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Broad epigenetic signature of maternal care in the brain of adult rats.

McGowan PO, Suderman M, Sasaki A, Huang TC, Hallett M, Meaney MJ, Szyf M - PLoS ONE (2011)

Bottom Line: In the rat, these effects are reversed by cross-fostering, demonstrating that they are defined by epigenetic rather than genetic processes.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.The results suggest for the first time that the epigenetic response to maternal care is coordinated in clusters across broad genomic areas.

View Article: PubMed Central - PubMed

Affiliation: Douglas Mental Health University Institute, Montreal, Quebec, Canada. patrick.mcgowan@utoronto.ca

ABSTRACT

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-α, -β, and -γ (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.

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Microarray validation.(a) H3K9 acetylation differences between High (white bars) and Low LG (black bars) adult offspring validated by qCHIP (see Methods). (b) (upper) DNA methylation differences between High and Low LG adult offspring detected by microarray analysis (H–L), showing gene location, and region analyzed. (lower) DNA methylation differences validated in the same manner as for H3K9 acetylation. (c) Gene expression differences between High LG and Low LG adult offspring (* = P<0.05). All real-time PCR reactions were performed in triplicate and results are displayed as mean +/− SEM.
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pone-0014739-g001: Microarray validation.(a) H3K9 acetylation differences between High (white bars) and Low LG (black bars) adult offspring validated by qCHIP (see Methods). (b) (upper) DNA methylation differences between High and Low LG adult offspring detected by microarray analysis (H–L), showing gene location, and region analyzed. (lower) DNA methylation differences validated in the same manner as for H3K9 acetylation. (c) Gene expression differences between High LG and Low LG adult offspring (* = P<0.05). All real-time PCR reactions were performed in triplicate and results are displayed as mean +/− SEM.

Mentions: 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 Pearson's 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 rather than differential methylation were ruled out for 12 regions (those validated by qChIP above) via DNA sequencing (data not shown). Of nine genes showing significant differences in gene expression between High and Low LG offspring, all were significantly more expressed among High LG offspring (Fig. 1c).


Broad epigenetic signature of maternal care in the brain of adult rats.

McGowan PO, Suderman M, Sasaki A, Huang TC, Hallett M, Meaney MJ, Szyf M - PLoS ONE (2011)

Microarray validation.(a) H3K9 acetylation differences between High (white bars) and Low LG (black bars) adult offspring validated by qCHIP (see Methods). (b) (upper) DNA methylation differences between High and Low LG adult offspring detected by microarray analysis (H–L), showing gene location, and region analyzed. (lower) DNA methylation differences validated in the same manner as for H3K9 acetylation. (c) Gene expression differences between High LG and Low LG adult offspring (* = P<0.05). All real-time PCR reactions were performed in triplicate and results are displayed as mean +/− SEM.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3046141&req=5

pone-0014739-g001: Microarray validation.(a) H3K9 acetylation differences between High (white bars) and Low LG (black bars) adult offspring validated by qCHIP (see Methods). (b) (upper) DNA methylation differences between High and Low LG adult offspring detected by microarray analysis (H–L), showing gene location, and region analyzed. (lower) DNA methylation differences validated in the same manner as for H3K9 acetylation. (c) Gene expression differences between High LG and Low LG adult offspring (* = P<0.05). All real-time PCR reactions were performed in triplicate and results are displayed as mean +/− SEM.
Mentions: 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 Pearson's 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 rather than differential methylation were ruled out for 12 regions (those validated by qChIP above) via DNA sequencing (data not shown). Of nine genes showing significant differences in gene expression between High and Low LG offspring, all were significantly more expressed among High LG offspring (Fig. 1c).

Bottom Line: In the rat, these effects are reversed by cross-fostering, demonstrating that they are defined by epigenetic rather than genetic processes.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.The results suggest for the first time that the epigenetic response to maternal care is coordinated in clusters across broad genomic areas.

View Article: PubMed Central - PubMed

Affiliation: Douglas Mental Health University Institute, Montreal, Quebec, Canada. patrick.mcgowan@utoronto.ca

ABSTRACT

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-α, -β, and -γ (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.

Show MeSH