Kai Ge, Ph.D.

Photo of Kai Ge
Scientific Focus Areas: Cell Biology, Chromosome Biology, Developmental Biology, Genetics and Genomics, Molecular Biology and Biochemistry

Professional Experience

  • Postdoctoral Fellow, The Rockefeller University, 2000–2003
  • Postdoctoral Fellow, The Wistar Institute, 1997–2000
  • Ph.D., Shanghai Institute of Biochemistry, Chinese Academy of Sciences, 1997
  • B.S., Fudan University, 1992

Research Goal

We study epigenomic regulation of PPARγ and adipogenesis (generation of fat tissue). We also use adipogenesis as a model system to understand epigenomic regulation of cell fate transition, with a focus on transcriptional enhancers.

Current Research

Epigenomic mechanisms, including histone modification and chromatin remodeling play critical roles in gene regulation. Histone acetylation correlates with gene activation while methylation correlates with either activation or repression, depending on the specific lysine (K) residue that gets methylated. Methylations on K4 and K36 of histone H3 (H3K4 and H3K36) correlate with gene activation, whereas methylations on K9 and K27 of histone H3 (H3K9 and H3K27) correlate with gene repression.

Enhancers control cell-type-specific gene expression and are critical for cell differentiation and tissue development. Primed enhancers are marked by H3K4 mono-methylation (H3K4me1). Active enhancers are further marked by H3K27 acetylation (H3K27ac). We identified CBP and p300 as the H3K27 acetyltransferases (EMBO J 2011). We also identified MLL3 (KMT2C) and MLL4 (KMT2D) as major H3K4me1 methyltransferases on enhancers (eLife 2013).

PPARγ is a master regulator of adipogenesis. It is a nuclear receptor and thus a ligand-activated transcription factor (TF). In search for novel PPARγ cofactors, we identified a nuclear protein complex that contains MLL3/MLL4 (MLL3/4) and the H3K27 demethylase UTX (JBC 2007, PNAS 2007).

Epigenomic regulation of enhancers

Combining mouse genetics with epigenomics and bioinformatics, we have shown:

  1. H3K4me1 methyltransferases MLL3/4 are required for enhancer activation and cell-type-specific gene expression in adipogenesis, myogenesis and ES cell differentiation (eLife 2013, PNAS 2016).  MLL3/4 are essential for development of embryos and adipose tissue, muscle, mammary gland, B cells, T cells, and heart.  MLL3/4 are mutated in many types of cancer as well as Kabuki syndrome and congenital heart disease.  Our findings suggest that mutations in MLL3/4 lead to enhancer dysfunction.  Such a mechanism may contribute to the pathogenesis of these developmental diseases and cancers (reviewed in Gene 2017). 
  2. Although enhancer priming by MLL3/4 is dispensable for cell-identity maintenance in ES and somatic cells, it controls cell fate transition by orchestrating H3K27 acetyltransferases CBP/p300-mediated enhancer activation (PNAS 2016, Nucleic Acids Res 2017).
  3. The epigenomic reader Brd4 binds to active enhancers to control cell identity gene induction in adipogenesis and myogenesis.  Our data suggest a model of sequential actions of epigenomic regulators on enhancers: 1) lineage-determining TFs recruit MLL3/4 to prime enhancer regions and label them with H3K4me1, 2) MLL3/4 facilitate the binding of CBP/p300, which activate enhancers and label them with H3K27ac, 3) Brd4 recognizes active enhancers and recruits Mediator and RNA Polymerase II to activate cell-type-specific gene expression (Nat Commun 2017). 
  4. UTX protein, but not its H3K27 demethylase activity, is required for ES cell differentiation and mouse development (PNAS 2012).  UTX likely functions through MLL3/4 to regulate enhancer activation in differentiation and development.  Interestingly, UTX demethylase activity is required for stem cell-mediated muscle regeneration (J Clin Invest 2016).

Epigenomic and transcriptional regulation of adipogenesis

We have shown that site-specific histone methyltransferases control expression of master regulators of adipogenesis [Reviewed in BBA 2012 and Cell Biosci 2014]:

  1. H3K4 methyltransferases MLL3/4 and associated PTIP directly control the induction of principal adipogenic TFs PPARγ and C/EBPα and are essential for adipogenesis (Cell Metab 2009, eLife 2013).
  2. H3K9 methyltransferase G9a represses PPARγ expression and adipogenesis (EMBO J 2013).
  3. H3K27 methyltransferase Ezh2 constitutively represses Wnt genes to facilitate adipogenesis (PNAS 2010).
  4. Depletion of Nsd2-mediated H3K36 methylation impairs adipose tissue development and function (Nat Commun 2018).

Using conditional knockout mice and preadipocytes, we found that although ligand-bound glucocorticoid receptor (GR) accelerates adipogenesis in culture, endogenous GR is dispensable for adipogenesis in culture and in mice (MCB 2017a). We also found that TFs KLF4 and Krox20 are dispensable for adipogenesis in culture and in mice (MCB 2017b). These unexpected results prompted us to study adipogenesis in vivo.

Epigenomic regulation of nuclear receptor target gene expression

We reported that two pairs of histone acetyltransferases (HATs), GCN5/PCAF and CBP/p300, are specifically required for H3K9 acetylation (H3K9ac) and H3K18/27 acetylation, respectively, in cells. CBP/p300 and their HAT activities are essential, while GCN5/PCAF and associated H3K9ac are dispensable, for nuclear receptor target gene expression (EMBO J 2011). GCN5/PCAF-mediated H3K9ac correlates well with, but is surprisingly dispensable for, the expression of endogenous interferon-β and the vast majority of active genes in fibroblasts. Instead, GCN5/PCAF repress interferon-β production and innate antiviral immunity in cells in a HAT-independent and non-transcriptional manner (EMBO Rep 2014). We are interested in epigenomic regulation of PPARγ and GR target gene expression. We showed that ligand-activated GR accelerates expression of early adipogenic genes in cells by recruiting CBP/p300 to activate C/EBPb-primed enhancers (MCB 2017a). We are investigating the role of H3K36 methylation in regulating PPARγ target gene expression.

Applying our Research

Understanding how epigenomic mechanisms regulate PPARγ and adipogenesis may provide new ways to treat obesity and type 2 diabetes. Synthetic PPARγ ligands have been used to treat millions of patients with type 2 diabetes. Investigating how epigenomic mechanisms regulate ligand-induced nuclear receptor target gene expression will help us better understand how synthetic PPARγ ligands act as antidiabetic agents.

Select Publications

Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation.
Jin Q, Yu LR, Wang L, Zhang Z, Kasper LH, Lee JE, Wang C, Brindle PK, Dent SY, Ge K.
EMBO J (2011 Jan 19) 30:249-62. Abstract/Full Text
H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation.
Lee JE, Wang C, Xu S, Cho YW, Wang L, Feng X, Baldridge A, Sartorelli V, Zhuang L, Peng W, Ge K.
Elife (2013 Dec 24) 2:e01503. Abstract/Full Text
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Research in Plain Language

Epigenetic mechanisms—factors other than an individual’s DNA sequence—play critical roles in regulating gene expression and cell differentiation. My laboratory studies epigenetic factors that regulate two processes: (1) adipogenesis—the process by which fat tissues are formed—and (2) nuclear receptor target gene expression, the process by which information from a gene is used in the development of a functional gene product.

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