All cells of our bodies have the same genes. Yet only some of them are used in any given cell type. So-called epigenetic mechanisms ensure that genes, which were not selected to be active, remain silent. We employ Drosopila and human cell culture models, genomics, genetics and numerical simulations to understand molecular mechanisms of epigenetic regulation by Polycomb and Trithorax proteins.
DNA elements that target Polycomb complexes to human genes.
Following our breakthrough study of a DNA element that targets Polycomb Repressive Complex 1 (PRC1) to human Cyclin D2 oncogene, we attempt to discover all such elements in the human genome. To this end, we use cultured human cell models, genomics, lentiviral transgenesis and CRISPR/Cas9-mediated precision genome editing.
Beyond the histone code: searching for non-histone targets of Trithorax group methylases.
Mutations in genes encoding Trithorax (Trx) and Ash1 proteins cause excessive Polycomb repression, severe developmental abnormalities and, in mammals, have been linked to multiple forms of cancer. In vitro, both Trx and Ash1 can methylate specific Lysines within histone H3. However, recent histone replacement experiments indicate that methylation of histone H3 is not how Ash1 or Trx stop Polycomb repression. To understand the true mechanism we need to discover other proteins methylated by Ash1 and Trx. We aim to do this by combining biochemical approaches with the power of Drosophila genetics.
Forecasting histone methylation by Polycomb complexes.
Polycomb complexes methylate histone H3 at Lysine 27 (H3K27) within repressed genes, which is an essential part of the epigenetic memory of Polycomb repression. Which genes are covered with methylated H3K27 in a given cell type? How is the dynamics of H3K27 methylation at specific genes affected by the number, affinity, and relative arrangement of DNA elements tethering Polycomb complexes to chromatin? To what extent will the level of methylated H3K27 at developmental genes (or oncogenes) change as cells speed up or slow down their cell cycle? Answers to these questions hold a great promise for controlled manipulation of cell fates. Yet, current technology does not allow addressing them experimentally, especially in clinical settings. To bridge this gap, we develop realistic numerical models, which, for starters, aim to forecasts H3K27 methylation by Drosophila Polycomb complexes.
Dorafshan E, Kahn TG, Glotov A, Savitsky M, Walther M, Reuter G, Schwartz YB. 2019. Ash1 counteracts Polycomb repression independent of histone H3 Lysine 36 methylation. EMBO Rep 20: e46762.
Cameron SR, Nandi S, Kahn TG, Barrasa JI, Stenberg P, Schwartz YB. 2018. PTE, a novel module to target Polycomb Repressive Complex 1 to the human cyclin D2 (CCND2) oncogene. J Biol Chem. 293:14342-14358.
Kahn TG, Dorafshan E, Schultheis D, Zare A, Stenberg P, Reim I, Pirrotta V, Schwartz YB. 2016. Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements. Nucleic Acids Res. 44:10132-10149.
Lee HG, Kahn TG, Simcox A, Schwartz YB, Pirrotta V. 2015. Genome-wide activities of Polycomb complexes control pervasive transcription. Genome Res. 25:1170-1181.
Schwartz YB, Linder-Basso D, Kharchenko PV, et al. 2012. Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res. 22:2188-2198.
Kharchenko PV, Alekseyenko AA, Schwartz YB, et al. 2011. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 471:480-485.