The continuum of Drosophila embryonic development at single-cell resolution

Abstract

Drosophila melanogaster is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost 1 million and gene expression in half a million nuclei from overlapping windows spanning the entirety of embryogenesis. Leveraging developmental asynchronicity within embryo collections, we applied deep neural networks to infer the age of each nucleus, resulting in continuous, multimodal views of molecular and cellular transitions in absolute time. We identify cell lineages; infer their developmental relationships; and link dynamic changes in enhancer usage, transcription factor (TF) expression, and the accessibility of TFs’ cognate motifs. With these data, the dynamics of enhancer usage and gene expression can be explored within and across lineages at the scale of minutes, including for precise transitions like zygotic genome activation.

A single-cell multi-omic atlas spanning the adult rhesus macaque brain

“…Given that families of TFs have similar binding motifs, it is often difficult to identify the specific TF in a given family that is responsible for enrichment in cell typespecific cCREs. To identify the most likely TF, we therefore employed our recently-developed approach [45, 65] that uses the computationally paired snRNA-seq and snATAC-seq data. In brief, this approach relies on the assumption that TFs will be highly expressed in cell types where they play a key role, while their associated motif should be enriched (or depleted) in that cell’s cCREs, indicating TF activation (or repression).…”

Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation

“…To understand the relationship between TF binding and chromatin accessibility, we performed ATAC-seq experiments 71,72 in a developmental time course of 30-minute intervals during the maternal-to-zygotic transition. This allowed us to measure how enhancers transition over time from a naturally closed state to a more accessible, primed state 50,[73][74][75][76][77] . The first embryo collection (1-1.5 h after egg laying, AEL) covers the time when Zelda begins to bind throughout the genome in the 8th nuclear cycle 36 , as well as the earliest stages of embryonic patterning.…”

Benchmarking strategies for cross-species integration of single-cell RNA sequencing data

“…Another valuable application is to compare cell types between human and model animals, with an aim of providing molecular guidance to select the most appropriate model for a particular tissue or disease. While more and more parallel biological processes, such as embryonic development 29,30,39,40 and aging 41 being characterized in several species at the cellular level, it is an exciting time to extend our knowledge base of cells, cell types and tissue functions in the area of development, evolution, health and disease.…”

“…Another valuable application is to compare cell types between human and model animals, with an aim of providing molecular guidance to select the most appropriate model for a particular tissue or disease. While more and more parallel biological processes, such as embryonic development 29,30,39,40 and aging 41 being characterized in several species at the cellular level, it is an exciting time to extend our knowledge base of cells, cell types and tissue functions in the area of development, evolution, health and disease. To obtain multi-modal data, cellular lineage information and cellular response under perturbation then compare cross-species will give a more comprehensive picture of cellular profile to deeper our understanding of the history, identity, and the behaviour of cells.…”