Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases

TLDR

Histone lysine methylation regulates gene expression, with reversible demethylation known for K4, K9, and K36, but enzymes removing methylation at H3K27 had remained unidentified. UTX and JMJD3, both containing JmjC domains, enzymatically remove H3K27 methylation in vitro, with activity dependent on a catalytically active JmjC domain. UTX and JMJD3 act as H3K27 demethylases, reducing di‑ and trimethylation in cells and demonstrating that H3K27 methylation is reversible and dynamically regulated by specific demethylases.

Abstract

Covalent modifications of histones, such as acetylation and methylation, play important roles in the regulation of gene expression. Histone lysine methylation has been implicated in both gene activation and repression, depending on the specific lysine (K) residue that becomes methylated and the state of methylation (mono-, di-, or trimethylation). Methylation on K4, K9, and K36 of histone H3 has been shown to be reversible and can be removed by site-specific demethylases. However, the enzymes that antagonize methylation on K27 of histone H3 (H3K27), an epigenetic mark important for embryonic stem cell maintenance, Polycomb-mediated gene silencing, and X chromosome inactivation have been elusive. Here we show the JmjC domain-containing protein UTX (ubiquitously transcribed tetratricopeptide repeat, X chromosome), as well as the related JMJD3 (jumonji domain containing 3), specifically removes methyl marks on H3K27 in vitro. Further, the demethylase activity of UTX requires a catalytically active JmjC domain. Finally, overexpression of UTX and JMJD3 leads to reduced di- and trimethylation on H3K27 in cells, suggesting that UTX and JMJD3 may function as H3K27 demethylases in vivo. The identification of UTX and JMJD3 as H3K27-specific demethylases provides direct evidence to indicate that similar to methylation on K4, K9, and K36 of histone H3, methylation on H3K27 is also reversible and can be dynamically regulated by site-specific histone methyltransferases and demethylases.