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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

Methylation and Athero-susceptible DMR distributions in genomic features. a: DNA methylation and b: DMR density in genomic features. For each genomic feature (intergenic, gene, etc.), DNA methylation or DMR density was computed as the number of reads or DMRs overlapping the portion of the genome covered by that feature type divided by the size of such portion of the genome. In this figure, the flanked gene was defined as the region from 10 kb upstream of the transcription start site to the end of the transcript. Intergenic regions were defined as the part of the genome not contained in that region. As gene models we used ENSEMBL 71 for Sscrofa10.2 (30,586 transcripts). n = 12 animals, 24 MeDIP seq libraries
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Fig4: Methylation and Athero-susceptible DMR distributions in genomic features. a: DNA methylation and b: DMR density in genomic features. For each genomic feature (intergenic, gene, etc.), DNA methylation or DMR density was computed as the number of reads or DMRs overlapping the portion of the genome covered by that feature type divided by the size of such portion of the genome. In this figure, the flanked gene was defined as the region from 10 kb upstream of the transcription start site to the end of the transcript. Intergenic regions were defined as the part of the genome not contained in that region. As gene models we used ENSEMBL 71 for Sscrofa10.2 (30,586 transcripts). n = 12 animals, 24 MeDIP seq libraries

Mentions: To characterize the relation of athero-susceptible DMRs to genomic features, we analyzed the density of DNA methylation and DMRs in functional genomic elements. As gene models we used ENSEMBL GENES 71 for Sscrofa10.2 (30,586 transcripts). Dot-blot data showed that the global methylation level is not significantly different between AA and DT (Additional file 1: Figure S3); however the distributions to features within each site (AA, DT) were significantly different. Consistent with Fig. 2, DNA methylation and DMRs were mostly enriched in the CGIs. Although methylation regions (MRs) density was comparable between 5’ and 3’UTR (Fig. 4a), athero-susceptible DMR density was 2.8-fold higher in the 5’UTR than in the 3’UTR (Fig. 4b). The enrichment of DMRs in the 5’UTR suggests a functional role of DMRs in contributing to the transcriptional activity of genes. Higher methylation and DMR densities were also noted in exons (Fig. 4a,b); 3.3-fold and 4.7-fold higher than in introns for methylation and DMR densities respectively. Numerous studies have shown that DNA methylation in the promoter, gene body and exons regulates transcription by promoter suppression, transcription elongation efficiency, alternative RNA splicing and exon recognition [22, 26, 27]. Thus, these data suggest that athero-susceptible DMRs functionally associate with gene regulation at the level of the 5’ UTR and individual gene/exons, consistent with a contribution to the heterogeneity of endothelia in diverse chemical and physical environments.Fig. 4


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)

Methylation and Athero-susceptible DMR distributions in genomic features. a: DNA methylation and b: DMR density in genomic features. For each genomic feature (intergenic, gene, etc.), DNA methylation or DMR density was computed as the number of reads or DMRs overlapping the portion of the genome covered by that feature type divided by the size of such portion of the genome. In this figure, the flanked gene was defined as the region from 10 kb upstream of the transcription start site to the end of the transcript. Intergenic regions were defined as the part of the genome not contained in that region. As gene models we used ENSEMBL 71 for Sscrofa10.2 (30,586 transcripts). n = 12 animals, 24 MeDIP seq libraries
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Methylation and Athero-susceptible DMR distributions in genomic features. a: DNA methylation and b: DMR density in genomic features. For each genomic feature (intergenic, gene, etc.), DNA methylation or DMR density was computed as the number of reads or DMRs overlapping the portion of the genome covered by that feature type divided by the size of such portion of the genome. In this figure, the flanked gene was defined as the region from 10 kb upstream of the transcription start site to the end of the transcript. Intergenic regions were defined as the part of the genome not contained in that region. As gene models we used ENSEMBL 71 for Sscrofa10.2 (30,586 transcripts). n = 12 animals, 24 MeDIP seq libraries
Mentions: To characterize the relation of athero-susceptible DMRs to genomic features, we analyzed the density of DNA methylation and DMRs in functional genomic elements. As gene models we used ENSEMBL GENES 71 for Sscrofa10.2 (30,586 transcripts). Dot-blot data showed that the global methylation level is not significantly different between AA and DT (Additional file 1: Figure S3); however the distributions to features within each site (AA, DT) were significantly different. Consistent with Fig. 2, DNA methylation and DMRs were mostly enriched in the CGIs. Although methylation regions (MRs) density was comparable between 5’ and 3’UTR (Fig. 4a), athero-susceptible DMR density was 2.8-fold higher in the 5’UTR than in the 3’UTR (Fig. 4b). The enrichment of DMRs in the 5’UTR suggests a functional role of DMRs in contributing to the transcriptional activity of genes. Higher methylation and DMR densities were also noted in exons (Fig. 4a,b); 3.3-fold and 4.7-fold higher than in introns for methylation and DMR densities respectively. Numerous studies have shown that DNA methylation in the promoter, gene body and exons regulates transcription by promoter suppression, transcription elongation efficiency, alternative RNA splicing and exon recognition [22, 26, 27]. Thus, these data suggest that athero-susceptible DMRs functionally associate with gene regulation at the level of the 5’ UTR and individual gene/exons, consistent with a contribution to the heterogeneity of endothelia in diverse chemical and physical environments.Fig. 4

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