Epigenetic mechanisms, in particular histone acetylation and methylation, play critical roles in regulating gene expression and cell differentiation. Histone acetylation generally correlates with gene activation. Histone lysine (K) methylation has been implicated in both gene activation and repression, depending on the specific K residue that gets methylated. For example, methylation at K4 of histone H3 (H3K4) is associated with gene activation, whereas methylation at K27 of histone H3 (H3K27) is associated with gene repression. Histone lysine methylation is dynamically regulated by site-specific methyltransferases and demethylases.
PPARγ is a master regulator of adipogenesis. It cooperates with another major adipogenic transcription factor C/EBPα to promote preadipocyte differentiation towards adipocyte. PPARγ is a nuclear receptor and thus a ligand-activated transcription factor. Synthetic PPARγ ligands have been used to treat type 2 diabetes, but have undesirable side effects. Investigating how epigenetic mechanisms regulate ligand-induced nuclear receptor target gene expression may help the next generation of diabetes drugs.
Identification and characterization of histone methyltransferases and demethylases
In search of novel transcription cofactors for PPARγ, we identified the nuclear protein PTIP. Through our research, we show the following:
- In cells, PTIP and a novel protein PA1 are both subunits of a histone H3K4 methyltransferase complex (i.e., the MLL3/MLL4 complex) that contains H3K4 methyltransferases MLL3 and MLL4, and the JmjC domain-containing protein UTX (JBC, 2007). [See Research Images Fig. 1.]
- The JmjC domain-containing proteins UTX and JMJD3 are histone H3K27-specific demethylases (PNAS, 2007). Based on the direct physical interaction between H3K4 methyltransferases MLL3/MLL4 and H3K27 demethylase UTX, we propose that by adding an active epigenetic marker (methylation on H3K4) and removing a repressive one (methylation on H3K27), the MLL3/MLL4 complex may use two distinct histone modifying activities to activate target gene expression synergistically. [See Research Images Fig. 2.] We are investigating the roles of PTIP, PA1, and associated histone modifying enzymes in epigenetic regulation of PPARγ and adipogenesis.
- UTX controls mesoderm differentiation of embryonic stem cells independent of its demethylase activity (PNAS, 2012). We are investigating enzymatic activity-dependent and activity-independent functions of UTX using knockin cells and mice.
- Enhancers play a central role in cell-type-specific gene expression and are marked by H3K4me1/2. We identify MLL3 and MLL4 as major mammalian H3K4 mono- and di-methyltransferases enriched on enhancers. MLL3 and MLL4 are essential for enhancer activation during cell differentiation (eLife, 2013).
Epigenetic regulation of adipogenesis by histone methylation
We use adipogenesis as a model system to study epigenetic regulation of cell differentiation. Through our research, we show the following:
- Histone H3K4 methylation regulator PTIP directly controls the induction of principal adipogenic transcription factors PPARγ and C/EBPα and is essential for adipogenesis (Cell Metabolism, 2009).
- Histone H3K27 methyltransferase Ezh2 uses its enzymatic activity to constitutively represses Wnt genes to facilitate adipogenesis. Acetylation and trimethylation on H3K27 appear to play opposing roles in regulating Wnt expression (PNAS, 2010).
- Histone H3K9 methyltransferase G9a represses PPARγ expression in an enzymatic activity-dependent manner but facilitates Wnt10a expression independent of its enzymatic activity. Accordingly, G9a represses adipogenesis (EMBO J, 2013).
These results provide an initial view of the epigenetic regulation of adipogenesis and suggest that site-specific histone methylations control expression of both positive and negative master regulators of adipogenesis. [Reviewed in BBA 2012 and Cell Biosci 2014; see Research Images Fig. 3.]
Epigenetic regulation of nuclear receptor target gene expression
We study how epigenetic mechanisms regulate nuclear receptor target gene expression. We report that the two pairs of histone acetyltransferases (HATs), GCN5/PCAF and CBP/p300, are specifically required for H3K9 acetylation (H3K9ac) and H3K18/27 acetylation (H3K18/27ac), respectively, in cells. Further, we show that CBP/p300 and their HAT activities are essential, while GCN5/PCAF and associated H3K9ac are dispensable, for ligand-induced nuclear receptor target gene expression. These results highlight the substrate and site specificities of HATs in cells, demonstrate the distinct roles of GCN5/PCAF- and CBP/p300-mediated histone acetylations in gene activation, and suggest an important role of CBP/p300-mediated H3K18/27ac in nuclear receptor target gene expression (EMBO J, 2011). Recently, we show that GCN5/PCAF-mediated H3K9ac correlates well with, but is surprisingly dispensable for, the expression of endogenous interferon-β (IFN-β) and the vast majority of active genes in fibroblasts. Instead, GCN5/PCAF repress IFN-β production and innate antiviral immunity in several cell types in a HAT-independent and non-transcriptional manner (EMBO Rep, 2014).
My laboratory uses adipogenesis and ligand-induced nuclear receptor target gene expression as model systems to study epigenetic regulation of gene expression and cell differentiation. Our current research is focused on the following projects:
- Enhancer regulation by H3K4 methyltransferases MLL3/MLL4
- Epigenetic regulation of adipogenesis by histone methylation
- Epigenetic regulation of nuclear receptor target gene expression