DNA methylation variation in Arabidopsis has a genetic basis and shows evidence of local adaptation

DNA methylation variation in Arabidopsis has a genetic basis and shows evidence of local adaptation

Manu J. Dubin, Pei Zhang, Dazhe Meng, Marie-Stanislas Remigereau, Edward J. Osborne, Francesco Paolo Casale, Phillip Drewe, André Kahles, Bjarni Vilhjálmsson, Joanna Jagoda, Selen Irez, Viktor Voronin, Qiang Song, Quan Long, Gunnar Rätsch, Oliver Stegle, Richard M. Clark, Magnus Nordborg
(Submitted on 21 Oct 2014)

Epigenome modulation in response to the environment potentially provides a mechanism for organisms to adapt, both within and between generations. However, neither the extent to which this occurs, nor the molecular mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects on DNA methylation were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association mapping revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) on the coding region of genes was not affected by growth temperature, but was instead strongly correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was correlated with elevated transcription levels for the genes affected. Genome-wide association mapping revealed that this effect was largely due to trans-acting loci, a significant fraction of which showed evidence of local adaptation. These findings constitute the first direct link between DNA methylation and adaptation to the environment, and provide a basis for further dissecting how environmentally driven and genetically determined epigenetic variation interact and influence organismal fitness.

Transcriptome Sequencing Reveals Widespread Gene-Gene and Gene-Environment Interactions

Transcriptome Sequencing Reveals Widespread Gene-Gene and Gene-Environment Interactions
Alfonso Buil, Andrew A Brown, Tuuli Lappalainen, Ana Viñuela, Matthew N Davies, Houfeng F Zheng, Brent J Richards, Daniel Glass, Kerrin S Small, Richard Durbin, Timothy D Spector, Emmanouil T Dermitzakis
doi: http://dx.doi.org/10.1101/010546

Understanding the genetic architecture of gene expression is an intermediate step to understand the genetic architecture of complex diseases. RNA-seq technologies have improved the quantification of gene expression and allow to measure allelic specific expression (ASE)1-3. ASE is hypothesized to result from the direct effect of cis regulatory variants, but a proper estimation of the causes of ASE has not been performed to date. In this study we take advantage of a sample of twins to measure the relative contribution of genetic and environmental effects on ASE and we found substantial effects of gene x gene (GxG) and gene x environment (GxE) interactions. We propose a model where ASE requires genetic variability in cis, a difference in the sequence of both alleles, but the magnitude of the ASE effect depends on trans genetic and environmental factors that interact with the cis genetic variants. We uncover large GxG and GxE effects on gene expression and likely complex phenotypes that currently remain elusive.

Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize

Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize

Jason G Wallace, Peter Bradbury, Nengyi Zhang, Yves Gibon, Mark Stitt, Edward Buckler
doi: http://dx.doi.org/10.1101/010207
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Phenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie functional variation. We present the results of combining genome-wide association analysis of 41 different phenotypes in ~5,000 inbred maize lines to analyze patterns of high-resolution genetic association among of 28.9 million single-nucleotide polymorphisms (SNPs) and ~800,000 copy-number variants (CNVs). We show that genic and intergenic regions have opposite patterns of enrichment, minor allele frequencies, and effect sizes, implying tradeoffs among the probability that a given polymorphism will have an effect, the detectable size of that effect, and its frequency in the population. We also find that genes tagged by GWAS are enriched for regulatory functions and are ~50% more likely to have a paralog than expected by chance, indicating that gene regulation and neofunctionalization are strong drivers of phenotypic variation. These results will likely apply to many other organisms, especially ones with large and complex genomes like maize.

Molecular phenotypes that are causal to complex traits can have low heritability and are expected to have small influence.

Molecular phenotypes that are causal to complex traits can have low heritability and are expected to have small influence.

Leopold Parts
doi: http://dx.doi.org/10.1101/009506

Work on genetic makeup of complex traits has led to some unexpected findings. Molecular trait heritability estimates have consistently been lower than those of common diseases, even though it is intuitively expected that the genotype signal weakens as it becomes more dissociated from DNA. Further, results from very large studies have not been sufficient to explain most of the heritable signal, and suggest hundreds if not thousands of responsible alleles. Here, I demonstrate how trait heritability depends crucially on the definition of the phenotype, and is influenced by the variability of the assay, measurement strategy, and the quantification approach used. For a phenotype downstream of many molecular traits, it is possible that its heritability is larger than for any of its upstream determinants. I also rearticulate via models and data that if a phenotype has many dependencies, a large number of small effect alleles are expected. However, even if these alleles do drive highly heritable causal intermediates that can be modulated, it does not imply that large changes in phenotype can be obtained.

Accounting for eXentricities: Analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases

Accounting for eXentricities: Analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases

Diana Chang, Feng Gao, Li Ma, Aaron Sams, Andrea Slavney, Yedael Waldman, Paul Billing-Ross, Aviv Madar, Richard Spritz, Alon Keinan
doi: http://dx.doi.org/10.1101/009464

Many complex human diseases are highly sexually dimorphic, which suggests a potential contribution of the X chromosome. However, the X chromosome has been neglected in most genome-wide association studies (GWAS). We present tailored analytical methods and software that facilitate X-wide association studies (XWAS), which we further applied to reanalyze data from 16 GWAS of different autoimmune diseases (AID). We associated several X-linked genes with disease risk, among which ARHGEF6 is associated with Crohn’s disease and replicated in a study of ulcerative colitis, another inflammatory bowel disease (IBD). Indeed, ARHGEF6 interacts with a gastric bacterium that has been implicated in IBD. Additionally, we found that the centromere protein CENPI is associated with three different AID; replicated a previously investigated association of FOXP3, which regulates genes involved in T-cell function, in vitiligo; and discovered that C1GALT1C1 exhibits sex-specific effect on disease risk in both IBDs. These and other X-linked genes that we associated with AID tend to be highly expressed in tissues related to immune response, display differential gene expression between males and females, and participate in major immune pathways. Combined, the results demonstrate the importance of the X chromosome in autoimmunity, reveal the potential of XWAS, even based on existing data, and provide the tools and incentive to appropriately include the X chromosome in future studies.

The genetic architecture of neurodevelopmental disorders

The genetic architecture of neurodevelopmental disorders

Kevin J Mitchell
doi: http://dx.doi.org/10.1101/009449

Neurodevelopmental disorders include rare conditions caused by identified single mutations, such as Fragile X, Down and Angelman syndromes, and much more common clinical categories such as autism, epilepsy and schizophrenia. These common conditions are all highly heritable but their genetics is considered to be “complex”. In fact, this sharp dichotomy in genetic architecture between rare and common disorders may be largely artificial. On the one hand, much of the apparent complexity in the genetics of common disorders may derive from underlying genetic heterogeneity, which has remained obscure until recently. On the other hand, even for supposedly Mendelian conditions, the relationship between single mutations and clinical phenotypes is rarely simple. The categories of monogenic and complex disorders may therefore merge across a continuum, with some mutations being strongly associated with specific syndromes and others having a more variable outcome, modified by the presence of additional genetic variants.

Genome-Wide Mapping In A House Mouse Hybrid Zone Reveals Hybrid Sterility Loci And Dobzhansky-Muller Interactions

Genome-Wide Mapping In A House Mouse Hybrid Zone Reveals Hybrid Sterility Loci And Dobzhansky-Muller Interactions
Leslie Turner, Bettina Harr
doi: http://dx.doi.org/10.1101/009373

Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone.