Table 1.

Summary of epigenetic regulatory changes in the intestinal epithelium

Epigenomic Feature	Intestinal Epithelial Process	References
3D chromatin looping	TADs are thought to be stable across cell types
	Genome-wide 3D chromatin interactions have not been mapped in the intestine
Chromatin accessiblity	Generally similar across intestinal epithelial cell populations	37, 40
	Secretory cells have specific accessible regions bound to secretory cell-specific TFs	32, 49
	These regions lose chromatin accessiblity when secretory cells dedifferentiate into ISCs	32
Histone Modifications
H3K4me1/2, H3K27ac	Overall similar across intestinal cell lineages	37, 40
	Differences correlate with dynamic gene expression	69
H3K27me3	Associated with promoters of silent genes and largely stable across cell types. About 200 ISC-specific genes show increases H3K27me3 levels in differentiated cells	31
	Loss of H3K27 methyltransferase activity permits reexpression of developmentally silenced genes, but ISC-specific genes are not reactivated in mature cells.	31
DNA methylation	Majority of enhancers have similar methylation profiles across intestinal epithelial cell types	30, 35
	Small differences occur at a subset of cell type-specific genes	58

ISC, intestinal stem cells; TADS, topological associating domains; TFs, transcription factors; 3D, three-dimensional.