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

Area of Science:

• Developmental biology
• Epigenetics
• Cell biology

Background:

• Cellular function and epigenomic patterns are influenced by developmental origins.
• Epigenomic patterns are often linked to the three embryonic germ layers.
• Understanding how developmental origin impacts epigenomes is crucial.

Purpose of the Study:

• To investigate the influence of developmental origin on cellular epigenomes.
• To identify surface ectoderm (SE)-differentially methylated regions (SE-DMRs).
• To compare epigenomes of SE-derived cells with those from other germ layers.

Main Methods:

• Comparative epigenomic analysis of cell types derived from surface ectoderm (SE), neural crest, and mesoderm.
• DNA methylome profiling of keratinocytes, breast luminal and myoepithelial cells, melanocytes, and dermal fibroblasts.
• Identification and characterization of SE-differentially methylated regions (SE-DMRs).

Main Results:

• Neonatal keratinocytes share more DNA methylation patterns with adult breast cells (SE-derived) than with melanocytes or fibroblasts.
• Surface ectoderm origin significantly contributes to DNA methylation patterning, independent of the immediate tissue environment.
• Hypomethylated SE-DMRs are located near genes with SE-relevant functions and are enriched for regulatory elements and transcription factor binding sites.

Conclusions:

• Epigenomic analysis of cells with common developmental origins reveals a distinct epigenetic signature.
• This signature reflects a shared gene regulatory network underlying cell function.
• Developmental origin is a key determinant of epigenomic patterning in differentiated cells.