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Single-cell epigenomics: quantifying epigenetic changes in individual cells using DamID

Periodic Reporting for period 4 - EpiID (Single-cell epigenomics: quantifying epigenetic changes in individual cells using DamID)

Reporting period: 2020-10-01 to 2021-09-30

Every cell in the human body descents from a single fertilized oocyte (egg) which consist of 50% each of the genetic information of both parents. However, the human body consists of hundreds of different cell types with very diverse functions despite all cells having the same genetic information (collectively named the genome). Different cell types cells arise as the fertilized oocyte divides to form the embryo. Cell-type diversification occurs through the activation of different regions of the genome in different cells. This process is directed by epigenetics, which involves the more or less tight packaging of the DNA in proteins collectively termed chromatin. Yet, how exactly cells take cell-fate decisions, and what the underlying epigenetic mechanism are, is poorly understood especially in early embryonic development. Thus to obtain better insight in this process, it is essential to develop techniques with which the identity of a cell can be determined in conjunction with the epigenetic regulatory state of that same single cell. For Q4 of our project, we finalized a new single-cell technique to measure epigenetic and transcriptomic states in individual cells. We implemented this technique to study gene regulation and genome organization in mouse and zebrafish embryogenesis. We obtained new insight into how transcription factor networks are controlled by chromatin states during cellular specification in mouse cells and uncovered potentially new roles for densely packed chromatin in providing mechanical stiffness to the notochord in zebrafish 15-somite stage. By implementing this technique, our group will continue to collect information on the contribution of epigenetics in directing cell choice in embryonic development in different organisms. The method and the publicly available computational pipeline will facilitate research of other research groups to study diverse biological questions.
The project involved the development of several new single-cell techniques to measure in single cells protein-DNA contacts and epigenetic states together with transcriptomics (mRNA). In addition, we have established protocols to implement these methods in early embryonic development in mouse and zebrafish model systems. We discovered an important role for the three-dimensional positioning of chromosomes in the first awaking of the genome just after fertilization of the oocyte. We also reported a remarkable variability in the spatial positioning of chromosomes in the nucleus as well as in the epigenetic states of individual cells of the same embryo. Future research by our group and others will have to determine the underlying biological implications of his cell-to-cell variability. In zebrafish embryos, we were able to map for the first time the single-cell epigenetics of an entire 15-somite embryo. Among other observations, this strategy resulted in the identification of an epigenetic state exclusively in notochord cells, that we think may contribute to providing these cells stiffness to withstand mechanical tension.
The techniques that we developed allow to obtain insights that can not be acquired with current state of the art techniques. The implementation of these techniques to early embryonic development will be indispensable to unravel the epigenetic mechanisms behind the first cell-fate decisions in diverse biological systems.