How epigenetic reprogramming modulates 3D chromatin organization in totipotent embryos

One of the most intriguing questions in biology is how a single cell (zygote) is generated that has the potential to give rise to all cell types of an organism, known as totipotency.

The overall purpose of this project is to gain mechanistic insights into the establishment of the totipotent state, in terms of 3D chromatin organization and zygotic genome activation (ZGA), summarized in two key aims:i)To test whether and how epigenetic reprogramming modulates the 3D chromatin structure in zygotes: The generation of a zygote is accompanied by Tet3-dependent active DNA demethylation of the paternal genome and asymmetry in histone modifications between the parental genomes.

Whether this alters chromatin organization and promotes transcription is poorly understood.

To test this, I will perturb Tet3 activity and perform single nucleus Hi-C (snHi-C) of zygotes to determine changes in genome architecture.

In addition, I will study the effect of the absence of Kdm4a on the different histone marks and the consequent potential effect on chromatin architecture.

This work will provide the first insights into how epigenetic reprogramming alters chromatin organization. ii) To study the mechanism of ZGA: The activation of embryonic transcription is crucial for the development of an organism. However, the essential activators of ZGA in mammals remain largely unidentified.

Based on work in Drosophila, a leading hypothesis is that ZGA is triggered by pioneer transcription factors. To identify these, I will participate in a targeted knockdown screen in embryos to identify factors required for ZGA. I will focus on one potential candidate and generate transgenic mouse strains to study its function in early embryos.

This high-risk high-gain aim has the potential to identify novel regulators of the mammalian ZGA.