Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease

Abstract

The enzymes catalyzing lysine and arginine methylation of histones are essential for maintaining transcriptional programs and determining cell fate and identity. Until recently, histone methylation was regarded irreversible. However, within the last few years, several families of histone demethylases erasing methyl marks associated with gene repression or activation have been identified, underscoring the plasticity and dynamic nature of histone methylation. Recent discoveries have revealed that histone demethylases take part in large multiprotein complexes synergizing with histone deacetylases, histone methyltransferases, and nuclear receptors to control developmental and transcriptional programs. Here we review the emerging biochemical and biological functions of the histone demethylases and discuss their potential involvement in human diseases, including cancer.

Figure 1.

Mechanisms of lysine demethylation by LSD1 and JMJC proteins. (A) LSD1 demethylates H3K4me2/me1 via an amine oxidation reaction using FAD as a cofactor. The imine intermediate is hydrolyzed to an unstable carbinolamine that subsequently degrades to release formaldehyde. (B) The JMJC proteins use αKG and iron (Fe) as cofactors to hydroxylate the methylated histone substrate. Fe(II) in the active site activates a molecule of dioxygen to form a highly reactive oxoferryl [Fe(IV) = O] species to react with the methyl group. The resulting carbinolamine intermediate spontaneously degrades to release formaldehyde. Throughout the figure, the wavy line indicates attachment to the peptide backbone.

Figure 2.

Phylogenetic tree of the JmjC family of demethylases. The names, synonyms, substrate specificities, and domain structures of the proteins are provided. The lists of synonyms may be longer, but due to space limitations only the most relevant are provided. Putative oncoproteins are in red and putative tumor suppressors are in green. (JmjC) Jumonji C domain; (JmjN) Jumonji N domain; (PHD) plant homeodomain; (Tdr) Tudor domain; (Arid) AT-rich interacting domain; (Fbox) F-box domain; (C5HC2) C5CHC2 zinc-finger domain; (CXXC) CXXC zinc-finger domain; (TPR) tetratricopeptide domain; (LRR) leucine-rich repeat domain; (TCZ) treble-clef zinc-finger domain; (PLAc) cytoplasmic phospholipase A2 catalytic subunit.

Figure 3.

Model for the involvement of demethylases/methyltransferases in transcriptional regulation of developmental genes. Histone methyltransferases and demethylases are found in the same complex, which methylates one mark while removing the opposing mark. The methylation pattern at a specific gene is determined by the equilibrium between activities of the two opposing complexes, exemplified here by the activating MLL2/UTX complex and the repressive PRC2/RBP2 complex (Agger et al. 2007; Pasini et al. 2008). Analogously, it has been shown that repressive complexes carrying K9 methyltransferase activity (G9a) may also contain H3K4 demethylase activities (Tahiliani et al. 2007). Correspondingly, it may be envisioned that H3K9 demethylases may form a part of activating complexes carrying methyltransferases to activating marks as H3K4.

Figure 4.

The involvement of demethylases in AR-mediated transcription. When bound to its ligands, androgen (A), the AR translocates to the nucleus to interact with histone demethylases on androgen-responsive elements (ARE) on specific genes. Through its interaction with JMJD2C, LSD1 or JMJD1A demethylation is triggered, removing the repressive H3K9 methylation and leading to the transcriptional induction of these androgen-responsive genes. Repressive complexes (RCO), possibly featuring H3K9-methyltransferase (KMT), HDAC, and H3K4 demethylase (JARID1) activities, may potentially act to prevent ligand-independent activation.

Figure 5.

Demethylases and histone modifications in senescence. (A) JMJD3 and p53 are transcribed from the same genomic region: chromosome 17p13.1. In response to oncogenic, replicative, or other types of stress (DNA damage, drug treatment, etc.) the tumor suppressors p53 and INK4A–ARF are induced, triggering senescence. JMJD3 or UTX may be involved in the transcriptional activation of the INK4A–ARF tumor suppressor locus by removing repressive K27 methylation from the gene (see B). In turn, p16 and p14ARF lead to the induction of pRB and p53, respectively, triggering senescence and/or apoptosis. (B) The compacted, transcriptionally silent chromatin structure of the INK4A–ARF locus serves to ensure cell cycle progression in normal “unstressed” cells and in some malignant cells. (Left panel) This silent state is maintained by H3K27 methylation mediated by the PcG proteins, and possibly also by the repressive activities of JARID1 proteins and other chromatin modifiers. When cells with intact tumor suppressor pathways are subjected to oncogenic stimuli or other types of stress, PcG proteins are displaced from the INK4A–ARF locus and K27 demethylases are possibly recruited to remove the repressive K27 methylation, leading to the expression of the INK4A– ARF locus and the induction of senescence. (C, left panel) In normal “unstressed” cells the transcription factor E2F mediates transcription, while the tumor suppressor pRB is maintained in an inactive phosphorylated state as a result of low p16 levels. During senescence induction, p16 is induced, causing hypophoshorylation of pRB. (Right panel) pRB subsequently recruits chromatin modifiers as HDAC, SUV39H1 (setting H3K9 methylation), SUV4H20 (setting H4K20 methylation), HP1, and possibly JARID1 proteins to silence euchromatic E2F target promoters and form SAHFs.

Figure 6.

Demethylases and histone modifications in X inactivation. Xist RNA associates with the X chromosome through unknown factor(s), and recruits an initial silencing activity. Demethylation of H3K4 is an early event in X inactivation, and most likely is mediated by JARID1 family members. HDAC activity is recruited, possibly through JARID1 members to deacetylate H3K9 and H3K27, probably in preparation for the subsequent repressive methylation of these marks. The PRC2 complex transiently associates with the inactivating X to methylate H3K27 and perhaps H3K9. The recruitment of PRC2 could be mediated through JARID1 members. Subsequently, PRC1 proteins transiently associate with the inactivating X chromosome, mediating histone H2A ubiquitinylation. Finally, localized Xist is indispensable for the accumulation of the histone variants macroH2A1 and macroH2A2 on the inactive X chromosome to form the so-called macrochromatin body.