Even though the DNA in all of our cells is nearly the same, it is epigenetic factors, including modifications to DNA, RNA, and chromatin that control the gene expression patterns in different cells, under various environmental conditions, and at specific times (1).
Post-translational modifications on histone tails function as a very complex code for controlling gene expression. Deciphering this code is at least as important as the genetic code for understanding its role in stem cell programming, maternal effects during fetal development, and potential reversibility in cancer therapies. However, it is also orders of magnitude more complex (2).
We study the molecular mechanisms driving the recognition of histone modifications, and how combinations of these chemical signals regulate protein interactions on the nucleus in both normal and disease states.
Major research efforts in the lab include:
- To uncover how multiple chromatin reader domains cooperatively regulate the activity of the MOZ histone acetyltransferase in acute myeloid leukemia
- To reveal how cross-talk between epigenetic marks modulates the function of histone binding proteins and chromatin remodeling enzymes
- To identify and functionally characterize how acetyllysine signaling and recognition contributes to the pathogenesis of parasitic infections
- To correlate how altered epigenetic modifications influence the progression of cancer
The human genome is compacted into chromatin, allowing nearly three meters of DNA to fit into the small volume of the nucleus. Chromatin is composed of DNA and proteins, and this DNA-protein complex is the template for a number of essential cell processes including transcription and replication. Understanding the role of chromatin's higher order structure in transcription control is important as loss of this regulation underlies many disease processes.
The basic structural unit of chromatin is the nucleosome. Nucleosomes are comprised of 147 base pairs of DNA wrapped around a core histone octamer. The histone octamer contains two molecules of each histone: H2A, H2B, H3, and H4. Each of these core histones contains two separate functional domains - (a) a modular domain, which interacts with the DNA and other histones and (b) a flexible tail domain that protrudes from the nucleosome. The tail domains can be modified by the reversible addition of chemical groups such as acetyl-, methyl-, and phospho- groups.
Modifications of the histone tail have been shown to be important in altering chromatin structure, facilitating access for DNA-binding transcription factors, but they also act as markers allowing non-histone proteins to interact with the chromatin. The "Histone Code Hypothesis" suggests that histone tail modifications constitute an epigenetic (beyond genes) code, which is read by other proteins.
It postulates that these proteins and protein complexes are able to recognize/read distinct tail modifications, just like a language or code. This consequently triggers downstream events resulting in unique and specific biological outcomes such as cell death; cell cycle regulation; and the transcription, repair, or replication of DNA.
Figure 1. Coordination of the H2AK5ac and H4K12ac histone ligands by the BRPF1 bromodomain. (A) The BRPF1 bromodomain (yellow) in complex with H2AK5ac (blue) ligand. Hydrogen bonds are indicated by a red dotted line. (B) The BRPF1 bromodomain (yellow) in complex with the H4K12ac (green ligand).
We are investigating the structure and function of chromatin binding domains, including the bromodomain, which interact specifically with acetylated histones. There are about 60 human bromodomain-containing proteins, and these nuclear proteins have a wide variety of biological activities (3).
Bromodomains bind to specific acetylation marks on histone tail (Figure 1) and tether associated proteins and enzymatic complexes to histones to regulate chromatin structure and gene expression (4). For example, the BRPF1 bromodomain is a subunit of the MOZ/MORF Histone Acetyltransferase (HAT) complex that plays an important role in hematopoiesis or blood development (Figure 2) (5).
Chromosomal translocations of the MOZ gene are associated with the development of acute myeloid leukemia (6,7). We have found that the bromodomain and other epigenetic reader domains within this complex are essential for targeting the MOZ HAT to its chromatin substrates and regulate its histone acetylation activity (8-10).
It is thought that disruption of MOZ's acetylation activity causes aberrant gene expression and transformation to the leukemic phenotype. Unlike genetic changes in cancer, epigenetic changes are potentially reversible. Recently it has become evident that chromatin reader domains, such as the PHD fingers and bromodomains found in the MOZ HAT complex, are druggable with small molecules.
Bromodomain inhibitors are rapidly being developed to treat disease and selective inhibition of epigenetic regulators is now recognized as a valuable therapeutic avenue (11).
Figure 2. The MOZ HAT complex is a hetero-tetramer composed of the monocytic leukemic zinc-finger (MOZ) catalytic subunit, the bromodomain-PHD finger protein 1 (BRPF1), inhibitor of growth 5 (ING5) and hEaf6 subunits. Epigenetic reader domains in the MOZ HAT complex recognize histone post-transitional modifications. Our model illustrates how recognition of histone modifications by various subunits within the MOZ HAT directs the complex to chromatin and regulates enzymatic activity.
However, how these protein modules differentiate between various histone marks to read the histone code is unknown. The focus of the Glass lab's research is aimed at determining the structures of chromatin binding domains, including the bromodomain and PHD finger, in complex with the histone tail to elucidate how histone tail modifications are recognized.
This research will aid in a deeper understanding of hwo chromatin remodeling complexes are targeted to the chromatin and regulate gene expression. A greater understanding of how these molecular signaling pathways function are regulated will provide insights into how they can be therapeutically manipulated and may help to identify new diagnostic markers and targets to prevent and treat disease.