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

Rebecca F. Lowdon, Bo Zhang, Misha Bilenky, Thea Mauro, Daofeng Li, Philippe Gascard, Mahvash Sigaroudinia, Peggy J. Farnham, Boris C. Bastian, Thea D. Tlsty, Marco A. Marra, Martin Hirst, Joseph F. Costello, Ting Wang, Jeffrey B. Cheng

Research output: Contribution to journalArticle

14 Citations (Scopus)

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.

Original languageEnglish (US)
Article number5442
JournalNature Communications
Volume5
DOIs
StatePublished - Nov 25 2014
Externally publishedYes

Fingerprint

Ectoderm
Keratinocytes
cells
Epigenomics
Melanocytes
fibroblasts
Fibroblasts
breast
genes
Skin
Breast
Histone Code
deoxyribonucleic acid
mammary glands
Genes
Germ Layers
glands
methylation
Neural Crest
Gene Regulatory Networks

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Chemistry(all)
  • Physics and Astronomy(all)

Cite this

Lowdon, R. F., Zhang, B., Bilenky, M., Mauro, T., Li, D., Gascard, P., ... Cheng, J. B. (2014). Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. Nature Communications, 5, [5442]. https://doi.org/10.1038/ncomms6442

Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. / Lowdon, Rebecca F.; Zhang, Bo; Bilenky, Misha; Mauro, Thea; Li, Daofeng; Gascard, Philippe; Sigaroudinia, Mahvash; Farnham, Peggy J.; Bastian, Boris C.; Tlsty, Thea D.; Marra, Marco A.; Hirst, Martin; Costello, Joseph F.; Wang, Ting; Cheng, Jeffrey B.

In: Nature Communications, Vol. 5, 5442, 25.11.2014.

Research output: Contribution to journalArticle

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 2014, 'Regulatory network decoded from epigenomes of surface ectoderm-derived cell types', Nature Communications, vol. 5, 5442. https://doi.org/10.1038/ncomms6442
Lowdon, Rebecca F. ; Zhang, Bo ; Bilenky, Misha ; Mauro, Thea ; Li, Daofeng ; Gascard, Philippe ; Sigaroudinia, Mahvash ; Farnham, Peggy J. ; Bastian, Boris C. ; Tlsty, Thea D. ; Marra, Marco A. ; Hirst, Martin ; Costello, Joseph F. ; Wang, Ting ; Cheng, Jeffrey B. / Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. In: Nature Communications. 2014 ; Vol. 5.
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