DNA Methylation dynamics during Gastrulation

Project Information

MeGa

Grant agreement ID: 751439

DOI

10.3030/751439

Project closed

EC signature date 22 March 2017

Start date 1 September 2018

End date 3 April 2021

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 195 454,80

EU contribution

€ 195 454,80

Coordinated by

THE BABRAHAM INSTITUTE
United Kingdom

Periodic Reporting for period 1 - MeGa (DNA Methylation dynamics during Gastrulation)

Reporting period: 2018-09-01 to 2020-08-31

Summary of the context and overall objectives of the project

The embryo development is a complex process in which a single totipotent cell generates a multicellular organism. During this process, hundreds of different cell types differentiate and acquire their own identity. This is orchestrated by large-scale changes in gene expression programs and a drastic remodeling of the epigenome. Epigenetic changes allow to activate the correct genes at the precise developmental stages at the same time they stabilize differentiated states once cell fate is specified. In mammals, studying how these changes occur is particularly challenging due to internal gestation and the complexity of developmental pathways. In addition, the static nature of sequencing technologies only allows the study of a developmental snapshot in time, substantially limiting the understanding of cell fate trajectories.

Using the mouse as a model, this project investigates the links between the epigenome and transcriptome during early development from a novel and unique temporal perspective. For this purpose, we have developed a novel single cell multiomic technology which records cell lineage relationships. The obtained information is used to monitor and understand the propagation of key developmental cell decisions throughout cell generations. This project also explores how DNA methylation marks contribute to lock in differentiated states preventing a return to less specialized fates. This is particularly important for stem cell therapies as failure to acquire these marks affects long-term cellular stability. The results of this project will also provide fundamental insights into the field of epigenetics, mammalian development and stem cell biology.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During the tenure of the Marie Sklodoska-Curie fellowship, I have developed a new method for simultaneous reporting lineage information and cellular state to study differentiation trajectories during embryo development. The method, based on CRISPR Cas9 technology, uses several barcoded guide RNAs and a Cre-inducible Cas9 protein. Upon activation, CRISPR-Cas9 is directed to make DNA double-stranded breaks that are subsequently repaired, frequently in an error-prone way, resulting in insertions or deletions. As mutagenesis continues, cells accumulate a combination of mutations that can be used to reconstruct their lineage history. The genetic mutations are captured in a polyA transcript which is sequenced together with the transcriptome and the epigenome of each cell. I have also developed a new computational method to connect molecular states (transcriptome and epigenome) with previous cellular activity (genetic mutations) at single cell resolution, thus directly connecting cell identities with the lineage of origin. A manuscript is currently in preparation, describing how cell’s history complement epigenetic and transcriptional information to characterize cell types and better understanding developmental trajectories.

This work has been presented at seminars at the host Institute and within the Cambridge scientific community. Furthermore, I will present our findings in the Single cell genomics 2022 meeting.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The results obtained in this multidisciplinary project contribute to increasing the knowledge of developmental biology and epigenetics. This project has also developed sophisticated technological and computational advances, which have wide-ranging applications including the study of clonality in regenerative and cancer biology. As such, this project is not only of scientific importance, but have potential medical relevance, benefiting the European Research Area. I have also benefited the European Research Area through a valuable exchange of ideas, knowledge and expertise and promoting international cooperation.

MeGa_summary