Description

Single cell changes in chromatin accessibility during metazoan development

James Reddington¹*, Darren Cusanovich²*, David Garfield¹*, Riza Daza², Raquel Marco-Ferreres¹, Rebecca Rodriguez Viales¹, Lena Christiansen³, Frank Steemers³, Jay Shendure^2$, Eileen Furlong^1$

*Joint first authors; ^$Co-corresponding authors

¹EMBL Heidelberg, Germany; ²University of Washington, Seattle, WA, USA; ³Illumina, Inc., San Diego, CA, USA

Embryonic development is characterised by the successive restriction of cell-fate that culminates in the complexity of cell-types observed in an adult organism.This emerging cellular heterogeneity poses a challenge to understand the regulation of embryonic cell-fate decisions, as genomic methods typically require large numbers of cells and therefore average out important biological differences.Here, we address this by examining the landscape of chromatin accessibility during Drosophila melanogaster embryogenesis at single-cell resolution. We applied sc-ATAC-seq to dissociated, intact nuclei from formaldehyde-fixed embryos at three developmental time-points, spanning early gastrulation through to terminal tissue differentiation, profiling 23,000 nuclei in total.These profiles provide a global view of the epigenetic landscape of emerging germ layers and are sufficient to group cells into diverse cell-types.By aggregating profiles across clusters of cells with similarly accessible chromatin we identify thousands of novel regulatory elements that are specifically accessible in subsets of tissue primordia or specified cell-types.For selected cell-clusters we show remarkable agreement with bulk measures of chromatin accessibility performed on pure populations of FACS isolated cells, validating this approach.We use this single-cell accessibility information to predict the spatial activity of novel developmental enhancers, which upon testing in transgenic embryos show near perfect accuracy.This data provides a first single-cell view of chromatin accessibility during embryonic progression, and demonstrates the power of ‘shotgun epigenetics’ of single cells, even from whole embryos, to resolve cell-types and define their regulatory landscapes.