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Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.

Lowdon RF, Zhang B, Bilenky M, Mauro T, Li D, Gascard P, Sigaroudinia M, Farnham PJ, Bastian BC, Tlsty TD, Marra MA, Hirst M, Costello JF, Wang T, Cheng JB - Nat Commun (2014)

Bottom Line: This suggests that SE origin contributes to DNA methylation patterning, while shared skin tissue environment has limited effect on epidermal keratinocytes.They are also enriched for enhancer- and promoter-associated histone modifications in SE-derived cells, and for binding motifs of transcription factors important in keratinocyte and mammary gland biology.Thus, epigenomic analysis of cell types with common developmental origin reveals an epigenetic signature that underlies a shared gene regulatory network.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, St Louis, Missouri 63108, USA.

ABSTRACT
Developmental history shapes the epigenome and biological function of differentiated cells. Epigenomic patterns have been broadly attributed to the three embryonic germ layers. Here we investigate how developmental origin influences epigenomes. We compare key epigenomes of cell types derived from surface ectoderm (SE), including keratinocytes and breast luminal and myoepithelial cells, against neural crest-derived melanocytes and mesoderm-derived dermal fibroblasts, to identify SE differentially methylated regions (SE-DMRs). DNA methylomes of neonatal keratinocytes share many more DMRs with adult breast luminal and myoepithelial cells than with melanocytes and fibroblasts from the same neonatal skin. This suggests that SE origin contributes to DNA methylation patterning, while shared skin tissue environment has limited effect on epidermal keratinocytes. Hypomethylated SE-DMRs are in proximity to genes with SE relevant functions. They are also enriched for enhancer- and promoter-associated histone modifications in SE-derived cells, and for binding motifs of transcription factors important in keratinocyte and mammary gland biology. Thus, epigenomic analysis of cell types with common developmental origin reveals an epigenetic signature that underlies a shared gene regulatory network.

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Identification and characterization of skin cell type-specific DMRs(a) Hypomethylation and hypermethylation percentages for each set of skin cell type-specific DMRs defined by comparison against the other two skin cell types. The total number for each set of cell type-specific DMRs is listed above the pie chart. DMRs are 500bp windows.(b) Histone modification patterns at skin cell type-specific hypomethylated DMRs.(c) Skin cell type RNA expression levels for genes with hypomethylated cell type-specific DMRs in their promoter regions. Each panel depicts expression values for a set of cell type-specific DMR-associated genes. Plotted values are RNA-seq RPKM values over exons, averaged (mean) over three biological replicates. For each boxplot, the middle line indicates the median value, top and bottom box edges are the third and first quartile boundaries respectively. The upper whisker is the highest data value within 1.5 times the interquartile range; the lower whisker indicates the lowest value within 1.5 times the interquartile range. The interquartile range is the distance between the first and third quartiles. Points indicate data beyond whiskers. Logarithmic scale transformations were applied before boxplot statistics were computed. RPKM distributions for a given set of cell type-specific DMR-associated genes in the specified cell type compared to other cell types were statistically significant (Wilcoxon ranked test, paired, * indicates P-value < 0.003, Keratinocyte-DMRs n = 602, Fibroblast-DMRs n = 108, Melanocyte-DMRs n = 74; K = keratinocytes, F = fibroblasts, M = melanocytes; Supplementary Tables 3–5).(d) Heat map depicting selected gene ontology terms enriched for keratinocyte, fibroblast, and melanocyte hypomethylated cell type-specific DMRs. K = keratinocytes, F = fibroblasts, M = melanocytes. Color intensity represents the negative log10 transformed p-value of enrichment of a given cell type-specific DMR set for association with the listed gene ontology term. Full datasets are in Supplementary Data 3.
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Figure 2: Identification and characterization of skin cell type-specific DMRs(a) Hypomethylation and hypermethylation percentages for each set of skin cell type-specific DMRs defined by comparison against the other two skin cell types. The total number for each set of cell type-specific DMRs is listed above the pie chart. DMRs are 500bp windows.(b) Histone modification patterns at skin cell type-specific hypomethylated DMRs.(c) Skin cell type RNA expression levels for genes with hypomethylated cell type-specific DMRs in their promoter regions. Each panel depicts expression values for a set of cell type-specific DMR-associated genes. Plotted values are RNA-seq RPKM values over exons, averaged (mean) over three biological replicates. For each boxplot, the middle line indicates the median value, top and bottom box edges are the third and first quartile boundaries respectively. The upper whisker is the highest data value within 1.5 times the interquartile range; the lower whisker indicates the lowest value within 1.5 times the interquartile range. The interquartile range is the distance between the first and third quartiles. Points indicate data beyond whiskers. Logarithmic scale transformations were applied before boxplot statistics were computed. RPKM distributions for a given set of cell type-specific DMR-associated genes in the specified cell type compared to other cell types were statistically significant (Wilcoxon ranked test, paired, * indicates P-value < 0.003, Keratinocyte-DMRs n = 602, Fibroblast-DMRs n = 108, Melanocyte-DMRs n = 74; K = keratinocytes, F = fibroblasts, M = melanocytes; Supplementary Tables 3–5).(d) Heat map depicting selected gene ontology terms enriched for keratinocyte, fibroblast, and melanocyte hypomethylated cell type-specific DMRs. K = keratinocytes, F = fibroblasts, M = melanocytes. Color intensity represents the negative log10 transformed p-value of enrichment of a given cell type-specific DMR set for association with the listed gene ontology term. Full datasets are in Supplementary Data 3.

Mentions: We identified 12,892 regions encompassing 193,202 CpGs with a DNA methylation status unique to one of the three skin cell types and consistent across all three individuals (Methods, Figure 2a, Supplementary Fig. 1–3, 4a, Supplementary Notes 1–3, Supplementary Table 1). The majority of these skin cell type-specific DMRs were hypomethylated (Figure 2a), suggesting potential cell type-specific regulatory activity at these regions4,12,13. 40–46% of the DMRs were intergenic and 5–9% were associated with RefSeq annotated gene promoters (Supplementary Fig. 5); non-CGI promoters were enriched among cell type-specific DMRs (Supplementary Note 4; Supplementary Table 2). 80–91% of hypomethylated cell type-specific DMRs overlapped with regulatory element-associated histone modifications in the same cell type (Figure 2b). Accordingly, hypomethylation of cell type-specific DMRs at gene promoters correlated with increased gene expression relative to the other two cell types where the DMR was hypermethylated (Figure 2c, Supplementary Tables 3–5). Gene Ontology (GO) analysis using the GREAT14 tool on hypomethylated cell type-specific DMRs showed strong enrichment for biological processes relevant to each cell type (e.g. extracellular matrix organization for fibroblasts (P-value=9.05E-45) and pigmentation for melanocytes (P-value=2.43E-06); Figure 2d; Supplementary Data 3). These data suggest skin cell type-specific DMRs occur primarily at distal enhancers and regulate genes relevant to each cell type.


Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.

Lowdon RF, Zhang B, Bilenky M, Mauro T, Li D, Gascard P, Sigaroudinia M, Farnham PJ, Bastian BC, Tlsty TD, Marra MA, Hirst M, Costello JF, Wang T, Cheng JB - Nat Commun (2014)

Identification and characterization of skin cell type-specific DMRs(a) Hypomethylation and hypermethylation percentages for each set of skin cell type-specific DMRs defined by comparison against the other two skin cell types. The total number for each set of cell type-specific DMRs is listed above the pie chart. DMRs are 500bp windows.(b) Histone modification patterns at skin cell type-specific hypomethylated DMRs.(c) Skin cell type RNA expression levels for genes with hypomethylated cell type-specific DMRs in their promoter regions. Each panel depicts expression values for a set of cell type-specific DMR-associated genes. Plotted values are RNA-seq RPKM values over exons, averaged (mean) over three biological replicates. For each boxplot, the middle line indicates the median value, top and bottom box edges are the third and first quartile boundaries respectively. The upper whisker is the highest data value within 1.5 times the interquartile range; the lower whisker indicates the lowest value within 1.5 times the interquartile range. The interquartile range is the distance between the first and third quartiles. Points indicate data beyond whiskers. Logarithmic scale transformations were applied before boxplot statistics were computed. RPKM distributions for a given set of cell type-specific DMR-associated genes in the specified cell type compared to other cell types were statistically significant (Wilcoxon ranked test, paired, * indicates P-value < 0.003, Keratinocyte-DMRs n = 602, Fibroblast-DMRs n = 108, Melanocyte-DMRs n = 74; K = keratinocytes, F = fibroblasts, M = melanocytes; Supplementary Tables 3–5).(d) Heat map depicting selected gene ontology terms enriched for keratinocyte, fibroblast, and melanocyte hypomethylated cell type-specific DMRs. K = keratinocytes, F = fibroblasts, M = melanocytes. Color intensity represents the negative log10 transformed p-value of enrichment of a given cell type-specific DMR set for association with the listed gene ontology term. Full datasets are in Supplementary Data 3.
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Figure 2: Identification and characterization of skin cell type-specific DMRs(a) Hypomethylation and hypermethylation percentages for each set of skin cell type-specific DMRs defined by comparison against the other two skin cell types. The total number for each set of cell type-specific DMRs is listed above the pie chart. DMRs are 500bp windows.(b) Histone modification patterns at skin cell type-specific hypomethylated DMRs.(c) Skin cell type RNA expression levels for genes with hypomethylated cell type-specific DMRs in their promoter regions. Each panel depicts expression values for a set of cell type-specific DMR-associated genes. Plotted values are RNA-seq RPKM values over exons, averaged (mean) over three biological replicates. For each boxplot, the middle line indicates the median value, top and bottom box edges are the third and first quartile boundaries respectively. The upper whisker is the highest data value within 1.5 times the interquartile range; the lower whisker indicates the lowest value within 1.5 times the interquartile range. The interquartile range is the distance between the first and third quartiles. Points indicate data beyond whiskers. Logarithmic scale transformations were applied before boxplot statistics were computed. RPKM distributions for a given set of cell type-specific DMR-associated genes in the specified cell type compared to other cell types were statistically significant (Wilcoxon ranked test, paired, * indicates P-value < 0.003, Keratinocyte-DMRs n = 602, Fibroblast-DMRs n = 108, Melanocyte-DMRs n = 74; K = keratinocytes, F = fibroblasts, M = melanocytes; Supplementary Tables 3–5).(d) Heat map depicting selected gene ontology terms enriched for keratinocyte, fibroblast, and melanocyte hypomethylated cell type-specific DMRs. K = keratinocytes, F = fibroblasts, M = melanocytes. Color intensity represents the negative log10 transformed p-value of enrichment of a given cell type-specific DMR set for association with the listed gene ontology term. Full datasets are in Supplementary Data 3.
Mentions: We identified 12,892 regions encompassing 193,202 CpGs with a DNA methylation status unique to one of the three skin cell types and consistent across all three individuals (Methods, Figure 2a, Supplementary Fig. 1–3, 4a, Supplementary Notes 1–3, Supplementary Table 1). The majority of these skin cell type-specific DMRs were hypomethylated (Figure 2a), suggesting potential cell type-specific regulatory activity at these regions4,12,13. 40–46% of the DMRs were intergenic and 5–9% were associated with RefSeq annotated gene promoters (Supplementary Fig. 5); non-CGI promoters were enriched among cell type-specific DMRs (Supplementary Note 4; Supplementary Table 2). 80–91% of hypomethylated cell type-specific DMRs overlapped with regulatory element-associated histone modifications in the same cell type (Figure 2b). Accordingly, hypomethylation of cell type-specific DMRs at gene promoters correlated with increased gene expression relative to the other two cell types where the DMR was hypermethylated (Figure 2c, Supplementary Tables 3–5). Gene Ontology (GO) analysis using the GREAT14 tool on hypomethylated cell type-specific DMRs showed strong enrichment for biological processes relevant to each cell type (e.g. extracellular matrix organization for fibroblasts (P-value=9.05E-45) and pigmentation for melanocytes (P-value=2.43E-06); Figure 2d; Supplementary Data 3). These data suggest skin cell type-specific DMRs occur primarily at distal enhancers and regulate genes relevant to each cell type.

Bottom Line: This suggests that SE origin contributes to DNA methylation patterning, while shared skin tissue environment has limited effect on epidermal keratinocytes.They are also enriched for enhancer- and promoter-associated histone modifications in SE-derived cells, and for binding motifs of transcription factors important in keratinocyte and mammary gland biology.Thus, epigenomic analysis of cell types with common developmental origin reveals an epigenetic signature that underlies a shared gene regulatory network.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, St Louis, Missouri 63108, USA.

ABSTRACT
Developmental history shapes the epigenome and biological function of differentiated cells. Epigenomic patterns have been broadly attributed to the three embryonic germ layers. Here we investigate how developmental origin influences epigenomes. We compare key epigenomes of cell types derived from surface ectoderm (SE), including keratinocytes and breast luminal and myoepithelial cells, against neural crest-derived melanocytes and mesoderm-derived dermal fibroblasts, to identify SE differentially methylated regions (SE-DMRs). DNA methylomes of neonatal keratinocytes share many more DMRs with adult breast luminal and myoepithelial cells than with melanocytes and fibroblasts from the same neonatal skin. This suggests that SE origin contributes to DNA methylation patterning, while shared skin tissue environment has limited effect on epidermal keratinocytes. Hypomethylated SE-DMRs are in proximity to genes with SE relevant functions. They are also enriched for enhancer- and promoter-associated histone modifications in SE-derived cells, and for binding motifs of transcription factors important in keratinocyte and mammary gland biology. Thus, epigenomic analysis of cell types with common developmental origin reveals an epigenetic signature that underlies a shared gene regulatory network.

Show MeSH
Related in: MedlinePlus