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

Periodic Reporting for period 3 - EpiID (Single-cell epigenomics: quantifying epigenetic changes in individual cells using DamID)

Reporting period: 2019-04-01 to 2020-09-30

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 having the same genetic information (collectively named the genome). Different 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 is, 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. Following the different steps of early embryonic development just after fertilization with such a technique will provide the first insights into how the initial cells of the embryo takes the very cell-fate decisions. The objective of this proposal is to develop such a technique and apply it to the first 3.5 days of early mouse embryonic development. In this period before implantation into the uterus, involves the diversification of cells into cells that contribute to the formation of the placenta and cells that will form the embryo proper. This research will provide the first detailed insight into the mechanism behind the first cell-fate decisions in life. With this research we expect to obtain basic knowledge into the fundamental process of cellular-specification and the molecular determinants involved. With this project we will collect valuable information for the improvement of reproductive strategies, and provide innovative new techniques for the research community.
So far the project involved the development of the new single-cell techniques to measure in single-cell different epigenetic states together with the cells identity (DNA output or mRNA). Furthermore, to apply these new techniques to early embryonic development we have set up the conditions in early mouse development. The second half of the project period will involve the further optimisation of the single-cell methods and the application of these to dissect the epigenetic regulatory trajectories of different cell types in early embryonic development.
The techniques that we are developing will allow to obtain insights that can not be acquired with current state of the art techniques. Implementing these techniques to early embryonic development we expect to start to unravel the epigenetic mechanisms behind the first cell-fate decisions.