A genome-wide comparative study of DNA methylation in great apes
Author(s): Hernando Herráez, I, Prado-Martínez, J, Garg, P, Fernandez-Callejo, M, Heyn, H, Hvilsom, C, Navarro, A, Esteller, M, Sharp, AJ, Marques-Bonet, T
It has been hypothesized that differences between humans and their closet relatives may be explained by changes in gene regulation rather in primary genome sequence. Epigenetic alterations are involved in many biological processes and have been under-explored in comparative genomics. Specifically, DNA methylation is still poorly understood in the context of recent human evolution. In this study, we performed a comparative analysis of CpG methylation patterns between 9 humans and 23 primates including all four species of great apes (chimpanzee, bonobo, gorilla and orangutan) using Illumina Methylation450 bead arrays. Using this approach, we were able to study the dynamics of DNA methylation and to identify regions showing species-specific methylation pattern among the great apes, including ~130 genes with a pattern unique to human. We also identified a significant positive relationship between the rate of coding variation and alterations of methylation at the promoter level, indicative of co-occurrence between evolution of protein sequence and gene regulation.
The Department of Physics, Chemistry and Biology
Behavioural epigenetics and the effects of domestication in the chicken
Author(s): Bélteky, J, Jensen, P
Environmental changes and selection puts pressure on an organism’s ability to adapt to new settings. An example where accelerated evolution in a short time-span has generated a large variety of phenotypes is seen in domestication, where artificial selection for desired traits have driven diversity not just from the founding origin but also in a range of different directions. Among the proposed explanations for this rapid change in phenotypes are epigenetic mechanisms. These are not only more frequent and flexible than genomic mutations, but their potential to shape individuals as well as their offspring make them viable targets for investigating the effects of environmental conditions or stimuli on an organism. With the chicken (Gallus gallus) as our model organism, we have been attempting to not only characterize behavioural differences between domestic chickens and their wild ancestors, but also specify genetic and epigenetic changes by looking at mutations, gene expression and epigenetic markers such as DNA methylation. Besides clear behaviour differences, we have found correlational changes between methylation patterns and gene expression, along with an enrichment of methylation in domestic chicken promoters. The genomic and epigenomic background, along with behavioural aspects, are currently being investigated in several projects including the effects of early stress, and an artificial selection line. Our hope is that the information generated from our experiments will give us insight in the stability and transmission of epigenetic markers, and let us expand the field of behavioural epigenetics. With knowledge about epigenetic changes in domestic animals, our understanding of their susceptibility to environmental changes such as stress or nutrition may help us in increasing animal welfare for both poultry and livestock.
Institute of Botany
Can epigenetic differentiation cause the formation of ecotypes? Insights from stable altitudinal variants in the mountain plant Heliosperma pusillum (Caryophyllaceae)
Author(s): Flatscher, R, Schönswetter, P, Paun, O, Frajman, B
Adaptation is a process which continuously moves populations towards better fit phenotypes. In its widest sense, it involves short-term effects such as mechanisms of short-term transcription regulation, and long term-effects which result from natural selection acting on different kinds of heritable variation (i.e. segregating [epi-]allelic variants). Variations in biotic and abiotic conditions thus often lead to the formation of “ecotypes”, i.e. distinct populations adapted to their specific habitat. If gene flow is limited, initial inter-fertility with other conspecific ecotypes may change into increasing divergence and incompatibility over time, and eventually result in speciation. An interesting example for multiple, independent origins of ecotypes is found in the mountain plant Heliosperma pusillum s.l., which comprises a widespread alpine ecotype inhabiting mountain creek banks and moist calcareous screes (H. pusillum s. str.), as well as a lowland ecotype with disjunct and locally limited distribution growing in gorges and under overhanging cliffs (H. veselskyi). AFLP fingerprints as well as non-coding chloroplast and nuclear sequences consistently indicate that there is no genome-wide genetic differentiation between these altitudinal variants which would mirror the conspicuous morphological and ecological differences. Nevertheless, morphology of the two types remains stable for at least one generation in offspring grown from seeds of high- and low altitude accessions in a common garden. We use methylation sensitive amplified polymorphism (MSAP) to test for genome-wide differences in DNA methylation in six pairs of high- and low altitude ecotypes from the Eastern Alps. We discuss the correlation of methylation patterns with evident phenotypic differences and the possible role of epigenetics in the initial phase of divergent evolution of ecotypes.
The environment as a source of epigenetic variations
Author(s): Leung, C, Breton, S, Angers, B
Asexual lineages may have a widespread distribution in absence of genetic variation. Epigenetic processes have been proposed as a mechanism enabling such a response to environmental heterogeneity and thus represent an alternative mechanism to explain the ecological success of genetically identical organisms. This study aims to determine whether epigenetics reflect how asexual organisms deal with environment heterogeneity. We compared epigenetic profiles of sympatric lineages of the clonal fish Chrosomus eos-neogaeus from lakes of the north-eastern North America. While individual epigenetic differences represent 20% of the observed variation, individuals of a given lineage within a lake cluster together. Sympatric lineages share numerous epigenetic modifications and “lake effect” account for more than 40% of the variation, suggesting similar response to environment. Similarly, a given lineage from different environments displays numerous epigenetic differences. Finally, genetic differences also contribute to an important part of variation. This may be explained by two non exclusive hypotheses: response to environment differs according to lineage and/or sympatric lineages coexist in different ecological niches. Altogether, theses results suggest a strong role of epigenetics when dealing with different environments in absence of genetic variation.