Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during early mammalian organogenesis

This repository contains the scripts to reproduce the Tet-TKO scNMT-seq analysis of the manuscript. It covers Figure 4 as well as Supplementary Figures 7-8. The source code for the Tet-TKO scNMT-seq, is available in this repository

Experimental design

We generated TET1/2/3 ^-/- (Tet-TKO) chimeric embryos following the study design of Pijuan-Sala et al 2019, in which Tet-TKO cells are marked by the fluorescent marker tdTomato thereby allowing collection of two fractions using FACS: a fluorescent fraction that contains Tet-TKO cells and a non-fluorescent fraction that contains WT host cells. We additionally use antibody staining to enrich for cells belonging to the primitive erythropoiesis trajectory. Single cells were collected and processed using scNMT-seq which profiles chromatin accessibility, DNA methylation and RNA transcription in parallel from the same cell.

Key results

• We find that primitive erythrocytes are associated with global methylation loss, independent of TET enzymes, likely mirroring the demethylation that occurs later in development during definitive erythropoiesis.

• Beyond this passive process, we discover coordinated demethylation of distal regulatory elements associated within the blood lineage that is TET-dependent and which provides a molecular explanation for the depletion of erythrocytes in Tet-TKO.

• We further show that TET-dependent demethylation of distal regulatory elements is a common feature of differentiation during early organogenesis.

Data

Raw data is available at GEO. Parsed data can be downloaded in progress....

Shiny app

We provide a shiny app that allows the user to explore the Tet-TKO scRNA-seq results here. Note that we currently do not have a shiny app to explore the scNMT-seq TET-TKO results.

Contact

For questions on the computational analysis: Ricard Argelaguet (ricard.argelaguet@gmail.com). For questions on the experimental work: Tim Lohoff (tlohoff431@gmail.com) or Stephen Clark (Stephen.Clark@babraham.ac.uk)