A study on changes of gene expression and chromatin accessibility during stepwise formation of intestinal organoids

Abstract

Differentiation is a fine-tuned process orchestrated by dynamic changes of gene regulatory network. Recent technical progress in genome-wide epigenetic profiling facilitates our understanding of the regulation of cell differentiation events. Epigenetic mechanisms such as histone modifications, DNA methylation, and chromatin structural alterations affect the overall gene expression patterns driving the change of cell fate. Using intestinal organoids imitating embryonic intestinal development as a model system, epigenetic dynamics together with gene expression program was explored to identify which factors or pathways mediate the differentiation process. Both transcriptome and chromatin accessibility information were collected from four stages towards intestinal organoids derived from embryonic stem cells. As expected, progressive changes of transcription profiles were confirmed so that intestinal function-related processes including lipid metabolism were gradually activated especially. The chromatin structure alterations indicated the differential involvement of Forkhead box family and CDX1/2 transcription factors at stage-specific accessible regions. Integration of chromatin accessibility-based footprints of transcription factor and gene expression patterns suggested that potential regulators such as HNF1A, HNF4A, CDX2, and ETS homology factor (EHF) might play roles in intestinal lineage specification. Of interest, the EHF seems to be related to increased chromatin accessibility during differentiation and it was highly expressed at intestinal organoid stage. Our results provided a new functional insight to develop chromatin structure-based epigenetic determinants like transcription factors specific to intestinal lineage specification.