The goal of the proposed research is (1) to measure spatially and temporally resolved chromatin dynamics in mammalian cells in interphase in vivo and (2) determine the origin and function of these dynamical behaviors by combining quantitative approaches derived from physical sciences with tools from molecular biology and biochemistry. The dynamic behavior of chromatin (DNA and associated proteins) has traditionally been studied by live cell microscopy of nuclear proteins, single genes, subchromosomal foci and chromosomal territories [Marshall et al. 1997;Belmont et al. 1998;Levi et al. 2005;Kumaran et al. 2008;Stixova et al. 2011]. Such studies are highly informative, but in practice one can only investigate a few sites simultaneously. Approaches that provide a picture of an overall chromatin dynamics have been slow to develop [Abney et al. 1997]. In the proposed research we will use our newly developed method of velocity correlation spectroscopy (VCS) [Zidovska et al. 2012a], combined with established methods like particle image velocimetry (PIV) and spatio-temporal image correlation spectroscopy (STICS), to measure high-resolution chromatin velocity maps and spatio-temporal evolution of chromatin dynamics over an entire nucleus for the first time (aim 1). In previous work using VCS we found local coherence in spatio-temporal chromatin dynamics, showing that chromatin dynamics is correlated over micron and second scale [Zidovska et al. 2012b]. Our preliminary studies also showed that chromatin dynamics uses ATP, but is independent of the cytoskeleton, hinting at nuclear ATPases being responsible for the observed dynamics. We will probe the origin of the observed chromatin dynamics by specifically inhibiting major nuclear ATPases (polymerase II, DNA polymerase and topoisomerase) using molecular poisons or RNA interference and analyzing the spatio-temporal changes in the pattern of measured chromatin dynamics (aim 2). An exciting preliminary finding showed that chromatin dynamics are largely blocked by a recently-described small molecule JQ1, which binds specifically to four BET family bromodomain proteins, antagonizing their binding to histones [Filippakopoulos et al. 2010]. By investigating how JQ1 blocks chromatin motility we will gain new information on the role of BET proteins in chromatin dynamics. Since JQ1 has demonstrated efficacy in translational models of poorly differentiated carcinoma, multiple myeloma and acute leukemia [Delmore et al. 2011;Zuber et al. 2011], this work may also help elucidate the cellular effects of a promising anti-cancer agent. Finally, we extend this approach to a small panel of cancer and non-cancer cell lines (aim 3) to ask whether chromatin dynamics are perturbed in cancer. If so, VCS analysis might prove useful as a diagnostic tool. Our discoveries in this project will provide a framework for a mechanistic picture of the origins and functional importance of chromatin dynamics in mammalian cells.
Our aim is to understand the origin and role of chromatin dynamics, in other words, how and why does chromatin - DNA and associated proteins - move in cell nucleus. By answering such fundamental question we will learn new biology and physics underlying chromatin dynamics. Such knowledge may trigger a new, mechanistic picture of chromatin dynamics, contributing to current efforts to understand mechanism of cancer as well as to help in search for an anti-cancer drug.
|Bruinsma, Robijn; Grosberg, Alexander Y; Rabin, Yitzhak et al. (2014) Chromatin hydrodynamics. Biophys J 106:1871-81|