Architecture of epigenetic reprogramming following Twist1-mediated epithelial-mesenchymal transition

Abstract

BackgroundEpithelial-mesenchymal transition (EMT) is known to impart metastasis and stemness characteristics in breast cancer. To characterize the epigenetic reprogramming following Twist1-induced EMT, we characterized the epigenetic and transcriptome landscapes using whole-genome transcriptome analysis by RNA-seq, DNA methylation by digital restriction enzyme analysis of methylation (DREAM) and histone modifications by CHIP-seq of H3K4me3 and H3K27me3 in immortalized human mammary epithelial cells relative to cells induced to undergo EMT by Twist1.ResultsEMT is accompanied by focal hypermethylation and widespread global DNA hypomethylation, predominantly within transcriptionally repressed gene bodies. At the chromatin level, the number of gene promoters marked by H3K4me3 increases by more than one fifth; H3K27me3 undergoes dynamic genomic redistribution characterized by loss at half of gene promoters and overall reduction of peak size by almost half. This is paralleled by increased phosphorylation of EZH2 at serine 21. Among genes with highly altered mRNA expression, 23.1% switch between H3K4me3 and H3K27me3 marks, and those point to the master EMT targets and regulators CDH1, PDGFRα and ESRP1. Strikingly, Twist1 increases the number of bivalent genes by more than two fold. Inhibition of the H3K27 methyltransferases EZH2 and EZH1, which form part of the Polycomb repressive complex 2 (PRC2), blocks EMT and stemness properties.ConclusionsOur findings demonstrate that the EMT program requires epigenetic remodeling by the Polycomb and Trithorax complexes leading to increased cellular plasticity. This suggests that inhibiting epigenetic remodeling and thus decrease plasticity will prevent EMT, and the associated breast cancer metastasis.

DNA Methylation Signature Reveals Cell Ontogeny of Renal Cell Carcinomas

“…The estimated false discovery rate (FDR) of DREAM is 0.7% and 2.1%, using 15% and 20% as a difference methylation cut-off, respectively. This was consistent with our previous results using blood and breast samples (15, 16). To determine whether DNA methylation alters gene expression, we examined the association of DNA methylation with promoter activity.…”

“…Sequencing was performed using Illumina Hiseq2000 at MD Anderson core facility. Mapping tags and algorithm of analysis have been previously reported (15, 16). …”

Environmental factors, epigenetics, and developmental origin of reproductive disorders

“…Segregation of genes into active, repressed, bivalent, or poised is often achieved by an intricate balance between H3K4me3 and H3K27me3 occupancy as reviewed by Weng et al (2012; [35]). The coordination of DNA methylation and histone modification, to define the transcriptional state and readiness of a cohort of genes, are commonly noted in most physiological and pathological states [36]. …”

Grainyhead-like 2 Reverses the Metabolic Changes Induced by the Oncogenic Epithelial–Mesenchymal Transition: Effects on Anoikis

“…The transcriptional reprogramming event known as the Epithelial to Mesenchymal transition (EMT) confers anoikis resistance and ultimately, increased metastatic potential (5). The increased phenotypic plasticity underlying transitions between epithelial and mesenchymal states is thought to be epigenetically driven (6–10). One additional manifestation of this increased plasticity, aside from EMT, is that cancer stem cell subpopulations emerge, that, like cells resulting from EMT, are resistant to anoikis; these contribute crucially to both metastasis and disease recurrence.…”