Epigenetic Studies in Wild House Mice
Epigenetic marks regulate gene activity by structuring the genome in open and closed chromatin conformations. Imprinting, gene dosage compensation and cellular differentiation are all regulated by secondary modifications of the DNA itself or of the histone proteins: A stem cell and a differentiated cell have different patterns of epigenetic marks. To date, most research on epigenetic mechanisms has been carried out on cell lines and inbred animals. This begs the question, how genetic diversity affects epigenetic diversity.
My epigenetic work at the MPI in Plšn centers on histone modifications that mark active genes in outbred mice. We measure histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac) by immunoprecipitation followed by genome-wide next-generation sequencing (ChIP-Seq) or quantitative PCR. One of the difficulties of the quantitative analysis of ChIP-Seq data is that peak sizes range over five orders of magnitude; for this we developed a suitable difference measure.
We chose measuring histone modifications rather than DNA methylation because we expect that the genomic diversity of our outbred mice interferes more with read mapping after bisulfite sequencing than after ChIP-Seq. Indeed, the mapping of our ChIP-Seq reads with up to two mismatches within the 36mer sequence reads yields a similar fraction of mapped reads to what is obtained when mapping reads from the standard mous strain (C57Bl/6) back onto the reference genome.
In order to work on epigenetic marks in wild or outbred animals, it is important to consider the possible effect of genomic diversity on the size of an epigenetic mark. For example, at loci that we know or suspect to harbour copy number variation, we can observe the genomic difference affecting the epigenetic signal. By comparing background noise at loci where the epigenetic signal is different between individuals, we are able to identify copy number loci from ChIP-Seq data. What is more difficult to determine is the influence of SNPs on the size of an epigenetic mark.
We are currently studying the effect of an environmental change on the epigenetic marks in wild mice. We subject mice to a different environment, for example a simulation of summer conditions, and investigate whether the different metabolic demands are reflected in the histone marks of liver tissue. Studies in inbred mice and rats that have been fed diets to induce a phenotype of obesity and diabetes have revealed that DNA methylation pattern change. At a few genes, such changes were transmitted by fathers to offspring, that is, in the absence of the intrauterine environment that could influence the DNA methylation pattern during the embryonal development. It turns out from our experiments that adaptation to a new environment induces small but quantitative changes of histone modification settings even in the absence of a toxic or disease-causing treatment. The bulk of these changes were not inherited, though, which is in line with the reports on DNA methylation changes being transmitted at only a very few loci.
Bšrsch-Haubold, A.G., Montero, I., Konrad, K., and Haubold, B. (2014) Genome-wide Quantitative Analysis of Histone H3 Lysine 4 Trimethylation in Wild House Mouse Liver: Environmental Change Causes Epigenetic Plasticity. PLoS One, DOI 10.1371/journal.pone.0097568
Krause, L., Haubold, B., Bšrsch-Haubold, A.G. (2015) Social Exclusion Changes Histone Modifications H3K4me3 and H3K27ac in Liver Tissue of Wild House Mice. PLoS One, DOI 10.1371/journal.pone.0133988
Supervision of Student Research Projects:
2013 Linda Krause Master Thesis, University of Lźbeck: "Quantitative epigenetische Analyse von Histonmodificationen in WildmŠusen"
2012 Megan Barclay M.Sc Biology: Research Project on Mouse Behaviour
2011 Rebecca Winkels Bachelor Thesis, University of Kiel: "Der Einflu§ von Umweltbedingungen auf epigenetische Marker"
2011 Tobias Brźgmann Master Student from the University of Hamburg: Research Project on measuring copy number variations
2010 Severin Uebbing Master Student from the University of Uppsala: Research Project on ChIP-qPCR