Single-cell temporal tracking of epigenetic DNA marks

Project Information

EpiTrack

Grant agreement ID: 742654

DOI

10.3030/742654

Project closed

EC signature date 21 April 2017

Start date 1 September 2017

End date 28 February 2023

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 499 875,00

EU contribution

€ 2 499 875,00

Coordinated by

VILNIAUS UNIVERSITETAS
Lithuania

Periodic Reporting for period 4 - EpiTrack (Single-cell temporal tracking of epigenetic DNA marks)

Reporting period: 2022-03-01 to 2023-02-28

Summary of the context and overall objectives of the project

Epigenetics, the study of the changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself, has taken centre stage in our understanding of gene regulation, cellular differentiation and human disease. The process of adding a methyl group to a DNA molecule (DNA methylation) is one of the most prevalent epigenetic modifications in mammals whereby three major DNA methylation enzymes (DNMT1, DNMT3a and DNMT3b) deposit tens of millions of these "diacritic marks" in the genome creating cell type-specific methylation patterns. Although DNA methylation has been extensively investigated, key mechanisms of these fascinating events remain obscure. The project aims to engineer an advanced cellular system (named liveTAG) that will give a comprehensive view of the roles that the three DNA methyltransferases play in establishing cell-specific genomic methylation patterns and how they govern cell variability and ability to differentiate during mammalian development. The study aims to deepen our understanding of epigenetic regulation in mammalian cells which has important implications in human development and disease.

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

Using CRISPR-CAS genome editing technology and new knowledge gained during the project we have successfully redesigned the DNMT1 methylase inside mouse cells for selective deposition of trackable chemical entities in DNA. In parallel, we have advanced our development of high resolution analytical tools for mapping the deposited chemical entities on the genome scale in single cells.

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 developed unique tools pave the way to selective chemical tracking of key epigenetic events underlying reprogramming of stem cells to other cell types during mammalian differentiation. These studies will provide new insights into the epigenetic regulation in mammalian cells which has important implications for our understanding human development and disease.

Strategy for small molecule-dependent chemical tagging of cognate methylation sites (liveTAG)