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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 surface ectoderm-DMRs(a) Venn diagram showing surface ectoderm-specific DMRs, defined as the overlap of keratinocyte, breast myoepithelial, and luminal epithelial cell DMRs.(b) Enrichment of H3K4me1, H3K4me3, H3K27ac, and DNAse I-hypersensitivity at SE-DMRs. Each heat map column represents histone modification ChIP-seq or DNAse-seq signal at 500bp SE-DMRs +/− 5 kb. Each heat map row represents a single hypomethylated SE-DMR, ordered by decreasing H3K4me1 signal, then increasing H3K4me3 signal.(c) Bar plot of enrichment values for top ten enriched TFBS motifs determined by motif scanning of hypomethylated SE-DMRs using FIMO47 (Methods). Enrichment based on hg19 genome background.(d) Selected gene ontology terms enriched for hypomethylated surface ectoderm-DMRs. P-value of enrichment calculated by GREAT14. Full list of enriched GO terms is in Supplementary Data 5.(e) Box plots showing RNA expression levels for genes with hypomethylated SE-DMRs in promoter regions. Skin cell type RNA-seq RPKM values over exons are averages (mean) of three biological replicates; luminal epithelial and myoepithelial values are a single biological replicate. 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 transformation was applied before boxplot statistics were computed. RPKM distributions for SE cell type expression levels vs. non-SE cell type expression levels are statistically significant (Wilcoxon-ranked test, paired, * indicates P-value < 0.02; n = 150 genes; Lum = breast luminal epithelial cells, Myo = breast myoepithelial cells, K= keratinocytes, F = fibroblasts, M = melanocytes; Supplementary Table 6).
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Figure 4: Identification and characterization of surface ectoderm-DMRs(a) Venn diagram showing surface ectoderm-specific DMRs, defined as the overlap of keratinocyte, breast myoepithelial, and luminal epithelial cell DMRs.(b) Enrichment of H3K4me1, H3K4me3, H3K27ac, and DNAse I-hypersensitivity at SE-DMRs. Each heat map column represents histone modification ChIP-seq or DNAse-seq signal at 500bp SE-DMRs +/− 5 kb. Each heat map row represents a single hypomethylated SE-DMR, ordered by decreasing H3K4me1 signal, then increasing H3K4me3 signal.(c) Bar plot of enrichment values for top ten enriched TFBS motifs determined by motif scanning of hypomethylated SE-DMRs using FIMO47 (Methods). Enrichment based on hg19 genome background.(d) Selected gene ontology terms enriched for hypomethylated surface ectoderm-DMRs. P-value of enrichment calculated by GREAT14. Full list of enriched GO terms is in Supplementary Data 5.(e) Box plots showing RNA expression levels for genes with hypomethylated SE-DMRs in promoter regions. Skin cell type RNA-seq RPKM values over exons are averages (mean) of three biological replicates; luminal epithelial and myoepithelial values are a single biological replicate. 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 transformation was applied before boxplot statistics were computed. RPKM distributions for SE cell type expression levels vs. non-SE cell type expression levels are statistically significant (Wilcoxon-ranked test, paired, * indicates P-value < 0.02; n = 150 genes; Lum = breast luminal epithelial cells, Myo = breast myoepithelial cells, K= keratinocytes, F = fibroblasts, M = melanocytes; Supplementary Table 6).

Mentions: In the absence of a strong skin tissue-specific epigenetic signature, we hypothesized that developmental origin is a major determinant of skin cell type epigenetic patterns. We explored this hypothesis by focusing on skin keratinocytes and breast epithelial cells, which are both derived from surface ectoderm15. Consistent with their shared developmental origin, neonatal skin keratinocytes clustered with adult breast epithelial cell types based on DNA methylation values at the DMRs previously identified in skin and non-skin cell pairwise comparisons (Figure 3c). To specifically define the DNA methylation signature of surface ectoderm-derived cell types, we identified DMRs for each of the surface ectodermal cell types in a pairwise manner compared to neonatal skin melanocytes and fibroblasts, which are derived from other embryonic germ layers (Supplementary Fig. 4c). There were 1,392 DMRs with the same methylation state exclusively in keratinocyte, breast myoepithelial, and breast luminal epithelial cells relative to the two other cell types, which we inferred to be surface ectoderm-specific DMRs (SE-DMRs) (Methods, Figure 4a). Therefore, common developmental origin influences surface ectoderm-derived cell epigenomes to a greater extent than does the shared skin tissue environment.


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 surface ectoderm-DMRs(a) Venn diagram showing surface ectoderm-specific DMRs, defined as the overlap of keratinocyte, breast myoepithelial, and luminal epithelial cell DMRs.(b) Enrichment of H3K4me1, H3K4me3, H3K27ac, and DNAse I-hypersensitivity at SE-DMRs. Each heat map column represents histone modification ChIP-seq or DNAse-seq signal at 500bp SE-DMRs +/− 5 kb. Each heat map row represents a single hypomethylated SE-DMR, ordered by decreasing H3K4me1 signal, then increasing H3K4me3 signal.(c) Bar plot of enrichment values for top ten enriched TFBS motifs determined by motif scanning of hypomethylated SE-DMRs using FIMO47 (Methods). Enrichment based on hg19 genome background.(d) Selected gene ontology terms enriched for hypomethylated surface ectoderm-DMRs. P-value of enrichment calculated by GREAT14. Full list of enriched GO terms is in Supplementary Data 5.(e) Box plots showing RNA expression levels for genes with hypomethylated SE-DMRs in promoter regions. Skin cell type RNA-seq RPKM values over exons are averages (mean) of three biological replicates; luminal epithelial and myoepithelial values are a single biological replicate. 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 transformation was applied before boxplot statistics were computed. RPKM distributions for SE cell type expression levels vs. non-SE cell type expression levels are statistically significant (Wilcoxon-ranked test, paired, * indicates P-value < 0.02; n = 150 genes; Lum = breast luminal epithelial cells, Myo = breast myoepithelial cells, K= keratinocytes, F = fibroblasts, M = melanocytes; Supplementary Table 6).
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Figure 4: Identification and characterization of surface ectoderm-DMRs(a) Venn diagram showing surface ectoderm-specific DMRs, defined as the overlap of keratinocyte, breast myoepithelial, and luminal epithelial cell DMRs.(b) Enrichment of H3K4me1, H3K4me3, H3K27ac, and DNAse I-hypersensitivity at SE-DMRs. Each heat map column represents histone modification ChIP-seq or DNAse-seq signal at 500bp SE-DMRs +/− 5 kb. Each heat map row represents a single hypomethylated SE-DMR, ordered by decreasing H3K4me1 signal, then increasing H3K4me3 signal.(c) Bar plot of enrichment values for top ten enriched TFBS motifs determined by motif scanning of hypomethylated SE-DMRs using FIMO47 (Methods). Enrichment based on hg19 genome background.(d) Selected gene ontology terms enriched for hypomethylated surface ectoderm-DMRs. P-value of enrichment calculated by GREAT14. Full list of enriched GO terms is in Supplementary Data 5.(e) Box plots showing RNA expression levels for genes with hypomethylated SE-DMRs in promoter regions. Skin cell type RNA-seq RPKM values over exons are averages (mean) of three biological replicates; luminal epithelial and myoepithelial values are a single biological replicate. 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 transformation was applied before boxplot statistics were computed. RPKM distributions for SE cell type expression levels vs. non-SE cell type expression levels are statistically significant (Wilcoxon-ranked test, paired, * indicates P-value < 0.02; n = 150 genes; Lum = breast luminal epithelial cells, Myo = breast myoepithelial cells, K= keratinocytes, F = fibroblasts, M = melanocytes; Supplementary Table 6).
Mentions: In the absence of a strong skin tissue-specific epigenetic signature, we hypothesized that developmental origin is a major determinant of skin cell type epigenetic patterns. We explored this hypothesis by focusing on skin keratinocytes and breast epithelial cells, which are both derived from surface ectoderm15. Consistent with their shared developmental origin, neonatal skin keratinocytes clustered with adult breast epithelial cell types based on DNA methylation values at the DMRs previously identified in skin and non-skin cell pairwise comparisons (Figure 3c). To specifically define the DNA methylation signature of surface ectoderm-derived cell types, we identified DMRs for each of the surface ectodermal cell types in a pairwise manner compared to neonatal skin melanocytes and fibroblasts, which are derived from other embryonic germ layers (Supplementary Fig. 4c). There were 1,392 DMRs with the same methylation state exclusively in keratinocyte, breast myoepithelial, and breast luminal epithelial cells relative to the two other cell types, which we inferred to be surface ectoderm-specific DMRs (SE-DMRs) (Methods, Figure 4a). Therefore, common developmental origin influences surface ectoderm-derived cell epigenomes to a greater extent than does the shared skin tissue environment.

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