Epigenetic landscape change analysis during human EMT sheds light on a key EMT mediator TRIM29.

Sung Kyung Choi,Gangning Liang,Peter A Jones,Jung Woo Eun,Kurinji Pandiyan,Suk Woo Nam,Jueng Soo You,Seong Hwi Hong,Xiaojing Yang

doi:10.18632/oncotarget.21681

Abstract

Epithelial to mesenchymal transition (EMT) is a key trans-differentiation process, which plays a critical role in physiology and pathology. Although gene expression changes in EMT have been scrutinized, study of epigenome is in its infancy. To understand epigenetic changes during TWIST-driven EMT, we used the AcceSssIble assay to study DNA methylation and chromatin accessibility in human mammary epithelial cells (HMECs). The DNA methylation changes were found to have functional significance in EMT – i.e. methylated genes were enriched for E-box motifs that can be recognized by TWIST, at the promoters suggesting a potential targeting phenomenon, whereas the demethylated regions were enriched for pro-metastatic genes, supporting the role of EMT in metastasis. TWIST-induced EMT triggers alterations in chromatin accessibility both independent of and dependent on DNA methylation changes, primarily resulting in closed chromatin conformation. By overlapping the genes, whose chromatin structure is changed during early EMT and a known “core EMT signature”, we identified 18 driver candidate genes during EMT, 14 upregulated and 4 downregulated genes with corresponding chromatin structure changes. Among 18 genes, we focused on TRIM29 as a novel marker of EMT. Although loss of TRIM29 is insufficient to suppress CDH, it is enough to induce CDH2 and VIM. Gene functional annotation analysis shows the involvement of TRIM29 in epidermal development, cell differentiation and cell migration. Taken together, our results provide a robust snapshot of chromatin state during human EMT and identify TRIM29 as a core mediator of EMT.

Highlights

Epithelial to mesenchymal transition (EMT) allows the trans-differentiation of epithelial and endothelial cell types to mesenchymal cells and plays important roles in normal development and disease progression [1, 2]
Since the Feinberg group claimed that DNA methylation does not change during TGF-beta induced EMT in the murine system [24], we focused our initial analysis on the methylation changes induced by TWIST in our human system
On performing a nonsupervised hierarchical clustering of the most variable probes across all time points, we observed that distinct groups of are methylated or demethylated genes are apparent in the TWIST expressing cells (Supplementary Figure 1C), demonstrating that changes in DNA methylation can accompany certain molecular transitions that result in EMT

Summary

Introduction

Epithelial to mesenchymal transition (EMT) allows the trans-differentiation of epithelial and endothelial cell types to mesenchymal cells and plays important roles in normal development and disease progression [1, 2]. EMT and the converse process of mesenchymal to epithelial transition (MET) are reversible; several rounds of EMT and MET are required for the proper differentiation of cells and organs during development [2]. Transcriptional repressors, such as SNAI1 (Snail), SNAI2 (Slug) and TWIST are key players in the process and have been shown to repress pro-epithelial/adhesion proteins, working in concert to induce the transformation of locally restricted epithelial cells into a migratory phenotype resulting in dramatic tissue re-organization [3]. Owing to the importance of EMT in tumorigenesis and wound healing, a deep understanding of the process and its players is required to manipulate the system for therapeutic purposes

Methods

Results

Conclusion