GSE110329
Effects of gene-by-environment interaction on the methylome of mice deficient for tryptophan hydroxylase 2 [MBD-seq]
Purpose: Investigation of effects of early adversity in mice deficient for brain serotonin on the methylome Methods: Following materal separation in early childhood and behavioural screening in adulthood, 4 moth old males, either wildtype or carrying a hetero- or homozygous knockout of the thryptophan hyroxylase 2 gene, were sacrificed, brains extracted, the amygdalae of both hemispheres dissected, blended and separated in two protions. From one of these portions DNA was processed by an external company, i.e. Nxt-Dx (Ghent, Belgium). DNA was sheared by sonication, followed by methyl binding domain (MBD) based capture, leading to an enrichment of methylated fragments. Subsequently, library preparation was performed followed by multiplexed paired-end sequencing with a read-length of 50 bp and an approximate output of 20 million reads/sample on the Illumina HiSeq4000 platform. Reads were mapped to the Mus musculus GRCm38.p5 genome  using Bowtie2 (v2.1.0) software in end-to-end & sensitive-mode. After mapping, coverage peaks were generated using MACS 14 peak caller (Zhang et al. 2008). Results: Either Tph2 genotype, early adversity as well as their interaction resulted in unique profiles of differentially enriched methylated peaks as well as expressed RNA. As expected, the effect sizes and significances were rather subtle and the overlap between top hits of methylome and transcriptome were marginal. Conclusion: Tph2, MS and their interaction induced changes in gene expression and DNA methylation, within a physiological range. The observed changes by MS seemed furthermore strongly influenced by the Tph2 genotype, ergo brain 5-HT availability. Overall design: RNA expression adn DNA methylation profiles affected by maternal separation, brain 5-HT deficiency and their interaction in adult male mice, were generated using MBD enrichment based and RNA deep sequencing MBD based capture (performed by Nxt-Dx, Ghent Belgium, http://www.nxt-dx.com/)