First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor

James D. Moody, Shiri Levy, Julie Mathieu, Yalan Xing, Woojin Kim, Cheng Dong, Wolfram Tempel, Aaron M. Robitaille, Luke T. Dang, Amy Ferreccio, Damien Detraux, Sonia Sidhu, Licheng Zhu, Lauren Carter, Chao Xu, Cristina Valensisi, Yuliang Wang, R. David Hawkins, Jinrong Min, Randall T. MoonStuart H. Orkin, David Baker, Hannele Ruohola-Baker

Research output: Contribution to journalArticlepeer-review


The polycomb repressive complex 2 (PRC2) histone methyltransferase plays a central role in epigenetic regulation in development and in cancer, and hence to interrogate its role in a specific developmental transition, methods are needed for disrupting function of the complex with high temporal and spatial precision. The catalytic and substrate recognition functions of PRC2 are coupled by binding of the N-terminal helix of the Ezh2 methylase to an extended groove on the EED trimethyl lysine binding subunit. Disrupting PRC2 function can in principle be achieved by blocking this single interaction, but there are few approaches for blocking specific protein–protein interactions in living cells and organisms. Here, we describe the computational design of proteins that bind to the EZH2 interaction site on EED with subnanomolar affinity in vitro and form tight and specific complexes with EED in living cells. Induction of the EED binding proteins abolishes H3K27 methylation in human embryonic stem cells (hESCs) and at all but the earliest stage blocks self-renewal, pinpointing the first critical repressive H3K27me3 marks in development.

Original languageEnglish
Pages (from-to)10125-10130
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number38
Publication statusPublished - 19 Sep 2017
Externally publishedYes


  • Epigenetics
  • Human early development
  • Human embryonic stem cell
  • Polycomb repressive complex
  • Rosetta protein design


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