Broad Epigenetic Signature of Maternal Care in the Brain of Adult Rats

et al. (2011) Broad Epigenetic Signature of Maternal Care in the Brain of Adult Rats. PLoS ONE 6(2): e14739. doi:10.1371/journal.pone.0014739 Broad Epigenetic Signature of Maternal Care in the Brain of Adult Rats Patrick O. McGowan 0 Matthew Suderman 0 Aya Sasaki 0 Tony C. T. Huang 0 Michael 0 Hallett 0 Michael J. Meaney 0 Moshe Szyf 0 Angela Sirigu, CNRS, France 0 1 Douglas Mental Health University Institute , Montreal, Quebec , Canada , 2 Sackler Program for Epigenetics and Developmental Psychobiology at McGill University, McGill University , Montreal, Quebec , Canada , 3 Centre for the Neurobiology of Stress, University of Toronto , Scarborough, Toronto, Ontario , Canada , 4 Department of Pharmacology and Therapeutics, McGill University , Montreal, Quebec , Canada , 5 McGill Centre for Bioinformatics , McGill University , Montreal, Quebec , Canada , 6 Singapore Institute for Clinical Sciences, Singapore, Republic of Singapore, 7 Experience-Based Brain and Biological Development Program of the Canadian Institute for Advanced Research , Toronto, Ontario , Canada Background: Maternal care is associated with long-term effects on behavior and epigenetic programming of the NR3C1 (GLUCOCORTICOID RECEPTOR) gene in the hippocampus of both rats and humans. In the rat, these effects are reversed by cross-fostering, demonstrating that they are defined by epigenetic rather than genetic processes. However, epigenetic changes at a single gene promoter are unlikely to account for the range of outcomes and the persistent change in expression of hundreds of additional genes in adult rats in response to differences in maternal care. Methodology/Principal Findings: We examine here using high-density oligonucleotide array the state of DNA methylation, histone acetylation and gene expression in a 7 million base pair region of chromosome 18 containing the NR3C1 gene in the hippocampus of adult rats. Natural variations in maternal care are associated with coordinate epigenetic changes spanning over a hundred kilobase pairs. The adult offspring of high compared to low maternal care mothers show epigenetic changes in promoters, exons, and gene ends associated with higher transcriptional activity across many genes within the locus examined. Other genes in this region remain unchanged, indicating a clustered yet specific and patterned response. Interestingly, the chromosomal region containing the protocadherin-a, -b, and -c (Pcdh) gene families implicated in synaptogenesis show the highest differential response to maternal care. Conclusions/Significance: The results suggest for the first time that the epigenetic response to maternal care is coordinated in clusters across broad genomic areas. The data indicate that the epigenetic response to maternal care involves not only single candidate gene promoters but includes transcriptional and intragenic sequences, as well as those residing distantly from transcription start sites. These epigenetic and transcriptional profiles constitute the first tiling microarray data set exploring the relationship between epigenetic modifications and RNA expression in both protein coding and non-coding regions across a chromosomal locus in the mammalian brain. - Funding: This study was supported by grants from the Canadian Institutes of Mental Health (CIHR) and the Sackler Foundation to MJM and MS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. The quality of parental care has a broad impact on mental health, including the risk for psychopathology [1,2,3,4,5]. Studies in the rat directly link the maternal care environment to long-term effects on neural systems that regulate stress [6,7] emotional function[8,9], learning and memory [10,11,12] and neuroplasticity [10,13,14,15]. Naturally occurring variations in maternal care in the first week of life in rats are associated with changes in brain and behavior that persist until adulthood [16]. These effects are reversed by cross-fostering, [7,9] demonstrating a causal link between maternal care and gene expression programming. In rats and humans, there is evidence that changes in gene expression as a function of early care are at least partly regulated by epigenetic mechanisms [6,17,18]. In rats, variations in maternal care in the first week of life are associated with alterations in DNA methylation and H3K9 acetylation of the NR3C1 promoter region, and gene expression of the GR17 splice variant of the NR3C1 gene in the hippocampus of adult offspring [6]. There is evidence that the expression of hundreds of additional genes in adult rats changes in response to differences in maternal care [19]. Some of these changes in gene expression can be reversed by pharmacological alterations of chromatin structure by the histone deacetylase inhibitor Trichostatin A (TSA) and the methyl donor Lmethionine [19,20]. The fact that the methyl donor L-methionine inhibits some of the genes influenced by maternal behavior supports the involvement of either DNA or histone methylation. The fact that a large number of genes are responsive to the effects of TSA and L-methionine implies that the epigenetic regulation of gene expression as a function of maternal care may be extensive. In the present study, we test this hypothesis by examining epigenetic and transcriptional changes associated with naturally occurring differences in maternal care. We obtained hippocampal samples from the adult offspring of rat mothers that differed in the frequency of pup licking/grooming in the first week of life (i.e. High vs Low LG adult offspring) and performed an analysis of DNA methylation, H3K9 acetylation and gene expression of a contiguous 7 million base pair region of rat chromosome 18 containing the NR3C1 gene at 100 bp spacing. To our knowledge, these epigenetic and transcriptional profiles constitute the first tiling microarray data set exploring the relationship between epigenetic modifications and RNA expression in both protein coding and non-coding regions across a chromosomal locus in the mammalian brain. Validation of microarray results To validate signals observed on our microarray and differences between High and Low LG offspring, we quantified changes in H3K9 acetylation, DNA methylation, and transcription. H3K9 acetylation differences in 7 regions (Fig. 1a) and DNA methylation differences in 12 regions (Fig. 1b) were validated by quantitative PCR (qChIP see Methods for details; [21]). Levels of DNA methylation validated by qChIP correlated significantly with levels of enrichment detected by microarray (R = 0.38, P = 0.0029 by Pearsons correlation; Fig. S1). DNA methylation differences were further confirmed for four genes by sequencing sodium bisulfite converted DNA (Fig. S2). False positives due to DNA polymorphism ra (...truncated)