ChromaDYN · Quantitative multimodal pulse-and-label time-resolved chromatin maps

Chromatin packages the eukaryotic genome in a highly dynamic fashion, with dramatic structural changes during every cell cycle. At the same time, chromatin provides remarkable stability for transcriptional regulation and genome organization, for example in maintaining gene expression programs and lineage identity during complex organismal development. A mechanism to propagate information through ‘disruptive’ transitions in the cell cycle, namely DNA replication and mitosis, is key in maintaining heritable, so-called ‘epigenetic’ chromatin states.Proteins that build and interact with chromatin, foremost histones, are much more than static architectural components. This motivates the development of time-resolved quantitative assays in the living cell, which will allow to capture dynamic features of chromatin states over timescales from minutes to days. Building on a synthetic biology toolbox, a quantitative multimodal pulse-and-label strategy will be developed. Following protein populations in both time and subcellular/genomic space, dynamic protein-protein interaction networks and chromatin maps will be captured.The project will use to state-of-the-art quantitative biochemical, imaging, genomics and proteomics readouts, including single-cell readouts. These will feed into mathematical models to describe the dynamics and potential heterogeneity/stochasticity of the system under study, predict its response to perturbations and guide mechanistic hypotheses. The project will systematically decipher mechanisms for propagating epigenetic chromatin states, starting with the fundamental rules of histone inheritance through replication and mitosis. Additional levels of complexity introduced through chromatin remodeling activities, nucleosome turnover and histone exchange will be integrated. Finally, the dynamics underlying developmental chromatin state transitions, including asymmetric cell fate decisions, will be resolved.