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
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.
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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.
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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.
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We further show that TET-dependent demethylation of distal regulatory elements is a common feature of differentiation during early organogenesis.
Raw data is available at GEO. Parsed data can be downloaded here
No longer hosted online, please contact Ricard if you are interested in using it.
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)