Single-nucleus chromatin landscapes during zebrafish early embryogenesis

Abstract

Vertebrate embryogenesis is a remarkable process, during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis-regulatory elements (CREs) and gene expression within the hierarchy of cell fate decisions. Here, we employed single-nucleus ATAC-seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis, including 3.3 hpf, 5.25 hpf, 6 hpf, 10 hpf, 12 hpf, 18 hpf and 24 hpf, obtained 51,620 high-quality nuclei and 23 clusters. Furthermore, by integrating snATAC-seq data with single-cell RNA-seq data, we described the dynamics of chromatin accessibility and gene expression across developmental time points, which validates the accuracy of the chromatin landscape data. Together, our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.

The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis

“…After quality control (see Methods ; Supplementary Figure 1C ), 10,518 nuclei were used for further analysis ( Supplementary Table 1 ). After duplication removal, the median numbers of unique fragments mapped to the nuclear genome range from ∼26,000 to ∼60,000 ( Supplementary Figure 1B ), which is at the higher end compared to the scATAC-seq atlases in other stages and adult tissues 15–17 . Peak calling using MACS2 from merged single nuclei (see Methods ) identified 446,501 open chromatin regions.…”

“…In zebrafish, several single-cell atlases have been generated in terms of gene expression 4–10 and chromatin accessibility. 15–17 They mainly focused on either the late stages of embryogenesis (mostly after gastrula) or adult tissues, partly due to the fact that early embryo development is driven by maternal factors in zebrafish. 2…”

“…12–14 A limited number of single-cell chromatin accessibility studies mainly focused on the post-gastrula stages or adult tissues. 15–17 Therefore, it is still not clear if and when cells become different at the chromatin level during early embryogenesis. In this study, we used a plate-based single-cell ATAC-seq (scATAC-seq) method 18,19 to investigate the chromatin accessibility states of 10,518 single embryonic nuclei from ZGA up to the dome stage.…”