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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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Regional variations in differences in histone acetylation, DNA methyation and gene expression between High and Low LG adult offspring.(a) The Pearson correlation of DNA methylation and H3K9 acetylation differences between the High and Low LG adult offspring for pairs of probes located at varying distances from each other. Error bars show 95% confidence intervals for the correlation values. Grey highlight shows the 95% confidence interval for correlations obtained from randomly selected probe pairs. (b) Enrichment of RDme (Regional Differences in DNA methylation) between High and Low LG adult offspring across all genes from the 5′ region to the 3′ region. Enrichment is quantified as increased frequency of RDme in a given gene region (number of RDme/bp). Significance is the quantile of this enrichment with respect to the distribution of randomly positioned RDme. A quantile above 0.975 indicates significant enrichment, and a quantile below 0.025 indicates significant depletion at the P = 0.05 level. Quantiles of hyperacetylated RDac/hypermethylated RDme in High compared to Low LG offspring (red) and quantiles of hypoacetylated RDac/hypomethylated RDme (blue) are shown. (c) Mean differences across all probes in DNA methylation, H3K9 acetylation and RNA expression levels between High LG and Low LG adult offspring are shown across all genes from the 5′ region to the 3′ region, with significant differences indicated by non-zero values. Line thickness denotes SEM.
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pone-0014739-g003: Regional variations in differences in histone acetylation, DNA methyation and gene expression between High and Low LG adult offspring.(a) The Pearson correlation of DNA methylation and H3K9 acetylation differences between the High and Low LG adult offspring for pairs of probes located at varying distances from each other. Error bars show 95% confidence intervals for the correlation values. Grey highlight shows the 95% confidence interval for correlations obtained from randomly selected probe pairs. (b) Enrichment of RDme (Regional Differences in DNA methylation) between High and Low LG adult offspring across all genes from the 5′ region to the 3′ region. Enrichment is quantified as increased frequency of RDme in a given gene region (number of RDme/bp). Significance is the quantile of this enrichment with respect to the distribution of randomly positioned RDme. A quantile above 0.975 indicates significant enrichment, and a quantile below 0.025 indicates significant depletion at the P = 0.05 level. Quantiles of hyperacetylated RDac/hypermethylated RDme in High compared to Low LG offspring (red) and quantiles of hypoacetylated RDac/hypomethylated RDme (blue) are shown. (c) Mean differences across all probes in DNA methylation, H3K9 acetylation and RNA expression levels between High LG and Low LG adult offspring are shown across all genes from the 5′ region to the 3′ region, with significant differences indicated by non-zero values. Line thickness denotes SEM.

Mentions: To index broad epigenetic changes observed across the locus, we defined a Regional Difference in DNA methylation and a Regional Difference H3K9 acetylation (RDme and RDac, respectively) as a statistically significant difference between High LG and Low LG offspring of at least 1000 bp containing at least one statistically significant probe per 1000 bp (see Methods S1 for details). Across the entire locus, we identified 723 RDme of which 373 are significantly hypermethylated and 350 are hypomethylated in High relative to Low LG offspring. We similarly identified 471 RDac of which 204 are hyperacetylated and 267 are hypoacetylated. We found that these broad epigenetic differences associated with maternal care are significantly co-localized within the locus, and were positively correlated at distances over 100 Kb (Fig. 3a). The data suggest that clustering of differentially methylated and acetylated regions is not exclusive to pathological responses under extreme selection as is the case in cancer but includes epigenetic responses to natural variations in maternal care, and may be characteristic of naturally occurring epigenetic responses.


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)

Regional variations in differences in histone acetylation, DNA methyation and gene expression between High and Low LG adult offspring.(a) The Pearson correlation of DNA methylation and H3K9 acetylation differences between the High and Low LG adult offspring for pairs of probes located at varying distances from each other. Error bars show 95% confidence intervals for the correlation values. Grey highlight shows the 95% confidence interval for correlations obtained from randomly selected probe pairs. (b) Enrichment of RDme (Regional Differences in DNA methylation) between High and Low LG adult offspring across all genes from the 5′ region to the 3′ region. Enrichment is quantified as increased frequency of RDme in a given gene region (number of RDme/bp). Significance is the quantile of this enrichment with respect to the distribution of randomly positioned RDme. A quantile above 0.975 indicates significant enrichment, and a quantile below 0.025 indicates significant depletion at the P = 0.05 level. Quantiles of hyperacetylated RDac/hypermethylated RDme in High compared to Low LG offspring (red) and quantiles of hypoacetylated RDac/hypomethylated RDme (blue) are shown. (c) Mean differences across all probes in DNA methylation, H3K9 acetylation and RNA expression levels between High LG and Low LG adult offspring are shown across all genes from the 5′ region to the 3′ region, with significant differences indicated by non-zero values. Line thickness denotes SEM.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3046141&req=5

pone-0014739-g003: Regional variations in differences in histone acetylation, DNA methyation and gene expression between High and Low LG adult offspring.(a) The Pearson correlation of DNA methylation and H3K9 acetylation differences between the High and Low LG adult offspring for pairs of probes located at varying distances from each other. Error bars show 95% confidence intervals for the correlation values. Grey highlight shows the 95% confidence interval for correlations obtained from randomly selected probe pairs. (b) Enrichment of RDme (Regional Differences in DNA methylation) between High and Low LG adult offspring across all genes from the 5′ region to the 3′ region. Enrichment is quantified as increased frequency of RDme in a given gene region (number of RDme/bp). Significance is the quantile of this enrichment with respect to the distribution of randomly positioned RDme. A quantile above 0.975 indicates significant enrichment, and a quantile below 0.025 indicates significant depletion at the P = 0.05 level. Quantiles of hyperacetylated RDac/hypermethylated RDme in High compared to Low LG offspring (red) and quantiles of hypoacetylated RDac/hypomethylated RDme (blue) are shown. (c) Mean differences across all probes in DNA methylation, H3K9 acetylation and RNA expression levels between High LG and Low LG adult offspring are shown across all genes from the 5′ region to the 3′ region, with significant differences indicated by non-zero values. Line thickness denotes SEM.
Mentions: To index broad epigenetic changes observed across the locus, we defined a Regional Difference in DNA methylation and a Regional Difference H3K9 acetylation (RDme and RDac, respectively) as a statistically significant difference between High LG and Low LG offspring of at least 1000 bp containing at least one statistically significant probe per 1000 bp (see Methods S1 for details). Across the entire locus, we identified 723 RDme of which 373 are significantly hypermethylated and 350 are hypomethylated in High relative to Low LG offspring. We similarly identified 471 RDac of which 204 are hyperacetylated and 267 are hypoacetylated. We found that these broad epigenetic differences associated with maternal care are significantly co-localized within the locus, and were positively correlated at distances over 100 Kb (Fig. 3a). The data suggest that clustering of differentially methylated and acetylated regions is not exclusive to pathological responses under extreme selection as is the case in cancer but includes epigenetic responses to natural variations in maternal care, and may be characteristic of naturally occurring epigenetic responses.

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