Research in my group focuses on the molecular mechanisms of epigenetic regulation and phosphoinositide signaling. We apply high field NMR spectroscopy, X-ray crystallography and a wide array of biochemical and molecular biology approaches to characterize the atomic-resolution structures and functions of chromatin- and lipid-binding proteins implicated in cancer and other human diseases.
The study of epigenetics and deciphering the ‘epigenetic code/language’ is the major direction in the lab. The genetic material of eukaryotic cells is packaged into the nucleus in the form of chromatin. Chromatin is made up of building blocks called nucleosomes. Each nucleosomal particle contains an octamer of four histone proteins, H2A, H2B, H3 and H4, around which genomic DNA is wound almost twice. The nucleosomes undergo recurrent structural rearrangements and are subject to posttranslational modifications (PTMs). A particularly large number of PTMs, or epigenetic marks, have been identified on the histone tails that protrude from the nucleosomal core and are freely accessible to histone acetyltransferases (HATs), histone deacetylases (HDACs), histone lysine methyltransferases (HKMTs), kinases, phosphatases and other enzymes capable of depositing or removing PTMs. The list of PTMs is expanding rapidly and includes, among others, acetylation and methylation of lysine residues, methylation of arginine residues, and phosphorylation of serine and threonine residues.
The histone PTMs are recognized by protein modules, referred to as epigenetic effectors, histone-binding domains or simply PTM ‘readers’. Binding of the effectors recruits various components of the epigenetic machinery to chromatin, mediating fundamental processes such as gene transcription, DNA replication and recombination, DNA damage response and chromatin remodeling. Chromatin-associating complexes often contain multiple readers within one or several subunits that show specificities for distinct PTMs. Coordinated recognition of a combination of PTMs can provide a lock-and-key type mechanism for targeting a particular genomic site and ensuring proper biological outcomes. The intricate relationship among the epigenetic components represents one of the most intriguing concepts in modern chromatin biology, which we have only begun to explore. Clearly, the spatial and temporal modulation of and crosstalk between histone PTMs, the PTM-writing, -erasing and -reading proteins play a crucial role in defining the epigenetic landscape.
Misreading of epigenetic marks has been linked to a host of human diseases including autoimmune and developmental abnormalities, addiction, schizophrenia and cancer. Thus, understanding the molecular mechanisms and functional importance of reader-PTM interactions is essential to understanding not only the basic principles of epigenetic regulation, but also the etiology of epimutation-induced human diseases. Our goal is to structurally characterize PHD fingers, Tudor, MBT and other epigenetic effectors and to establish the significance of reading of the epigenetic marks (Fig. 1).
Another research direction is aimed at elucidating the mechanisms of membrane anchoring by PI-binding proteins (Fig. 2). PIs are generated through mono-, bis- and tris-phosphorylation of the inositol headgroup of PtdIns. Each PI has a unique stereochemistry and is involved in distinct biological responses. Collectively, seven known PI isoforms create a remarkably complex signaling network, which could be viewed through a ‘PI code’ model. The level and activity of PIs are tightly regulated by PI kinases, phosphatases and phospholipases that either initiate or terminate signaling cascades by phosphorylating, dephosphorylating and hydrolyzing PIs. Individual PIs are highly concentrated in different intracellular membranes, such as the plasma membrane, or membranes of early endosomes, multivesicular bodies and Golgi. PIs form specific docking sites for lipid-binding effectors, including the ANTH, ENTH, FYVE, PH and PX domain-containing proteins. Interactions of these domains with PIs are required for many fundamental processes including growth, differentiation, vesicular trafficking, cytoskeletal rearrangement and survival of cells. Many PI-binding proteins are involved in down-regulation of proliferative pathways through internalizing oncogenic growth factor receptors. We are interested in defining the molecular basis of activation and recruitment of the PI-binding proteins to the membranes.