Our laboratory is interested in understanding the molecular mechanisms by which chromatin signaling networks effect nuclear and epigenetic programs, and how disruption in these mechanisms contribute to cancer and other pathologic states. Our work centers on the biology of protein lysine methylation, a principal chromatin-regulatory mechanism thought to be involved in directing epigenetic processes. We study how lysine methylation events on histone and non-histone nuclear factors are generated, sensed, and transduced, and how these chemical marks integrate with other modification and nuclear signaling systems to govern diverse functions.
Major research efforts in the lab include:
Investigation of the catalytic, biological, and pathologic functions for diverse lysine methyltransferase enzymes present in the human and yeast proteomes
Identification and functional characterization of protein domains that sense and transduce histone modification events
Identification and biological characterization of novel lysine methylation events on non-histone chromatin-regulatory proteins
Develop high-throughput technologies to study the broad spectrum of chromatin modification present in the human epigenome
I. Investigation of the catalytic, biological, and pathologic functions for diverse lysine methyltransferase enzymes present in the human proteome. We have generated an expression library containing the majority of the greater than fifty protein lysine methyltransferase (PKMT) enzymes predicted to be present in the human proteome. While several of these enzymes have been implicated in human disease, the catalytic activity and substrate specificity for many of these enzymes and how such activities relate to disease pathogenesis, is presently not clear. We are conducting studies employing molecular, biochemical, genomic, and cellular strategies to understand the physiologic and pathologic action for several of these factors, with an emphasis on PKMTs implicated in cancer, aging, and inflammation regulation.
II. Identification and functional characterization of protein domains that sense and transduce histone modification events. Elucidation of the protein modules present within chromatin-regulatory factors that recognize the broad spectrum of post-translational modifications present on histone proteins is critical for understanding how chromatin dynamics influence fundamental nuclear processes. The PHD finger is an evolutionarily conserved zinc finger motif common to chromatin-associated proteins, and mutations within PHD fingers of many proteins are associated with cancers and genetic disorders. We have discovered that the PHD finger present in the tumor suppressor ING2 [Full Text PDF] as well as several other PHD fingers [Full Text PDF; Full Text PDF] found on diverse nuclear proteins, including the recombinase RAG2 (in collaboration with the Oettinger lab [Full Text PDF], function as highly selective recognition modules for histone H3 trimethylated at lysine 4 (H3K4me3). These studies, in conjunction with work from several other groups (see figure below), have demonstrated that PHD finger constitute the largest known class of chromatin effectors to date and have uncovered new paradigms of how histone methylation impacts on biology. We utilize a number of approaches to identify and characterize new effector domains that modulate chromatin dynamics to influence key nuclear programs.
III. Identification and biological characterization of novel lysine methylation events on non-histone chromatin-regulatory proteins. In addition to histone proteins, several other proteins undergo lysine methylation (for example, p53[Full Text PDF; Full Text PDF], indicating that this modification may be a common mechanism for modulating protein-protein interactions and signaling pathways. We are utilizing a combination of biochemical and proteomic strategies to purify and identify non-histone chromatin-regulatory proteins that are modified by lysine methylation. We then employ strategies and principles developed for the study of histone methylation to understand the enzymes, effectors, and signaling networks that are linked to these diverse methylation events.
IV. Develop high-throughput technologies to study the broad spectrum of chromatin modification present in the human epigenome. The molecular mechanism linking the vast number of histone PTMs to biological outcomes requires knowledge of the proteins that recognize distinct histone species. These effector proteins define the functional consequences of specific modifications by transducing molecular events at chromatin to biological outcomes. Thus, the elucidation of histone PTM readers is critical for understanding how chromatin dynamics contribute to epigenetic programs. To aid in the discovery of novel readers we utilize protein array technology for proteome-wide, high-throughput coverage of the human epigenome [Full Text PDF]. We are interested in developing second-generation arrays that will allow us to probe multivalent interactions between chromatin-modifying complexes and chromatin.