Affiliations: 1) Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, Paris, France; 2) Menzies Institute for Medical Research, University of Tasmania, Australia
Keywords: n. other (chromatin states during differentiation); d. intestinal stem cells
Adult stem cells self-renew and differentiate into one or several cell types, thus ensuring tissue homeostasis. Understanding their regulation is crucial to have a better comprehension of uncontrolled proliferation and altered differentiation mechanisms occurring during tumorigenesis and age-dependent functional decline of tissues. Here, we aim to better understand what chromatin states are associated with adult stem cell activity in vivo in a homeostatic tissue using the Drosophila adult intestine as a model. Our lab has previously provided evidence of roles of conserved chromatin factors in controlling intestinal stem cell (ISC) proliferation (Gervais et al, 2019), highlighting their importance in the regulation of the intestinal lineage. Here, we expanded on these studies to investigate chromatin state changes associated with stem cell differentiation at the genome-wide scale. By generating cell-type specific whole-genome binding maps of 5 chromatin proteins (RNA Pol II, Brahma, Polycomb, HP1 and H1) using Targeted DamID and performing subsequent Hidden Markov modelling to define chromatin states, we found that 7 major chromatin states exist in the ISC lineage. Examining these states at specific genes revealed dynamic changes within the lineage. First, ISC-specific transcription factors such as esg, klu, Sox100B become marked by the Blue (Polycomb-enriched) state in differentiated cells. In contrast, components of signaling pathways regulating ISC activity are found in distinct states depending on the differentiated cell type, suggesting that they are repressed in different ways. In addition, the key transcription regulators of lineage specification including pros and pdm1 undergo a transition from the Blue state (Polycomb-enriched) to active states upon differentiation, suggesting a role for Polycomb group proteins in repressing these genes in ISCs. While these data suggest a regulatory function of Polycomb-marked chromatin for control of the transcriptional hierarchy within the ISC lineage, we find that genes involved in differentiated cell physiology are instead associated with Histone H1- enriched Black chromatin. Indeed, physiology and metabolic activity-related genes follow a transition from the Black state in ISCs to active states upon their activation, suggesting a previously uncharacterized mode of regulation of physiology-related genes. On-going work will highlight the biological relevance of these chromatin transitions by perturbing specific states and studying the subsequent transcriptional changes and effects on proliferation and differentiation in the intestinal lineage. Overall, the extensive characterization of chromatin state changes during differentiation will provide a valuable resource to better understand the regulatory programs that control cell fate and identity, as well as physiological functions in this homeostatic tissue.