Chaperone-Histone Determinants of Cell Identity, Lineage Fate and Transitions – CHIFT

How is cellular identity established during differentiation? How can it be maintained or changed during development, specifically during the choice between symmetric and asymmetric divisions? To what extent can somatic cell fate be challenged or rewired? Answering these fundamental questions is key to understanding how dedicated cells sustain or change their phenotype in the organism. This is an increasingly important societal issue for human health, as understanding how defects at this level contribute to the onset of diseases such as cancer will provide critical knowledge to deroute disease, or improve cellular therapy for regenerative medicine by efficiently manipulating this process.
Much of the information the cell needs to set its identity is conveyed by DNA sequence-specific transcription factors, which orchestrate cell-type specific transcriptional programs. However, the availability of transcription factors does not suffice to induce cell fate changes: it is increasingly clear that changes in cell fate need to overcome epigenetic barriers that lead to resistance to reprogramming and differentiation.
Chromatin organization and epigenomic features are intimately linked to cell identity and plasticity acting precisely with transcription factors to impact both gene expression and genome stability. At the crossroads of these processes, it is increasingly clear that histone variants and histone chaperones are essential regulators of cellular plasticity in the adult nervous system, notably during development, and they have a strong impact on cell reprogramming and differentiation. In this context, our initative CHIFT (Chaperone-Histone Determinants of Cell Identity, Lineage Fate and Transitions) is propelled by recent findings, including our own, providing first evidence that histone chaperones and variants are a relevant entry point to manipulating more efficiently cell identity switches, notably including reprogramming into pluripotency. We believe that these findings are a game-changer, both confirming that histone variant dynamics are critical for cell identity and demonstrating that this property can be exploited to enhance the efficiency of synthetic biology and, potentially, regenerative medicine. Our goal is thus to investigate the role of chromatin assembly mechanisms with specific histone variants in establishment, maintenance and reprogramming of mouse cell identity with a particular focus on chromatin barriers and accelerators of identity switching.
Our project will build upon validated mouse transgenic tools (published or generated by our consortium) to dissect the mechanisms linking histone chaperones and cell identity in mouse primary cells and tissue. We will focus on adult muscle lineage progression from stemness to renewal, to activation and differentiation. We will pay particular attention to asymmetrically dividing muscle stem cells, to dissect how repartition of parental epigenetic features can impact cell identity and fate. To address these points, we will develop new tools that allow us to assay for the first time chaperone-mediated dynamics of specific histone variants in physiological settings. We will develop novel strategies to obtain spatially and temporally resolved cartography of nucleosome organization and histone dynamics, combining classical approaches (epifluorescence, confocal microscopy, chromatin immunoprecipitation) with innovative methods (super-resolution microscopy, time-resolved chromatin immunoprecipitation). Together, we expect that CHIFT will reveal mechanisms of cell identity determination based on the fine, context-dependent modulation of chromatin organization by histone chaperones.