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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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Distribution of DNA methylation across the mouse genome and various types of genomic elements in the developing heart. A, Cartoon depicting the genic regions (enhancer, promoter and genebody). B, Violin plot (a combination of a box plot and a kernel density plot) showing the distributions of tag counts for all ACGT (top) or differential methylated (bottom) sites in different genomic regions. As number of tag counts is inversely correlated to level of CG methylation, these plots indicate that gene promoters and regulatory regions exhibit significantly lower levels of DNA methylation than genomic background, and repetitive sequences are highly methylated. Plots in orange and yellow are for data from E11.5 and E14.5, respectively. TES indicates transcription end sites; TSS, transcription start sites.
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fig02: Distribution of DNA methylation across the mouse genome and various types of genomic elements in the developing heart. A, Cartoon depicting the genic regions (enhancer, promoter and genebody). B, Violin plot (a combination of a box plot and a kernel density plot) showing the distributions of tag counts for all ACGT (top) or differential methylated (bottom) sites in different genomic regions. As number of tag counts is inversely correlated to level of CG methylation, these plots indicate that gene promoters and regulatory regions exhibit significantly lower levels of DNA methylation than genomic background, and repetitive sequences are highly methylated. Plots in orange and yellow are for data from E11.5 and E14.5, respectively. TES indicates transcription end sites; TSS, transcription start sites.

Mentions: We then catalogued the ACGT sites into genic sites (−50 kb of transcription start sites [TSS] to +0.5 kb of transcription end sites [TES] and intergenic sites) (Figure 2A), with the former further separated into 3 types: promoter proximal sites (−5 kb to +0.5 kb of TSS), gene body sites (+0.5 kb of TSS to TES), and promoter distal or enhancer sites (Figure 2B, top panel), and also determined the distribution of ACGT tag counts across the genome by intersecting the genome‐wide ACGT methylation profiles with several genomic features, including CpG islands, CTCF‐binding sites, RefSeq genes, repetitive elements, and regulatory elements (Figure 2B, bottom panel). The gene annotation, CpG islands, and repeats were downloaded from the UCSC browser. Additionally, lists of regulatory elements for embryonic hearts were obtained from previous studies, including 3596 P300 binding sites identified for E11.5 hearts, 69 073 P300‐marked enhancers, 14 874 CTCF sites, and 45 981 regions with the H3K27ac modification (a histone mark for active enhancer) for E14.5.40–42


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)

Distribution of DNA methylation across the mouse genome and various types of genomic elements in the developing heart. A, Cartoon depicting the genic regions (enhancer, promoter and genebody). B, Violin plot (a combination of a box plot and a kernel density plot) showing the distributions of tag counts for all ACGT (top) or differential methylated (bottom) sites in different genomic regions. As number of tag counts is inversely correlated to level of CG methylation, these plots indicate that gene promoters and regulatory regions exhibit significantly lower levels of DNA methylation than genomic background, and repetitive sequences are highly methylated. Plots in orange and yellow are for data from E11.5 and E14.5, respectively. TES indicates transcription end sites; TSS, transcription start sites.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

fig02: Distribution of DNA methylation across the mouse genome and various types of genomic elements in the developing heart. A, Cartoon depicting the genic regions (enhancer, promoter and genebody). B, Violin plot (a combination of a box plot and a kernel density plot) showing the distributions of tag counts for all ACGT (top) or differential methylated (bottom) sites in different genomic regions. As number of tag counts is inversely correlated to level of CG methylation, these plots indicate that gene promoters and regulatory regions exhibit significantly lower levels of DNA methylation than genomic background, and repetitive sequences are highly methylated. Plots in orange and yellow are for data from E11.5 and E14.5, respectively. TES indicates transcription end sites; TSS, transcription start sites.
Mentions: We then catalogued the ACGT sites into genic sites (−50 kb of transcription start sites [TSS] to +0.5 kb of transcription end sites [TES] and intergenic sites) (Figure 2A), with the former further separated into 3 types: promoter proximal sites (−5 kb to +0.5 kb of TSS), gene body sites (+0.5 kb of TSS to TES), and promoter distal or enhancer sites (Figure 2B, top panel), and also determined the distribution of ACGT tag counts across the genome by intersecting the genome‐wide ACGT methylation profiles with several genomic features, including CpG islands, CTCF‐binding sites, RefSeq genes, repetitive elements, and regulatory elements (Figure 2B, bottom panel). The gene annotation, CpG islands, and repeats were downloaded from the UCSC browser. Additionally, lists of regulatory elements for embryonic hearts were obtained from previous studies, including 3596 P300 binding sites identified for E11.5 hearts, 69 073 P300‐marked enhancers, 14 874 CTCF sites, and 45 981 regions with the H3K27ac modification (a histone mark for active enhancer) for E14.5.40–42

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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Related in: MedlinePlus