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

Gabriel G Malouf12, Joseph H Taube35, Yue Lu1, Tapasree Roysarkar35, Shoghag Panjarian6, Marcos RH Estecio1, Jaroslav Jelinek1, Jumpei Yamazaki1, Noel J-M Raynal1, Hai Long1, Tomomitsu Tahara1, Agata Tinnirello3, Priyanka Ramachandran3, Xiu-Ying Zhang4, Shoudan Liang4, Sendurai A Mani35* and Jean-Pierre J Issa16*

Author Affiliations

1 Department of Leukemia, the University of Texas MD Anderson Cancer Center, Houston, TX, USA

2 Department of Medical Oncology, Groupe Hospitalier Pitié - Salpêtrière, Assistance Publique Hopitaux de Paris, Faculty of Medicine Pierre et Marie Curie, Institut Universitaire de Cancérologie, Paris, France

3 Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

4 Department of Bioinformatics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA

5 Metastasis Research Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

6 Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA, USA

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Genome Biology 2013, 14:R144  doi:10.1186/gb-2013-14-12-r144

Published: 24 December 2013

Abstract

Background

Epithelial-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.

Results

EMT 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.

Conclusions

Our 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.