Previous and current research
Our laboratory studies the biochemical mechanisms by which chromatin-modifying enzymes and chromatin-binding proteins regulate gene transcription. In particular, our work is focused on the molecular mechanisms by which chromatin proteins encoded by the Polycomb group (PcG) and the trithorax group (trxG) of genes maintain transcriptional states of target genes. PcG and trxG proteins are two evolutionary conserved sets of regulatory factors that control a plethora of developmental processes in both animals and plants. PcG proteins act as repressors that keep target genes inactive in cells where these genes should not be expressed, while trithorax group proteins promote transcription of the same target genes in other cells. Although the PcG/trxG system is best known for its role in maintaining spatially restricted expression of developmental regulator genes in animals and plants, it is also used for processes ranging from X-chromosome inactivation in mammals to the control of flowering time in plants.
We study the PcG/trxG system in the model system Drosophila, using an integrated approach that combines a variety of biochemical, biophysical, genetic and genomic assays. One focus of our research during the past years has been the biochemical purification of PcG protein complexes and to understand their molecular mechanisms. We thus found that PcG protein complexes contain enzymatic activities that add or remove particular post-translational modifications at specific lysine residues in histone proteins. These include a histone methyltransferase and a histone deubiquitylase. Our analysis of PcG protein complexes also revealed that they contain subunits that allow these complexes to bind to specific post-translational modifications such as methylated lysines on histone proteins. From discovering these activities in vitro, we then proceeded to dissect how they regulate gene expression in vivo, by studying where PcG and trxG protein complexes bind to target genes in Drosophila and how their enzymatic activities modify target gene chromatin. By comparing the chromatin of target genes in wild-type and mutant Drosophila strains and by performing structure/function analyses of PcG proteins in Drosophila, we have obtained critical insight into the mechanisms by which these chromatin-modifying and -binding activities regulate gene transcription. For these studies we use the combination of detailed in-depth analyses at the single gene level and global analyses at the level of the entire genome.
Future projects and goals
The strength of our approach is the combination of Drosophila genetics and global genome-wide analyses in vivo with detailed in-depth biophysical and biochemical analyses in vitro. Examples of current studies in the lab include dissecting the mechanisms of chromatin complexes in vitro, measuring the stability of post-translational modifications on histone proteins in vivo, analyzing the role of protein GlcNAcylation in Polycomb repression, or functional testing of the ‘histone code’ in Drosophila. Our long-term goal is to understand how gene transcription states are controlled by the Polycomb /trithorax system and how they are propagated through replication and cell division.