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Single-base resolution of mouse offspring brain methylome reveals epigenome modifications caused by gestational folic acid.

Barua S, Kuizon S, Chadman KK, Flory MJ, Brown WT, Junaid MA - Epigenetics Chromatin (2014)

Bottom Line: Maternal nutrients affecting one-carbon metabolism during gestation can exert long-term effects on the health of the progeny.Quantitative real time reverse transcription-polymerase chain reaction confirmed altered expression of several genes.Our findings provide a foundation for future studies to explore the influence of gestational FA on genetic/epigenetic susceptibility to altered development and disease in offspring.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Developmental Biochemistry, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA. mohammed.junaid@opwdd.ny.gov.

ABSTRACT

Background: Epigenetic modifications, such as cytosine methylation in CpG-rich regions, regulate multiple functions in mammalian development. Maternal nutrients affecting one-carbon metabolism during gestation can exert long-term effects on the health of the progeny. Using C57BL/6 J mice, we investigated whether the amount of ingested maternal folic acid (FA) during gestation impacted DNA methylation in the offspring's cerebral hemispheres. Reduced representation bisulfite sequencing at single-base resolution was performed to analyze genome-wide DNA methylation profiles.

Results: We identified widespread differences in the methylation patterns of CpG and non-CpG sites of key developmental genes, including imprinted and candidate autism susceptibility genes (P <0.05). Such differential methylation of the CpG and non-CpG sites may use different mechanisms to alter gene expressions. Quantitative real time reverse transcription-polymerase chain reaction confirmed altered expression of several genes.

Conclusions: These finding demonstrate that high maternal FA during gestation induces substantial alteration in methylation pattern and gene expression of several genes in the cerebral hemispheres of the offspring, and such changes may influence the overall development. Our findings provide a foundation for future studies to explore the influence of gestational FA on genetic/epigenetic susceptibility to altered development and disease in offspring.

No MeSH data available.


Related in: MedlinePlus

Distribution of differentially methylated sites in CpG island sequences. (a) Male low maternal folic acid (LMFA) versus high maternal folic acid (HMFA). (b) Female LMFA versus HMFA.
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Figure 1: Distribution of differentially methylated sites in CpG island sequences. (a) Male low maternal folic acid (LMFA) versus high maternal folic acid (HMFA). (b) Female LMFA versus HMFA.

Mentions: The final DNA methylation map presented in this study represents the summary of three biological replicates [12,13], with each mouse collected from an independent litter. On average, the sequence depths of unique CpG sites in our study were 4,647,138 (11 times) for male and 4,410,480 (14 times) for female DNA samples (Additional file 1: Table S1), and about 90% of the CpG islands were covered. To investigate the differentially methylated regions (DMRs), sequence alignment and Fisher’s exact test or t test were performed for each CpG site that had at least five reads covered. Results of global methylation comparison revealed that approximately 16% of the CpG sites were differentially methylated in both male and female pups from HMFA (n = 43,010 for male, n = 57,602 for female). The majority of the CpG island-associated DMRs were either intergenic or in introns, whereas 18% to 19% were in exons, and approximately 7% were in promoter regions (Figure 1a, b). Several genes involved in neural functioning, brain development, and synaptic plasticity were differentially methylated (P <0.05) in the CpG sites of the offspring from HMFA (Tables 1, 2, 3 and 4, Additional file 2: Table S2, Additional file 3: Table S3, Additional file 4: Table S5, and Additional file 5: Table S6). The results of high-resolution global DNA methylation profiling indicated that maternal FA induces significant changes in the overall methylation patterns in the brains of the offspring. The correlations of the distribution of methylation ratios in male and female pups for the corresponding sites in LMFA and HMFA are shown in Additional file 6: Figures S1-S6, and the distributions of the overlapped sites between LMFA and HMFA male with that of LMFA and HMFA female differential methylation sites (P <0.05) are shown as a hexbin plot in Additional file 7: Figures S7-S9.


Single-base resolution of mouse offspring brain methylome reveals epigenome modifications caused by gestational folic acid.

Barua S, Kuizon S, Chadman KK, Flory MJ, Brown WT, Junaid MA - Epigenetics Chromatin (2014)

Distribution of differentially methylated sites in CpG island sequences. (a) Male low maternal folic acid (LMFA) versus high maternal folic acid (HMFA). (b) Female LMFA versus HMFA.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3928622&req=5

Figure 1: Distribution of differentially methylated sites in CpG island sequences. (a) Male low maternal folic acid (LMFA) versus high maternal folic acid (HMFA). (b) Female LMFA versus HMFA.
Mentions: The final DNA methylation map presented in this study represents the summary of three biological replicates [12,13], with each mouse collected from an independent litter. On average, the sequence depths of unique CpG sites in our study were 4,647,138 (11 times) for male and 4,410,480 (14 times) for female DNA samples (Additional file 1: Table S1), and about 90% of the CpG islands were covered. To investigate the differentially methylated regions (DMRs), sequence alignment and Fisher’s exact test or t test were performed for each CpG site that had at least five reads covered. Results of global methylation comparison revealed that approximately 16% of the CpG sites were differentially methylated in both male and female pups from HMFA (n = 43,010 for male, n = 57,602 for female). The majority of the CpG island-associated DMRs were either intergenic or in introns, whereas 18% to 19% were in exons, and approximately 7% were in promoter regions (Figure 1a, b). Several genes involved in neural functioning, brain development, and synaptic plasticity were differentially methylated (P <0.05) in the CpG sites of the offspring from HMFA (Tables 1, 2, 3 and 4, Additional file 2: Table S2, Additional file 3: Table S3, Additional file 4: Table S5, and Additional file 5: Table S6). The results of high-resolution global DNA methylation profiling indicated that maternal FA induces significant changes in the overall methylation patterns in the brains of the offspring. The correlations of the distribution of methylation ratios in male and female pups for the corresponding sites in LMFA and HMFA are shown in Additional file 6: Figures S1-S6, and the distributions of the overlapped sites between LMFA and HMFA male with that of LMFA and HMFA female differential methylation sites (P <0.05) are shown as a hexbin plot in Additional file 7: Figures S7-S9.

Bottom Line: Maternal nutrients affecting one-carbon metabolism during gestation can exert long-term effects on the health of the progeny.Quantitative real time reverse transcription-polymerase chain reaction confirmed altered expression of several genes.Our findings provide a foundation for future studies to explore the influence of gestational FA on genetic/epigenetic susceptibility to altered development and disease in offspring.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Developmental Biochemistry, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA. mohammed.junaid@opwdd.ny.gov.

ABSTRACT

Background: Epigenetic modifications, such as cytosine methylation in CpG-rich regions, regulate multiple functions in mammalian development. Maternal nutrients affecting one-carbon metabolism during gestation can exert long-term effects on the health of the progeny. Using C57BL/6 J mice, we investigated whether the amount of ingested maternal folic acid (FA) during gestation impacted DNA methylation in the offspring's cerebral hemispheres. Reduced representation bisulfite sequencing at single-base resolution was performed to analyze genome-wide DNA methylation profiles.

Results: We identified widespread differences in the methylation patterns of CpG and non-CpG sites of key developmental genes, including imprinted and candidate autism susceptibility genes (P <0.05). Such differential methylation of the CpG and non-CpG sites may use different mechanisms to alter gene expressions. Quantitative real time reverse transcription-polymerase chain reaction confirmed altered expression of several genes.

Conclusions: These finding demonstrate that high maternal FA during gestation induces substantial alteration in methylation pattern and gene expression of several genes in the cerebral hemispheres of the offspring, and such changes may influence the overall development. Our findings provide a foundation for future studies to explore the influence of gestational FA on genetic/epigenetic susceptibility to altered development and disease in offspring.

No MeSH data available.


Related in: MedlinePlus