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DNA methylation is developmentally regulated for genes essential for cardiogenesis.

Chamberlain AA, Lin M, Lister RL, Maslov AA, Wang Y, Suzuki M, Wu B, Greally JM, Zheng D, Zhou B - J Am Heart Assoc (2014)

Bottom Line: Quantitative real-time PCR analysis of 350 genes with differential DNA methylation showed that the expression of 181 genes is developmentally regulated, and 79 genes have correlative changes between methylation and expression, including hyaluronan synthase 2 (Has2).Required for heart valve formation, Has2 expression in the developing heart valves is downregulated at E14.5, accompanied with increased DNA methylation in its enhancer.Genetic knockout further showed that the downregulation of Has2 expression is dependent on DNA methyltransferase 3b, which is co-expressed with Has2 in the forming heart valve region, indicating that the DNA methylation change may contribute to the Has2 enhancer's regulating function.

View Article: PubMed Central - PubMed

Affiliation: Division of Hematology, Department of Genetics, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY (A.A.C., M.L., A.A.M., Y.W., M.S., B.W., J.M.G., D.Z.).

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Limited DNA methylation changes between E11.5 and E14.5 hearts. A, The tag counts for all ACGT sites in E11.5 (x‐axis) and E14.5 (y‐axis) are highly correlated. The depth of the color represents the density of points in a plotting area (n=2). B, Confirmation of stable global methylation by Luminometric Methylation Assay (LUMA) (n=2). Error bars represent standard error.
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fig01: Limited DNA methylation changes between E11.5 and E14.5 hearts. A, The tag counts for all ACGT sites in E11.5 (x‐axis) and E14.5 (y‐axis) are highly correlated. The depth of the color represents the density of points in a plotting area (n=2). B, Confirmation of stable global methylation by Luminometric Methylation Assay (LUMA) (n=2). Error bars represent standard error.

Mentions: To study the importance of DNA methylation in heart development, we carried out a genome‐wide cytosine methylation analysis of E11.5 and E14.5 mouse embryonic hearts using MSFE/MPS with HpyCH4IV, a methylation‐sensitive restriction enzyme recognizing ACGT. A total of 75 278 236 and 28 496 681 sequencing reads were obtained from the 2 E11.5 replicates that were mapped to 1 522 872 and 1 447 993 ACGT sites, respectively, while 89 562 687 and 65 198 805 reads were generated from the 2 E14.5 replicates that were mapped to 1 442 766 and 1 490 463 sites, respectively. At both stages, the reads from the 2 replicates covered >83% of the total 1 756 340 ACGT sites in the mouse genome. The Pearson's correlation coefficients were 0.894 and 0.896 between the 2 replicates for E11.5 and E14.5, respectively (data not shown); indicating that the quality of the data was high. The majority of ACGT sites had highly similar and correlated tag counts between E11.5 and E14.5 (Figure 1A), suggesting at the global level no significant methylation changes occurred between the 2 developmental stages. This finding of genome‐wide stable DNA methylation in the developing hearts was supported by the LUMA data (Figure 1B).


DNA methylation is developmentally regulated for genes essential for cardiogenesis.

Chamberlain AA, Lin M, Lister RL, Maslov AA, Wang Y, Suzuki M, Wu B, Greally JM, Zheng D, Zhou B - J Am Heart Assoc (2014)

Limited DNA methylation changes between E11.5 and E14.5 hearts. A, The tag counts for all ACGT sites in E11.5 (x‐axis) and E14.5 (y‐axis) are highly correlated. The depth of the color represents the density of points in a plotting area (n=2). B, Confirmation of stable global methylation by Luminometric Methylation Assay (LUMA) (n=2). Error bars represent standard error.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4309105&req=5

fig01: Limited DNA methylation changes between E11.5 and E14.5 hearts. A, The tag counts for all ACGT sites in E11.5 (x‐axis) and E14.5 (y‐axis) are highly correlated. The depth of the color represents the density of points in a plotting area (n=2). B, Confirmation of stable global methylation by Luminometric Methylation Assay (LUMA) (n=2). Error bars represent standard error.
Mentions: To study the importance of DNA methylation in heart development, we carried out a genome‐wide cytosine methylation analysis of E11.5 and E14.5 mouse embryonic hearts using MSFE/MPS with HpyCH4IV, a methylation‐sensitive restriction enzyme recognizing ACGT. A total of 75 278 236 and 28 496 681 sequencing reads were obtained from the 2 E11.5 replicates that were mapped to 1 522 872 and 1 447 993 ACGT sites, respectively, while 89 562 687 and 65 198 805 reads were generated from the 2 E14.5 replicates that were mapped to 1 442 766 and 1 490 463 sites, respectively. At both stages, the reads from the 2 replicates covered >83% of the total 1 756 340 ACGT sites in the mouse genome. The Pearson's correlation coefficients were 0.894 and 0.896 between the 2 replicates for E11.5 and E14.5, respectively (data not shown); indicating that the quality of the data was high. The majority of ACGT sites had highly similar and correlated tag counts between E11.5 and E14.5 (Figure 1A), suggesting at the global level no significant methylation changes occurred between the 2 developmental stages. This finding of genome‐wide stable DNA methylation in the developing hearts was supported by the LUMA data (Figure 1B).

Bottom Line: Quantitative real-time PCR analysis of 350 genes with differential DNA methylation showed that the expression of 181 genes is developmentally regulated, and 79 genes have correlative changes between methylation and expression, including hyaluronan synthase 2 (Has2).Required for heart valve formation, Has2 expression in the developing heart valves is downregulated at E14.5, accompanied with increased DNA methylation in its enhancer.Genetic knockout further showed that the downregulation of Has2 expression is dependent on DNA methyltransferase 3b, which is co-expressed with Has2 in the forming heart valve region, indicating that the DNA methylation change may contribute to the Has2 enhancer's regulating function.

View Article: PubMed Central - PubMed

Affiliation: Division of Hematology, Department of Genetics, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY (A.A.C., M.L., A.A.M., Y.W., M.S., B.W., J.M.G., D.Z.).

Show MeSH
Related in: MedlinePlus