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Arterial endothelial methylome: differential DNA methylation in athero-susceptible disturbed flow regions in vivo.

Jiang YZ, Manduchi E, Stoeckert CJ, Davies PF - BMC Genomics (2015)

Bottom Line: Gender-specific DMRs associated with ciliogenesis that may be linked to defects in cilia development were also identified in AA DMRs.An endothelial methylome analysis identifies epigenetic DMR characteristics associated with transcriptional regulation in regions of atherosusceptibility in swine aorta in vivo.The data represent the first methylome blueprint for spatio-temporal analyses of lesion susceptibility predisposing to endothelial dysfunction in complex flow environments in vivo.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology & Laboratory Medicine and Institute for Medicine & Engineering, Perelman School of Medicine, University of Pennsylvania, 1010 Vagelos Building, 3340 Smith Walk, Philadelphia, PA, 19104, USA. jyizhou@mail.med.upenn.edu.

ABSTRACT

Background: Atherosclerosis is a heterogeneously distributed disease of arteries in which the endothelium plays an important central role. Spatial transcriptome profiling of endothelium in pre-lesional arteries has demonstrated differential phenotypes primed for athero-susceptibility at hemodynamic sites associated with disturbed blood flow. DNA methylation is a powerful epigenetic regulator of endothelial transcription recently associated with flow characteristics. We investigated differential DNA methylation in flow region-specific aortic endothelial cells in vivo in adult domestic male and female swine.

Results: Genome-wide DNA methylation was profiled in endothelial cells (EC) isolated from two robust locations of differing patho-susceptibility:--an athero-susceptible site located at the inner curvature of the aortic arch (AA) and an athero-protected region in the descending thoracic (DT) aorta. Complete methylated DNA immunoprecipitation sequencing (MeDIP-seq) identified over 5500 endothelial differentially methylated regions (DMRs). DMR density was significantly enriched in exons and 5'UTR sequences of annotated genes, 60 of which are linked to cardiovascular disease. The set of DMR-associated genes was enriched in transcriptional regulation, pattern specification HOX loci, oxidative stress and the ER stress adaptive pathway, all categories linked to athero-susceptible endothelium. Examination of the relationship between DMR and mRNA in HOXA genes demonstrated a significant inverse relationship between CpG island promoter methylation and gene expression. Methylation-specific PCR (MSP) confirmed differential CpG methylation of HOXA genes, the ER stress gene ATF4, inflammatory regulator microRNA-10a and ARHGAP25 that encodes a negative regulator of Rho GTPases involved in cytoskeleton remodeling. Gender-specific DMRs associated with ciliogenesis that may be linked to defects in cilia development were also identified in AA DMRs.

Conclusions: An endothelial methylome analysis identifies epigenetic DMR characteristics associated with transcriptional regulation in regions of atherosusceptibility in swine aorta in vivo. The data represent the first methylome blueprint for spatio-temporal analyses of lesion susceptibility predisposing to endothelial dysfunction in complex flow environments in vivo.

No MeSH data available.


Related in: MedlinePlus

DNA methylation and DMRs in HOXA loci and the relationships to mRNA expression. a: The UCSC Genome Browser was used to visualize DNA methylation level of CpG sites in AA (blue lines) and DT (purple lines) in HOXA loci (chr18). Bar = 10 kb. 1 = 100 % methylated, 0 = unmethylated. DMRs are shown as blue and purple regions, which represent AA hypermethylation and hypomethylation respectively (n = 12 animals, FDR < 0.1). The positions of CpG islands (green) and HOX genes (dark red) are shown. mRNA expression in DT and AA was measured for HOXA1-A7, HOXA10 AND HOXA13. b: Relative (AA/DT) gene expression plotted against relative DMR demonstrating an inverse relationship
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Fig6: DNA methylation and DMRs in HOXA loci and the relationships to mRNA expression. a: The UCSC Genome Browser was used to visualize DNA methylation level of CpG sites in AA (blue lines) and DT (purple lines) in HOXA loci (chr18). Bar = 10 kb. 1 = 100 % methylated, 0 = unmethylated. DMRs are shown as blue and purple regions, which represent AA hypermethylation and hypomethylation respectively (n = 12 animals, FDR < 0.1). The positions of CpG islands (green) and HOX genes (dark red) are shown. mRNA expression in DT and AA was measured for HOXA1-A7, HOXA10 AND HOXA13. b: Relative (AA/DT) gene expression plotted against relative DMR demonstrating an inverse relationship

Mentions: The prominence of HOX gene association with DMRs warranted further evaluation of these relationships. The recent identification of HOXA5 methylation in disturbed flow in mouse carotid endothelium20 led us to examine HOXA loci in more detail in our large animal model. Figure 6a shows a high resolution map of 18 DMRs clustering at gene- and CGI-rich regions of HOXA loci on chr18. Hypermethylated or hypomethylated DMR regions tended to be contiguous, perhaps associated with higher-order chromatin structure [36]. For example, 11 consecutive DMRs spanning 15 kb in the HOXA4 to HOXA7 locus were hypermethylated in AA.Fig. 6


Arterial endothelial methylome: differential DNA methylation in athero-susceptible disturbed flow regions in vivo.

Jiang YZ, Manduchi E, Stoeckert CJ, Davies PF - BMC Genomics (2015)

DNA methylation and DMRs in HOXA loci and the relationships to mRNA expression. a: The UCSC Genome Browser was used to visualize DNA methylation level of CpG sites in AA (blue lines) and DT (purple lines) in HOXA loci (chr18). Bar = 10 kb. 1 = 100 % methylated, 0 = unmethylated. DMRs are shown as blue and purple regions, which represent AA hypermethylation and hypomethylation respectively (n = 12 animals, FDR < 0.1). The positions of CpG islands (green) and HOX genes (dark red) are shown. mRNA expression in DT and AA was measured for HOXA1-A7, HOXA10 AND HOXA13. b: Relative (AA/DT) gene expression plotted against relative DMR demonstrating an inverse relationship
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
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getmorefigures.php?uid=PMC4492093&req=5

Fig6: DNA methylation and DMRs in HOXA loci and the relationships to mRNA expression. a: The UCSC Genome Browser was used to visualize DNA methylation level of CpG sites in AA (blue lines) and DT (purple lines) in HOXA loci (chr18). Bar = 10 kb. 1 = 100 % methylated, 0 = unmethylated. DMRs are shown as blue and purple regions, which represent AA hypermethylation and hypomethylation respectively (n = 12 animals, FDR < 0.1). The positions of CpG islands (green) and HOX genes (dark red) are shown. mRNA expression in DT and AA was measured for HOXA1-A7, HOXA10 AND HOXA13. b: Relative (AA/DT) gene expression plotted against relative DMR demonstrating an inverse relationship
Mentions: The prominence of HOX gene association with DMRs warranted further evaluation of these relationships. The recent identification of HOXA5 methylation in disturbed flow in mouse carotid endothelium20 led us to examine HOXA loci in more detail in our large animal model. Figure 6a shows a high resolution map of 18 DMRs clustering at gene- and CGI-rich regions of HOXA loci on chr18. Hypermethylated or hypomethylated DMR regions tended to be contiguous, perhaps associated with higher-order chromatin structure [36]. For example, 11 consecutive DMRs spanning 15 kb in the HOXA4 to HOXA7 locus were hypermethylated in AA.Fig. 6

Bottom Line: Gender-specific DMRs associated with ciliogenesis that may be linked to defects in cilia development were also identified in AA DMRs.An endothelial methylome analysis identifies epigenetic DMR characteristics associated with transcriptional regulation in regions of atherosusceptibility in swine aorta in vivo.The data represent the first methylome blueprint for spatio-temporal analyses of lesion susceptibility predisposing to endothelial dysfunction in complex flow environments in vivo.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology & Laboratory Medicine and Institute for Medicine & Engineering, Perelman School of Medicine, University of Pennsylvania, 1010 Vagelos Building, 3340 Smith Walk, Philadelphia, PA, 19104, USA. jyizhou@mail.med.upenn.edu.

ABSTRACT

Background: Atherosclerosis is a heterogeneously distributed disease of arteries in which the endothelium plays an important central role. Spatial transcriptome profiling of endothelium in pre-lesional arteries has demonstrated differential phenotypes primed for athero-susceptibility at hemodynamic sites associated with disturbed blood flow. DNA methylation is a powerful epigenetic regulator of endothelial transcription recently associated with flow characteristics. We investigated differential DNA methylation in flow region-specific aortic endothelial cells in vivo in adult domestic male and female swine.

Results: Genome-wide DNA methylation was profiled in endothelial cells (EC) isolated from two robust locations of differing patho-susceptibility:--an athero-susceptible site located at the inner curvature of the aortic arch (AA) and an athero-protected region in the descending thoracic (DT) aorta. Complete methylated DNA immunoprecipitation sequencing (MeDIP-seq) identified over 5500 endothelial differentially methylated regions (DMRs). DMR density was significantly enriched in exons and 5'UTR sequences of annotated genes, 60 of which are linked to cardiovascular disease. The set of DMR-associated genes was enriched in transcriptional regulation, pattern specification HOX loci, oxidative stress and the ER stress adaptive pathway, all categories linked to athero-susceptible endothelium. Examination of the relationship between DMR and mRNA in HOXA genes demonstrated a significant inverse relationship between CpG island promoter methylation and gene expression. Methylation-specific PCR (MSP) confirmed differential CpG methylation of HOXA genes, the ER stress gene ATF4, inflammatory regulator microRNA-10a and ARHGAP25 that encodes a negative regulator of Rho GTPases involved in cytoskeleton remodeling. Gender-specific DMRs associated with ciliogenesis that may be linked to defects in cilia development were also identified in AA DMRs.

Conclusions: An endothelial methylome analysis identifies epigenetic DMR characteristics associated with transcriptional regulation in regions of atherosusceptibility in swine aorta in vivo. The data represent the first methylome blueprint for spatio-temporal analyses of lesion susceptibility predisposing to endothelial dysfunction in complex flow environments in vivo.

No MeSH data available.


Related in: MedlinePlus