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Inter- and intra-individual variation in allele-specific DNA methylation and gene expression in children conceived using assisted reproductive technology.

Turan N, Katari S, Gerson LF, Chalian R, Foster MW, Gaughan JP, Coutifaris C, Sapienza C - PLoS Genet. (2010)

Bottom Line: We found substantial variation in allele-specific methylation at both loci in both groups.Our results show that in vitro conception is associated with aberrant methylation patterns at the IGF2/H19 locus.It is possible that this developmental difference has an effect on placental and fetal growth.

View Article: PubMed Central - PubMed

Affiliation: Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America.

ABSTRACT
Epidemiological studies have reported a higher incidence of rare disorders involving imprinted genes among children conceived using assisted reproductive technology (ART), suggesting that ART procedures may be disruptive to imprinted gene methylation patterns. We examined intra- and inter-individual variation in DNA methylation at the differentially methylated regions (DMRs) of the IGF2/H19 and IGF2R loci in a population of children conceived in vitro or in vivo. We found substantial variation in allele-specific methylation at both loci in both groups. Aberrant methylation of the maternal IGF2/H19 DMR was more common in the in vitro group, and the overall variance was also significantly greater in the in vitro group. We estimated the number of trophoblast stem cells in each group based on approximation of the variance of the binomial distribution of IGF2/H19 methylation ratios, as well as the distribution of X chromosome inactivation scores in placenta. Both of these independent measures indicated that placentas of the in vitro group were derived from fewer stem cells than the in vivo conceived group. Both IGF2 and H19 mRNAs were significantly lower in placenta from the in vitro group. Although average birth weight was lower in the in vitro group, we found no correlation between birth weight and IGF2 or IGF2R transcript levels or the ratio of IGF2/IGF2R transcript levels. Our results show that in vitro conception is associated with aberrant methylation patterns at the IGF2/H19 locus. However, very little of the inter- or intra-individual variation in H19 or IGF2 mRNA levels can be explained by differences in maternal DMR DNA methylation, in contrast to the expectations of current transcriptional imprinting models. Extraembryonic tissues of embryos cultured in vitro appear to be derived from fewer trophoblast stem cells. It is possible that this developmental difference has an effect on placental and fetal growth.

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Related in: MedlinePlus

Allele-specific methylation at the IGF2/H19 DMR.(A) 56 informative in vivo individuals, and (B) 45 informative in vitro individuals. M/P represents the DNA methylation ratio between maternal and paternal alleles (see text). Each individual is represented as vertical data-set of M/P ratios from cord blood, cord and five sections of placenta. Individuals were ranked based on the degree of scatter (intra-individual variation) observed.
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pgen-1001033-g001: Allele-specific methylation at the IGF2/H19 DMR.(A) 56 informative in vivo individuals, and (B) 45 informative in vitro individuals. M/P represents the DNA methylation ratio between maternal and paternal alleles (see text). Each individual is represented as vertical data-set of M/P ratios from cord blood, cord and five sections of placenta. Individuals were ranked based on the degree of scatter (intra-individual variation) observed.

Mentions: Figure 1 shows the distribution of M/P methylation ratios observed from 56 informative in vivo (Figure 1A) and 45 informative in vitro (Figure 1B) individuals. The M/P ratios were measured for cord blood, cord and five sections of placenta from each informative individual. The data are represented as a series of symbols on a vertical line, ranked from individuals showing the greatest range of variation on the left side of the graph to individuals showing the least range of variation on the right side of the graph. The distribution of individual M/P methylation ratios in cord blood (red circles in Figure 1) shows that the great majority of informative individuals have <15% methylation on the maternal allele in both groups. Approximately 8% of the population examined here has ≥15% of methylation of CpG sites on the maternal allele in cord blood. These findings are similar to those reported previously by Sandovici et al. (2003) for M/P methylation ratios measured in peripheral blood samples from the CEPH families [28]. The distribution of individual M/P methylation ratios in cord showed a similar pattern to that observed in cord blood (Figure 1), while the five sections of placenta taken from each individual showed a broad range of intra-individual variation in M/P methylation ratios.


Inter- and intra-individual variation in allele-specific DNA methylation and gene expression in children conceived using assisted reproductive technology.

Turan N, Katari S, Gerson LF, Chalian R, Foster MW, Gaughan JP, Coutifaris C, Sapienza C - PLoS Genet. (2010)

Allele-specific methylation at the IGF2/H19 DMR.(A) 56 informative in vivo individuals, and (B) 45 informative in vitro individuals. M/P represents the DNA methylation ratio between maternal and paternal alleles (see text). Each individual is represented as vertical data-set of M/P ratios from cord blood, cord and five sections of placenta. Individuals were ranked based on the degree of scatter (intra-individual variation) observed.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2908687&req=5

pgen-1001033-g001: Allele-specific methylation at the IGF2/H19 DMR.(A) 56 informative in vivo individuals, and (B) 45 informative in vitro individuals. M/P represents the DNA methylation ratio between maternal and paternal alleles (see text). Each individual is represented as vertical data-set of M/P ratios from cord blood, cord and five sections of placenta. Individuals were ranked based on the degree of scatter (intra-individual variation) observed.
Mentions: Figure 1 shows the distribution of M/P methylation ratios observed from 56 informative in vivo (Figure 1A) and 45 informative in vitro (Figure 1B) individuals. The M/P ratios were measured for cord blood, cord and five sections of placenta from each informative individual. The data are represented as a series of symbols on a vertical line, ranked from individuals showing the greatest range of variation on the left side of the graph to individuals showing the least range of variation on the right side of the graph. The distribution of individual M/P methylation ratios in cord blood (red circles in Figure 1) shows that the great majority of informative individuals have <15% methylation on the maternal allele in both groups. Approximately 8% of the population examined here has ≥15% of methylation of CpG sites on the maternal allele in cord blood. These findings are similar to those reported previously by Sandovici et al. (2003) for M/P methylation ratios measured in peripheral blood samples from the CEPH families [28]. The distribution of individual M/P methylation ratios in cord showed a similar pattern to that observed in cord blood (Figure 1), while the five sections of placenta taken from each individual showed a broad range of intra-individual variation in M/P methylation ratios.

Bottom Line: We found substantial variation in allele-specific methylation at both loci in both groups.Our results show that in vitro conception is associated with aberrant methylation patterns at the IGF2/H19 locus.It is possible that this developmental difference has an effect on placental and fetal growth.

View Article: PubMed Central - PubMed

Affiliation: Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America.

ABSTRACT
Epidemiological studies have reported a higher incidence of rare disorders involving imprinted genes among children conceived using assisted reproductive technology (ART), suggesting that ART procedures may be disruptive to imprinted gene methylation patterns. We examined intra- and inter-individual variation in DNA methylation at the differentially methylated regions (DMRs) of the IGF2/H19 and IGF2R loci in a population of children conceived in vitro or in vivo. We found substantial variation in allele-specific methylation at both loci in both groups. Aberrant methylation of the maternal IGF2/H19 DMR was more common in the in vitro group, and the overall variance was also significantly greater in the in vitro group. We estimated the number of trophoblast stem cells in each group based on approximation of the variance of the binomial distribution of IGF2/H19 methylation ratios, as well as the distribution of X chromosome inactivation scores in placenta. Both of these independent measures indicated that placentas of the in vitro group were derived from fewer stem cells than the in vivo conceived group. Both IGF2 and H19 mRNAs were significantly lower in placenta from the in vitro group. Although average birth weight was lower in the in vitro group, we found no correlation between birth weight and IGF2 or IGF2R transcript levels or the ratio of IGF2/IGF2R transcript levels. Our results show that in vitro conception is associated with aberrant methylation patterns at the IGF2/H19 locus. However, very little of the inter- or intra-individual variation in H19 or IGF2 mRNA levels can be explained by differences in maternal DMR DNA methylation, in contrast to the expectations of current transcriptional imprinting models. Extraembryonic tissues of embryos cultured in vitro appear to be derived from fewer trophoblast stem cells. It is possible that this developmental difference has an effect on placental and fetal growth.

Show MeSH
Related in: MedlinePlus