastenmüller, G.
AU  - Wang-Sattler, R.
AU  - Strauch, K.
AU  - Gieger, C.
AU  - Aulchenko, Y.S.*
AU  - Ried, J.S.
C1  - 44874
C2  - 37068
CY  - Bethesda
SP  - 707-718
TI  - Non-additive effects of genes in human metabolomics.
JO  - Genetics
VL  - 200
IS  - 3
PB  - Genetics Society America
PY  - 2015
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - Genome duplication is thought to be central to the evolution of morphological complexity, and some polyploids enjoy a variety of capabilities that transgress those of their diploid progenitors. Comparison of genomic sequences from several tetraploid (AtDt) Gossypium species and genotypes with putative diploid A and D genome progenitor species revealed that unidirectional DNA exchanges between homeologous chromosomes were the predominant mechanism responsible for allelic differences between the Gossypium tetraploids and their diploid progenitors. HeGCE gradually subsided, declining to rates similar to random mutation during radiation of the polyploid into multiple clades and species. Despite occurring in a common nucleus, preservation of HeGCE is asymmetric in the two tetraploid subgenomes. At to Dt conversion is far more abundant than the reciprocal, is enriched in heterochromatin, is highly correlated with GC content and transposon distribution, and may silence abundant A-genome-derived retrotransposons. Dt to At conversion is abundant in euchromatin and genes, frequently reversing losses of gene function. The long-standing observation that the non-spinnable-fibered D genome contributes to the superior yield and quality of tetraploid cotton fibers may be explained by accelerated Dt to At conversion during cotton domestication and improvement, increasing dosage of alleles from the spinnable-fibered A genome. HeGCE may provide an alternative to (rare) reciprocal DNA exchanges between chromosomes in heterochromatin, where genes have ~5x greater abundance of Dt to At conversion than does adjacent intergenic DNA. Spanning exon-to-gene-sized regions, HeGCE is a natural non-invasive means of gene transfer with the precision of transformation, potentially important in genetic improvement of many crop plants.
AU  - Guo, H.*
AU  - Wang, X.*
AU  - Gundlach, H.
AU  - Mayer, K.F.X.
AU  - Peterson, D.G.*
AU  - Scheffler, B.E.*
AU  - Chee, P.W.*
AU  - Paterson, A.H.*
C1  - 31659
C2  - 34620
CY  - Bethesda
SP  - 1153-1163
TI  - Extensive and biased intergenomic non-reciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (cotton).
JO  - Genetics
VL  - 197
IS  - 4
PB  - Genetics Society America
PY  - 2014
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - Targeted mouse mutants are instrumental for the analysis of gene function in health and disease. We recently provided proof-of-principle for the fast-track mutagenesis of the mouse genome, using transcription activator-like effector nucleases (TALENs) in one-cell embryos. Here we report a routine procedure for the efficient production of disease-related knockin and knockout mutants, using improved TALEN mRNAs that include a plasmid-coded poly(A) tail (TALEN-95A), circumventing the problematic in vitro polyadenylation step. To knock out the C9orf72 gene as a model of frontotemporal lobar degeneration, TALEN-95A mutagenesis induced sequence deletions in 41% of pups derived from microinjected embryos. Using TALENs together with mutagenic oligodeoxynucleotides, we introduced amyotrophic lateral sclerosis patient-derived missense mutations in the fused in sarcoma (Fus) gene at a rate of 6.8%. For the simple identification of TALEN-induced mutants and their progeny we validate high-resolution melt analysis (HRMA) of PCR products as a sensitive and universal genotyping tool. Furthermore, HRMA of off-target sites in mutant founder mice revealed no evidence for undesired TALEN-mediated processing of related genomic sequences. The combination of TALEN-95A mRNAs for enhanced mutagenesis and of HRMA for simplified genotyping enables the accelerated, routine production of new mouse models for the study of genetic disease mechanisms.
AU  - Panda, S.
AU  - Wefers, B.
AU  - Ortiz, O.
AU  - Floß, T.
AU  - Schmid, B.*
AU  - Haass, C.*
AU  - Wurst, W.
AU  - Kühn, R.
C1  - 28239
C2  - 33023
SP  - 703-713
TI  - Highly efficient targeted mutagenesis in mice using TALENs.
JO  - Genetics
VL  - 195
IS  - 3
PB  - Genetics Soc. Amer.
PY  - 2013
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - The increasing evidence of fetal developmental effects on postnatal life, the Still unknown fetal growth mechanisms impairing offspring generated by somatic nuclear transfer techniques, and the impact on stillbirth and dystocia in conventional reproduction have generated increasing attention toward mammalian fetal growth. We identified a highly significant quantitative trait locus (QTL) affecting fetal growth on bovine chromosome 6 in a specific resource Population, which was set tip by consistent rise of embryo transfer and foster mothers and, thus, enabled dissection of fetal-specific genetic components of fetal growth. Merging our data with results from other cattle populations differing in historical and geographical origin and with comparative data from human whole-genome association mapping suggests that a nonsynonymous polymorphism in the non-SMC condensin I complex, Subunit G (NCAPG) gene, NCAPG c.1326T>G, is the potential cause of tire identified QTL resulting in divergent bovine fetal growth. NCAPG gene expression data in fetal placentomes with different NCAPG c.1326T>G genotypes, which are in line with recent results about differential NCAPG expression in placentomes from studies on assisted reproduction techniques, indicate that the NCAPG locus may give valuable information on the specific mechanisms regulating fetal growth in mammals.
AU  - Eberlein, A.*
AU  - Takasuga, A.*
AU  - Setoguchi, K.*
AU  - Pfuhl, R.*
AU  - Flisikowski, K.*
AU  - Fries, R.*
AU  - Klopp, N.
AU  - Fürbass, R.*
AU  - Weikard, R.*
AU  - Kühn, C.*
C1  - 2222
C2  - 27131
SP  - 951-964
TI  - Dissection of genetic factors modulating fetal growth in cattle indicates a substantial role of the non-SMC condensin I complex, subunit G (NCAPG) gene.
JO  - Genetics
VL  - 183
IS  - 3
PB  - Genetics Society of America
PY  - 2009
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - In the mouse pax6 function is critical in a dose-dependent manner for proper eye development. pax6 Configuous gene deletions were shown to be homozygous lethal at an early embryonic stage. Heterozygotes express belly spotting and extreme microphthalmia. The eye phenotype is more Severe than in heterozygous pax6, intragenic null mutants, raising the possibility that deletions are functionally different. from intragenic null mutations or that a region distinct from Pax6 included in the deletions affects eye phenotype. we recovered and identified the exact regions deleted in three new Pax6 deletions. All are homozygous lethal at an early embryonic stage. None express belly spotting. One expresses extreme microphthalmia and two express the milder eye phenotype similar to Pax6 intragenic null mutants. Analysis of Pax6 expression levels and the major isoforms excluded the hypothesis that the deletions expressing extreme microphthalmia are directly due to the action of pax6 and functionally different from intragenic null mutations. A region distinct from Pax6 containing eight genes was identified for bell), spotting. A second region containing one gene (Rcn I) was identified for the extreme microphthalmia phenotype. Rcn1 is a Ca+2 -binding protein, resident in the endoplasmic reticulum, participates in the secretory pathway and expressed in the eye. Our results suggest that deletion of Rcn1 directly or indirectly contributes to the eye phenotype in Pax6 contiguous gene deletions.
AU  - Favor, J.
AU  - Bradley, A.*
AU  - Conte, N.*
AU  - Janik, D.*
AU  - Pretsch, W.
AU  - Reitmeir, P.
AU  - Rosemann, M.
AU  - Schmahl, W.*
AU  - Wienberg, J.*
AU  - Zaus, I.
C1  - 1865
C2  - 26436
CY  - Baltimore
SP  - 1077-1088
TI  - Analysis of Pax6 contiguous gene deletions in the mouse, Mus musculus, identifies regions distinct from Pax6 responsible for extreme small-eye and belly-spotting phenotypes.
JO  - Genetics
VL  - 182
IS  - 4
PB  - Genetics
PY  - 2009
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - In this study we extend the mouse Pax6 mutant allelic series to include a homozygous and hemizygous viable hypomorph allele. The Pax6(132-14Neu) allele is a Phe272Ile missense mutation within the third helix of the homeodomain. The mutant Pax6 homeodomain shows greatly reduced binding activity to the P3 DNA binding target. Glucagon-promoter activation by the entire mutant Pax6 product of a reporter gene driven by the G1 paired and homeodomain DNA binding target was slightly increased. We constructed mutant Pax6 genotypes such that Pax6 activity ranged between 100 and 0% and show that the extent of eye development is progressively reduced as Pax6 activity decreased. Two apparent thresholds identify three groups in which the extent of eye development abruptly shifted from complete eye at the highest levels of Pax6 to a rudimentary eye at intermediate levels of Pax6 to very early termination of eye development at the lowest levels of Pax6. Of the two Pax6-positive regions that participate in eye development, the surface ectoderm, which develops into the lens vesicle and the cornea, is more sensitive to reduced levels of Pax6 activity than the optic vesicle, which develops into the inner and outer retinal layers.
AU  - Favor, J.
AU  - Gloeckner, C.J.
AU  - Neuhäuser-Klaus, A.
AU  - Pretsch, W.
AU  - Sandulache, R.
AU  - Saule, S.*
AU  - Zaus, I.
C1  - 1555
C2  - 25472
SP  - 1345-1355
TI  - Relationship of Pax6 activity levels to the extent of eye development in the mouse, Mus musculus.
JO  - Genetics
VL  - 179
IS  - 3
PB  - GSA
PY  - 2008
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - The basement membrane is important for proper tissue development, stability, and physiology. Major components of the basement membrane include laminins and type IV collagens. The type IV procollagens Col4a1 and Col4a2 form the heterotrimer [alpha1(IV)]2[alpha2(IV)], which is ubiquitously expressed in basement membranes during early developmental stages. We present the genetic, molecular, and phenotypic characterization of nine Col4a1 and three Col4a2 missense mutations recovered in random mutagenesis experiments in the mouse. Heterozygous carriers express defects in the eye, the brain, kidney function, vascular stability, and viability. Homozygotes do not survive beyond the second trimester. Ten mutations result in amino acid substitutions at nine conserved Gly sites within the collagenous domain, one mutation is in the carboxy-terminal noncollagenous domain, and one mutation is in the signal peptide sequence and is predicted to disrupt the signal peptide cleavage site. Patients with COL4A2 mutations have still not been identified. We suggest that the spontaneous intraorbital hemorrhages observed in the mouse are a clinically relevant phenotype with a relatively high predictive value to identify carriers of COL4A1 or COL4A2 mutations.
AU  - Favor, J.
AU  - Gloeckner, C.J.
AU  - Janik, D.*
AU  - Klempt, M.*
AU  - Neuhäuser-Klaus, A.
AU  - Pretsch, W.
AU  - Schmahl, W.*
AU  - Quintanilla-Fend, L.
C1  - 4853
C2  - 24687
SP  - 725-736
TI  - Type IV procollagen missense mutations associated with defects of the eye, vascular stability, the brain, kidney function and embryonic or postnatal viability in the mouse, Mus musculus: An extension of the Col₄a₁allelic series and the identification of the first twoCol₄a₂ mutant alleles.
JO  - Genetics
VL  - 175
IS  - 2
PB  - HighWire Press
PY  - 2007
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - The Notch signaling pathway is an evolutionarily conserved transduction pathway involved in embryonic patterning and regulation of cell fates during development. Recent studies have demonstrated that this pathway is integral to a complex system of interactions, which are also involved in distinct human diseases. Delta1 is one of the known ligands of the Notch receptors. Mice homozygous for a loss-of-function allele of the Delta1 gene Dll1lacZ/lacZ die during embryonic development. Here, we present the results of two phenotype-driven modifier screens. Heterozygous Dll1lacZ knockout animals were crossed with ENU-mutagenized mice and screened for dysmorphological, clinical chemical, and immunological variants that are dependent on the Delta1 loss-of-function allele. First, we show that mutagenized heterozygous Dll1lacZ offspring have reduced body weight and altered specific clinical chemical parameters, including changes in metabolites and electrolytes relevant for kidney function. In our mutagenesis screen we have successfully generated 35 new mutant lines. Of major interest are 7 mutant lines that exhibit a Dll1lacZ/+-dependent phenotype. These mutant mouse lines provide excellent in vivo tools for studying the role of Notch signaling in kidney and liver function, cholesterol and iron metabolism, cell-fate decisions, and during maturation of T cells in the immune system.
AU  - Rubio-Aliaga, I.
AU  - Soewarto, D.
AU  - Wagner, S.
AU  - Klaften, M.
AU  - Fuchs, H.
AU  - Kalaydjiev, S.
AU  - Busch, D.H.
AU  - Klempt, M.
AU  - Rathkolb, B.
AU  - Wolf, E.
AU  - Abe, K.
AU  - Zeiser, S.
AU  - Przemeck, G.K.H.
AU  - Beckers, J.
AU  - Hrabě de Angelis, M.
C1  - 2364
C2  - 24344
SP  - 1451-1463
TI  - A genetic screen for modifiers of the delta1-dependent notch signaling function in the mouse.
JO  - Genetics
VL  - 175
IS  - 3
PB  - HighWire Press
PY  - 2007
SN  - 0016-6731
ER  - 

TY  - JOUR
AU  - Binladen, J.*
AU  - Wiuf, C.*
AU  - Gilbert, M.T.P.*
AU  - Bunce, M.*
AU  - Barnett, R.*
AU  - Larson, G.*
AU  - Greenwood, A.D.
AU  - Haile, J.*
AU  - Ho, S.Y.W.*
AU  - Hanson, A.J.*
AU  - Willerslev, E.*
C1  - 1705
C2  - 23506
SP  - 733-741
TI  - Assessing the fidelity of ancient DNA sequences amplified from nuclear genes.
JO  - Genetics
VL  - 172
PY  - 2006
SN  - 0016-6731
ER  - 

TY  - JOUR
AU  - Noguchi, Y.*
AU  - Kurima, K.*
AU  - Makishima, T.*
AU  - Hrabě de Angelis, M.
AU  - Fuchs, H.
AU  - Frolenkov, G.*
AU  - Kitamura, K.*
AU  - Griffith, A.J.*
C1  - 4827
C2  - 23856
SP  - 2111-2119
TI  - Multiple quantitative trait loci modify cochlear hair cell degeneration in the Beethoven (tmc1Bth) mouse model of progressive hearing loss DFNA36.
JO  - Genetics
VL  - 173
PY  - 2006
SN  - 0016-6731
ER  - 

TY  - JOUR
AU  - Graw, J.
AU  - Pretsch, W.
AU  - Löster, J.
C1  - 22318
C2  - 21138
SP  - 1035-1041
TI  - Mutation in Intron 6 of the Hamster Mitf Gene Leads to Skipping of the Subsequent Exon and Creates a Novel Animal Model for the Human Waardenburg Syndrome Type II.
JO  - Genetics
VL  - 164
PY  - 2003
SN  - 0016-6731
ER  - 

TY  - JOUR
AU  - Kokubu, C.
AU  - Wilm, B.
AU  - Kokubu, T.
AU  - Wahl, M.
AU  - Rodrigo, I.
AU  - Sakai, N.
AU  - Santagati, F.
AU  - Hayashizaki, Y.*
AU  - Suzuki, M.*
AU  - Yamamura, K.*
AU  - Abe, K.*
AU  - Imai, K.
C1  - 10163
C2  - 21185
SP  - 299-307
TI  - Undulated short-tail Deletion Mutation in the Mouse Ablates Pax1 and Leads to Ectopic Activation of Neighboring Nkx2-2 in Domains That Normally Express Pax1.
JO  - Genetics
VL  - 165
PY  - 2003
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - We previously reported close physical linkage between Pax9 and Nkx2-9 in the human, mouse, and pufferfish (Fugu rubripes) genomes. In this study, we analyzed cis-regulatory elements of the two genes by comparative sequencing in the three species and by transgenesis in the mouse. We identified two regions including conserved noncoding sequences that possessed specific enhancer activities for expression of Pax9 in the medial nasal process and of Nkx2-9 in the ventral neural tube. Remarkably, the latter contained the consensus Gli-binding motif. Interestingly, the identified Pax9 cis-regulatory sequences were located in an intron of the neighboring gene Slc25a21. Close examination of an extended genomic interval around Pax9 revealed the presence of strong synteny conservation in the human, mouse, and Fugu genomes. We propose such an intersecting organization of cis-regulatory sequences in multigenic regions as a possible mechanism that maintains evolutionary conserved synteny.
AU  - Santagati, F.
AU  - Abe, K.*
AU  - Schmidt, V.*
AU  - Schmitt-John, T.*
AU  - Suzuki, M.*
AU  - Yamamura, K.*
AU  - Imai, K.
C1  - 33183
C2  - 21184
SP  - 235-242
TI  - Identification of Cis-regulatory elements in the mouse Pax9/Nkx2-9 genomic region: Implication for evolutionary conserved synteny.
JO  - Genetics
VL  - 165
IS  - 1
PY  - 2003
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - A novel ENU-induced mutation in the mouse leading to a nuclear and cortical opacity of the eye lens (ENU418) was mapped to proximal chromosome 1 by a genome-wide mapping approach. It suggests that the cluster of gamma-crystallin encoding genes (Cryg) and the betaA2-crystallin encoding gene Cryba2 are excellent candidate genes. An A --> G exchange in the middle of intron 1 of the Cryge gene was found as the only alteration cosegregating with the cataractous phenotype. The mutation was confirmed by the presence of a novel restriction site for ApaI in the corresponding genomic DNA fragment. The mutation represses splicing of intron 1; the additional 92 by in the corresponding cDNA leads to a frameshift and the expression of a novel hybrid protein containing 3 amino acids of the gammaE-crystallin at the N terminus, but 153 novel amino acids. The Cryge(ENU418) protein has a calculated molecular mass of similar to15.6 kD and an alkaline isoelectric point (pH 10.1) and is predicted to have two hydrophobic domains. Western blot analysis using a polyclonal antibody against the hydrophilic C-terminal part of the Cryge(ENU418)-specific protein demonstrated its stable expression in the cataractous lenses; it was not found in the wild types. Histological analysis of the cataractous lenses indicated that the expression of the new protein disrupts the cellular structure of the eye lens.
AU  - Graw, J.
AU  - Neuhäuser-Klaus, A.
AU  - Löster, J.
AU  - Klopp, N.
AU  - Favor, J.
C1  - 10161
C2  - 20413
SP  - 1633-1640
TI  - Ethylnitrosourea-Induced Base Pair Substitution Affects Splicing of the Mouse gammaE-Crystallin Encoding Gene Leading to the Expression of a Hybrid Protein and to a Cataract.
JO  - Genetics
VL  - 161
PB  - GSA
PY  - 2002
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - Phenotype-based mutagenesis experiments will increase the mouse mutant resource, generating mutations at previously unmarked loci as well as extending the allelic series at known loci. Mapping, molecular characterization, and phenotypic analysis of nine independent Pax6 mutations of the mouse recovered in mutagenesis experiments is presented. Seven mutations result in premature termination of translation and all express phenotypes characteristic of null alleles, suggesting that Pax6 function requires all domains to be intact. Of major interest is the identification of two possible hypomorph mutations: Heterozygotes express less severe phenotypes and homozygotes develop rudimentary eyes and nasal processes and survive up to 36 hr after birth. Pax6(4Neu) results in an amino acid substitution within the third helix of the homeodomain. Three-dimensional modeling indicates that the amino acid substitution interrupts the homeodomain recognition alpha-helix, which is critical for DNA binding. Whereas cooperative dimer binding of the mutant homeodomain to a paired-class DNA target sequence was eliminated, weak monomer binding was observed. Thus, a residual function of the mutated homeodomain may explain the hypomorphic nature of the Pax6(4Neu) allele. Pax6(7Neu) is a base pair substitution in the Kozak sequence and results in a reduced level of Pax6 translation product. The Pax6(4Neu) and Pax6(7Neu) alleles may be very useful for gene-dosage studies.
AU  - Favor, J.
AU  - Peters, H.
AU  - Hermann, T.
AU  - Schmahl, W.*
AU  - Chatterjee, B.
AU  - Neuhäuser, K.A.*
AU  - Sandulache, R.
C1  - 21987
C2  - 20516
SP  - 1689-1700
TI  - Molecular characterization of Pax62Neu through Pax610Neu: An extension of the Pax6 allelic series and the identification of two possible hypomorph alleles in the mouse Mus musculus.
JO  - Genetics
VL  - 159
PY  - 2001
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - A novel ENU-induced mutation in the mouse leading to a nuclear and zonular opacity of the eye lens (Aey1) was mapped to chromosome 1 between the markers D1Mit303 and D1Mit332. On the basis of the chromosomal position, the gamma -crystallin encoding gene cluster (Cryg) and the beta A2-crystallin encoding gene Cryba2 were tested as candidate genes. An A --> T mutation destroys the start codon of the Cryge gene in the mutants; this mutation was confirmed by the absence of a restriction site for NcoI in the corresponding genomic fragment of homozygous mutants. The next in-frame start codon is 129 bp downstream; this predicted truncated gammaE-crystallin consists of 131 amino acids, resulting in a molecular mass of 14 kD. However, another open reading frame was observed just 19 bp do downstream of the regular Cryge start codon, resulting in a protein of 119 amino acids and a calculated molecular weight of 13 kD. Western blot analysis using polyclonal antibodies against gamma -crystallins or the novel Aeyl-specific protein demonstrated the specific expression of the Aeyl protein in the cataractous lenses only; the truncated form of the gammaE-crystallin could not be detected. Therefore, it is concluded that the novel protein destroys the sensitive cellular structure of the eye lens.
AU  - Graw, J.
AU  - Klopp, N.
AU  - Löster, J.
AU  - Soewarto, D.
AU  - Fuchs, H.
AU  - Becker-Follmann, J.*
AU  - Reis, A.*
AU  - Wolf, E.*
AU  - Balling, R.
AU  - Hrabě de Angelis, M.
C1  - 10160
C2  - 19843
SP  - 1313-1320
TI  - Ethylnitrosourea-induced mutation in mice leads to the expression of a novel protein in the eye and to dominant cataracts.
JO  - Genetics
VL  - 157 
IS  - 3
PB  - Genetics Society of America
PY  - 2001
SN  - 0016-6731
ER  - 

TY  - JOUR
AU  - Pretsch, W.
AU  - Merkle, S.
AU  - Favor, J.
AU  - Werner, T.
C1  - 20309
C2  - 13498
SP  - 161-170
TI  - A Mutation Affecting the Lactate Dehydrogenase Locus Ldh-1 in the Mouse. - II. Mechanism of the LDH-A Deficiency Associated with Hemolytic Anemia.
JO  - Genetics
VL  - 135
PY  - 1993
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - A procarbazine hydrochloride-induced mutation at the Ldh-1 structural locus encoding the A subunit of lactate dehydrogenase (LDH) was used to study the molecular and metabolic basis of severe hemolytic anemia due to LDH-A deficiency in the mouse. The mutant allele designated Ldh-1(a-m/Neu) codes for an enzyme that as homotetramer differs from the wild-type enzyme by a marked instability, acidic shift of the pH profile, increased K(m) for pyruvate and altered inhibition by high concentrations of this substrate. Except for the latter, all these altered properties of the mutant protein contribute to the diminished LDH activity in heterozygous and homozygous mutant individuals. Impaired energy metabolism of erythrocytes indicated by a relatively low ATP concentration is suggested to result in cell death at the end of the reticulocyte stage leading to the expression of hemolytic anemia with extreme reticulocytosis and hyperbilirubinemia. Despite the severe anemia, affected homozygous mutants exhibit approximately normal body weight and do not show noticeable impairment of viability or fertility. To date no such condition is observed in man. This discrepancy is likely due to the fact that in human erythrocytes both LDH-A and LDH-B subunits are expressed such that homozygotes for a LDH-A or LDH-B deficiency would not result in a comparably extreme LDH activity deficiency.
AU  - Pretsch, W.
AU  - Merkle, S.
AU  - Favor, J.
AU  - Werner, T.
C1  - 40328
C2  - 0
SP  - 161-170
TI  - A mutation affecting the lactate dehydrogenase locus Ldh-1 in the mouse. II. Mechanism of the LDH-A deficiency associated with hemolytic anemia.
JO  - Genetics
VL  - 135
IS  - 1
PY  - 1993
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - Two ethylnitrosourea-induced heterozygous mouse mutants with approximately 58 and 50% of wild-type lactate dehydrogenase (LDH) activity and a γ-ray- induced heterozygous mutant with 50% of wild-type LDH activity in blood, liver and spleen (expressing predominantly the Ldh-1 gene) were recovered in mutagenicity experiments following spermatogonial treatment. Physiological and genetic studies revealed no indications for differences in fertility as well as hematological or other physiological traits between heterozygotes of each mutant line and wild types. This suggests that neither the mutations in the heterozygous state per se nor the resulting approximate 42 to 50% LDH deficiency affect metabolism and fitness. Physicochemical and immunological studies clearly demonstrated that the two mutations with 50% deficiency in heterozygotes result from null alleles of the Ldh-1 structural locus, generating neither enzyme activity nor immunological cross-reacting material. In contrast, the heterozygous mutant with approximately 58% of normal blood LDH activity was shown to be due to a Ldh-1 allele creating protein subunits, which in random assortment with wild-type subunits in vivo exhibit a reduced specific activity and further alterations of kinetic and physicochemical characteristics. All the mutations in the homozygous state were found to be lethal at an early postimplantation stage of embryonic development, probably due to a block of glycolysis with the corresponding loss of the main source of metabolic energy during this ontogenetic stage. The distinct physiological consequences of the total absence of a functioning LDH-A subunit in mice and humans are discussed. The key role regarding the presence as well as developmental pattern of isozymes in estimating the impact of enzyme-activity mutations on the phenotype of an organism is emphasized.
AU  - Merkle, S.
AU  - Favor, J.
AU  - Graw, J.
AU  - Hornhardt, S.V.
AU  - Pretsch, W.
C1  - 40494
C2  - 38539
SP  - 413-421
TI  - Hereditary lactate dehydrogenase A-subunit deficiency as cause of early postimplantation death of homozygotes in Mus musculus.
JO  - Genetics
VL  - 131
IS  - 2
PY  - 1992
SN  - 0016-6731
ER  - 

TY  - JOUR
AB  - Four heterozygous triosephosphate isomerase (TPI) mutants the approximately 50% reduced activity in blood compared to wild type were detected in offspring of 1-ethyl-1-nitrosourea treated male mice Breeding experiments displayed an autosomal, dominant mode of inheritance for the mutations. All mutations were found to be homozygous lethal at an early postimplantation stage of embryonic development, probably due to a total lack of TPI activity and consequently to the inability to utilize glucose as a source of metabolic energy. Although activity alteration was also found in liver, lung, kidney, spleen, heart, brain and muscle the TPI deficiency in heterozygotes has no influence on the following physiological traits: hematological parameters, plasma glucose, glucose consumption of blood cells, body weight and organo-somatic indices of liver, spleen, heart, kidney and lung. Biochemical investigations of TPI in the four mutant lines indicated no difference of physicochemical properties compared to the wild type. Results from immunoinactivation assays indicate that the decrease of enzyme activity corresponds to a decrease in the level of an immunologically active moiety. It is suggested that the mutations have affected the Tpi-1 structural locus and resulted in alleles which produce no detectable enzyme activity and no immunologically cross-reacting material. The study furthermore suggests one functional TPI gene per haploid genome in the erythrocyte and seven other tested organs of the mouse.
AU  - Merkle, S.
AU  - Pretsch, W.
C1  - 42087
C2  - 38194
SP  - 837-844
TI  - Characterization of triosephosphate isomerase mutants with reduced enzyme activity in Mus musculus.
JO  - Genetics
VL  - 123
IS  - 4
PY  - 1989
SN  - 0016-6731
ER  - 

TY  - JOUR
AU  - Eckardt-Schupp, F.
AU  - Siede, W.
AU  - Game, J.C.
C1  - 41254
C2  - 36603
SP  - 83-90
TI  - The RAD24 (= RS1) gene product of Saccharomyces cerevisiae participates in two different pathways of DNA repair.
JO  - Genetics
VL  - 115
IS  - 1
PY  - 1987
SN  - 0016-6731
ER  -