Genetic variation modulates susceptibility to aberrant DNA hypomethylation and imprint deregulation in naïve pluripotent stem cells.

Naïve pluripotent stem cells (nPSC) frequently undergo pathological and not readily reversible loss of DNA methylation marks at imprinted gene loci. This abnormality poses a hurdle for using pluripotent cell lines in biomedical applications and underscores the need to identify the causes of imprint instability in these cells. We show that nPSCs from inbred mouse strains exhibit pronounced strain-specific susceptibility to locus-specific deregulation of imprinting marks during reprogramming to pluripotency and upon culture with MAP kinase inhibitors, a common approach to maintain naïve pluripotency. Analysis of genetically highly diverse nPSCs from the Diversity Outbred (DO) stock confirms that genetic variation is a major determinant of epigenome stability in pluripotent cells. We leverage the variable DNA hypomethylation in DO lines to identify several trans-acting quantitative trait loci (QTLs) that determine epigenome stability at either specific target loci or genome-wide. Candidate factors encoded by two multi-target QTLs on chromosomes 4 and 17 suggest specific transcriptional regulators that contribute to DNA methylation maintenance in nPSCs. We propose that genetic variants represent candidate biomarkers to identify pluripotent cell lines with desirable properties and might serve as entry points for the targeted engineering of nPSCs with stable epigenomes. Highlights: Naïve pluripotent stem cells from distinct inbred mouse strains exhibit variable DNA methylation levels at imprinted gene loci.The vulnerability of pluripotent stem cells to loss of genomic imprinting caused by MAP kinase inhibition strongly differs between inbred mouse strains.Genetically diverse pluripotent stem cell lines from Diversity Outbred mouse stock allow the identification of quantitative trait loci controlling DNA methylation stability.Genetic variants may serve as biomarkers to identify naïve pluripotent stem cell lines that are epigenetically stable in specific culture conditions.

Glutathione S-transferase copy number variation alters lung gene expression.

The glutathione S-transferase (GST) enzymes catalyse the conjugation of xenobiotics to glutathione. Based on reports that inherited copy number variations (CNVs) modulate some GST gene expression levels, and that the small airway epithelium (SAE) and alveolar macrophages (AMs) are involved early in the pathogenesis of smoking-induced lung disease, we asked: do germline CNVs modulate GST expression levels in SAE and AMs? Microarrays were used to survey GST gene expression and determine CNVs genotypes in SAE and AMs obtained by bronchoscopy from current smokers and nonsmokers. 26% of subjects were null for both GSTM1 alleles, with reduced GSTM1 mRNA levels seen in both SAE and AMs. 30% of subjects had homozygous deletions of GSTT1, with reduced mRNA levels in both tissues. Interestingly, GSTT2B exhibited homozygous deletion in the blood of 27% of subjects and was not expressed in SAE in the remainder of subjects, but was expressed in AMs of heterozygotes and wild-type subjects, proportionate to genotype. These data show a germline CNV-mediated linear relationship of genotype with expression level, suggesting minimal compensation of gene expression levels in heterozygotes, consistent with GST polymorphisms playing a role in the risk of smoking-associated, xenobiotic-induced lung disease.

Brain-derived neurotrophic factor as a model system for examining gene by environment interactions across development.

There has been a dramatic rise in gene x environment studies of human behavior over the past decade that have moved the field beyond simple nature versus nurture debates. These studies offer promise in accounting for more variability in behavioral and biological phenotypes than studies that focus on genetic or experiential factors alone. They also provide clues into mechanisms of modifying genetic risk or resilience in neurodevelopmental disorders. Yet, it is rare that these studies consider how these interactions change over the course of development. In this paper, we describe research that focuses on the impact of a polymorphism in a brain-derived neurotrophic factor (BDNF) gene, known to be involved in learning and development. Specifically we present findings that assess the effects of genotypic and environmental loadings on neuroanatomic and behavioral phenotypes across development. The findings illustrate the use of a genetic mouse model that mimics the human polymorphism, to constrain the interpretation of gene-environment interactions across development in humans.

Penicillium implicatum causes a destructive rot of pomegranate fruits.

In this study Penicillium implicatum Biourge was found to be the cause of a destructive rot of stored pomegranate (Punica granata) fruits. This species has not previously been reported to cause disease of the fruit. The ability of the strain to decay pomegranates as well as some varieties of apples (Jonagold, Selena and Vanda) under laboratory conditions after inoculation with conidia into the subcutaneous layer of healthy fruits was demonstrated. The fungus was also found on mouldy stamens of pomegranates.

Is the genotype-phenotype map modular? A statistical approach using mouse quantitative trait loci data.

Various theories about the evolution of complex characters make predictions about the statistical distribution of genetic effects on phenotypic characters, also called the genotype-phenotype map. With the advent of QTL technology, data about these distributions are becoming available. In this article, we propose simple tests for the prediction that functionally integrated characters have a modular genotype-phenotype map. The test is applied to QTL data on the mouse mandible. The results provide statistical support for the notion that the ascending ramus region of the mandible is modularized. A data set comprising the effects of QTL on a more extensive portion of the phenotype is required to determine if the alveolar region of the mandible is also modularized.

Hox cluster genomics in the horn shark, Heterodontus francisci.

Reconstructing the evolutionary history of Hox cluster origins will lead to insights into the developmental and evolutionary significance of Hox gene clusters in vertebrate phylogeny and to their role in the origins of various vertebrate body plans. We have isolated two Hox clusters from the horn shark, Heterodontus francisci. These have been sequenced and compared with one another and with other chordate Hox clusters. The results show that one of the horn shark clusters (HoxM) is orthologous to the mammalian HoxA cluster and shows a structural similarity to the amphioxus cluster, whereas the other shark cluster (HoxN) is orthologous to the mammalian HoxD cluster based on cluster organization and a comparison with noncoding and Hox gene-coding sequences. The persistence of an identifiable HoxA cluster over an 800-million-year divergence time demonstrates that the Hox gene clusters are highly integrated and structured genetic entities. The data presented herein identify many noncoding sequence motifs conserved over 800 million years that may function as genetic control motifs essential to the developmental process.

Modeling the evolution of genetic architecture: A continuum of alleles model with pairwise AxA epistasis.

A continuum of alleles model with pair-wise AxA epistasis is proposed and its transmission genetic, and variational properties are analysed. The basic idea is that genes control the values of underlying variables, which affect the genotypic value of phenotypic characters proportional to a "scaling factor". Epistasis is the influence of one gene on the average effect of another gene. In this model, epistasis is introduced as a mutational effect of one gene on the scaling factors of another gene. In accordance with empirical results, the model assumes that the average direct effect of mutations is zero, as is the average epistatic effect. The model predicts that, on average, a mutation at one locus increases the expected mutational variance of mutations at another interacting locus. The increase in mutational variance is predicted to be equal to the variance of the pair-wise epistatic effects. This result is consistent with the observation that mutant phenotypes tend to be more variable than the wildtype phenotype. Another generic result of this model is that the frequency of canalizing mutations can at most be equal to the frequency of de-canalizing mutations. Furthermore, it is predicted that the mutational variance of a character increases at least linearly with the size of the character; hence this model is scale variant. In the case of two characters it is shown that the dimensionality of the locus-specific mutational effect distribution is invariant, i.e. the rank of the mutational covariance matrix M is invariant. While in additive models the mutational covariance matrix is always and entirely invariant, the invariance in the case of epistatic models is unexpected. Epistatic interactions can change the magnitude of the mutational (co)variances at a locus and can thus influence the structure of the mutational covariance matrix. However, in the present model the dimensionality of the mutational effect distribution remains the same. A consequence of this result is that, in this model, the genetic architecture of a set of characters is always evolvable i.e. no hard constraints can evolve.