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Effects of gene-by-environment interaction on the methylome of mice deficient for tryptophan hydroxylase 2 [MBD-seq]

ABSTRACT: Effects of gene-by-environment interaction on the methylome of mice deficient for tryptophan hydroxylase 2 [MBD-seq]

PROVIDER: PRJNA433809 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6706400_1.fastq.gz	Fastqsanger.gz
	SRR6706400_2.fastq.gz	Fastqsanger.gz
	SRR6706410_1.fastq.gz	Fastqsanger.gz
	SRR6706410_2.fastq.gz	Fastqsanger.gz
	SRR6706420_1.fastq.gz	Fastqsanger.gz

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Effects of gene-by-environment interaction on the methylome of mice deficient for tryptophan hydroxylase 2 [MBD-seq]

Project description: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.

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Effects of gene-by-environment interaction on the transcriptome of mice deficient for tryptophan hydroxylase 2 [RNA-seq]

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Effects of gene-by-environment interaction on the transcriptome and methylome of mice deficient for tryptophan hydroxylase 2

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