Pleiotropic Functions of H3K27Me3 Demethylases in Immune Cell Differentiation

Abstract

The trimethylation of histone H3 lysine 27 (H3K27Me3) contributes to gene repression, notably through recruitment of Polycomb complexes, and has long been considered essential to maintain cell identity. Whereas H3K27Me3 was thought to be stable and not catalytically reversible, the discovery of the Utx and Jmjd3 demethylases changed this notion, raising new questions on the role of these enzymes in gene expression and cell differentiation. Recent studies have demonstrated critical roles for Utx and Jmjd3 in the development and function of immune cells, and revealed both demethylase and demethylase-independent activities of these enzymes. I review these finding here, and discuss the current understanding of the mechanisms that underlie the broad, yet highly cell- and gene-specific, impact of these enzymes in vivo.

Figure 1. Schematic structure of Kdm6 family proteins

Uty, Utx and Jmjd3 are schematically depicted with their JmjC domain shown as a blue box and Utx and Uty tetratricopeptide repeats (TPR) shown as red boxes. Amino-acid residue numbers are shown in black, whereas numbers in white over black background indicate percent aminoacid identity between the regions of the molecules delineated by dashed lines. Black bars in Uty JmjC domain indicate mutations at positions 947 and 955 responsible for the lack of catalytic activity [33].

Figure 2. H3K27Me3 homeostasis

H3 K27 (blue) is methylated by PRC2-associated methyl transferases (Ezh2, as shown, or Ezh1), resulting in mono-, di-, or trimethylation (H3K27Me3, shown, middle). Kdm6 family enzymes Jmjd3 and Utx can demethylate H3K27Me3 into its di- or monomethyl forms (not shown for simplicity). H3K27Me3 recruits PRC1 complexes through their Cbx subunits (Cbx4–8). Additional subunits common to most PRC1 complexes are depicted, including ubiquitin ligases Ring1A or 1B, and a member of the Polycomb group RING fingers (PCGF) family of proteins (e.g. Bmi1) [13, 15].

Figure 3. Promoter-specific impact of Jmjd3 and Utx on H3K27Me3 demethylation in developing thymocytes

H3K27Me3 decoration at the promoter regions of S1pr1 and Zbtb7b (encoding the transcription factor Thpok) are schematically depicted in wild-type CD4⁺CD8⁺ (DP) and CD4⁺CD8⁻ (CD4 SP) thymocytes, and in CD4 SP thymocytes with disrupted Jmjd3 and Utx (original data from Ref. [50]). Normally, both promoters undergo almost complete H3K27Me3 removal as non-dividing DP thymocytes differentiate into CD4 SP cells, and are active in CD4 SP but not DP thymocytes. The overlapping activities of Jmjd3 and Utx are required for H3K27Me3 removal at and expression of S1pr1 in CD4 SP thymocytes. In contrast, Jmjd3 and Utx have little impact on H3K27Me3 removal at and expression of Zbtb7b.

Figure 4. Demethylase-dependent and –independent effects of Jmjd3 and Utx on transcription

The figure illustrates two potential mechanistic contributions of Jmjd3 or Utx to transcriptional activation. (a) schematic depiction of a gene promoter region, represented in an inactive state with extensive H3K27 (light blue ovals) trimethylation (red symbols) on nucleosomes. H3K4 (dark blue ovals) is not methylated. H3K27Me3-recruited PRC1 inhibits transcription. (b) Transcription factor (TF) mediated recruitment of Jmjd3 causes catalytic H3K27Me3 demethylation and relieves PRC1-mediated transcriptional repression (top). Jmjd3-independent mechanisms (not shown, e.g. transcription factor recruitment) result in transcription activation, associated with H3K4 trimethylation (bottom). In (c), a transcription factor recruits Utx, which promotes catalytic H3K27Me3 demethylation, thereby relieving PRC1-mediated repression (top), and associates with a Ktm2-family H3K4 methyl-transferase, resulting in H3K4 trimethylation (bottom). Note that (i) both Jmjd3 and Utx have been shown to associate with Ktm2 complexes, (ii) whether Jmjd3 or Utx molecules associated with MLL complexes exert demethylase activity (as depicted in [c]) remains to be determined, and (iii) the existence of promoters enriched in both H3K4Me3 and H3K27Me3 suggests that H3K4 trimethylation can take place before H3K27Me3 demethylation.

Figure 5. Potential impact of Jmjd3 and Utx on Brg1-mediated chromatin remodeling

(a) Schematic depiction of a transcriptionally inactive gene promoter, in which DNA sequences around the transcription start site (red lines) are wrapped around a nucleosome, preventing RNA the recruitment of a transcription initiation complex. (b) DNA-bound T bet recruits a Jmjd3-Brg1 complex. The chromatin remodeling activity associated with Brg1 mobilizes nucleosomes away from the transcription start site (b), allowing RNA polymerase II recruitment and transcription initiation (c).