清华大学医学院蓝勋团队近期取得重要工作进展，他们研究利用SPATAC-seq在单细胞分辨率下绘制斑马鱼胚胎发生的染色质可及性图谱。相关研究成果2024年7月8日在线发表于《自然—细胞生物学》杂志上。

据介绍，目前对于决定斑马鱼胚胎发生过程中每种细胞类型独特身份和功能调控程序的动态可及性元件缺乏详细的研究。

研究人员提出了SPATAC-seq：一种使用测序的基于分裂池连接的转座酶可及染色质测定法。使用SPATAC-seq，研究人员分析了从球体阶段到早期幼虫突出嘴阶段的20个发育阶段中超过80万个单细胞核的染色质可及性。利用这个染色质可及性图谱，研究人员鉴定了604种细胞状态，并推断了它们的发育关系。

研究人员还鉴定了959040个候选顺式调控元件（cCRE），并描述了发育特异性cCRE，以及定义不同细胞身份的转录因子。增强子报告基因测定证实，大多数测试的cCRE在受限的细胞类型或组织中表现出增强的绿色荧光蛋白表达。最后，研究人员探索了驱动色素和脊索细胞分化的基因调控程序。

总之，这一研究为探索斑马鱼胚胎发生中细胞命运决定的驱动因子提供了宝贵的开放资源。

附：英文原文

Title: Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq

Author: Sun, Keyong, Liu, Xin, Xu, Runda, Liu, Chang, Meng, Anming, Lan, Xun

Issue&Volume: 2024-07-08

Abstract: Currently, the dynamic accessible elements that determine regulatory programs responsible for the unique identity and function of each cell type during zebrafish embryogenesis lack detailed study. Here we present SPATAC-seq: a split-pool ligation-based assay for transposase-accessible chromatin using sequencing. Using SPATAC-seq, we profiled chromatin accessibility in more than 800,000 individual nuclei across 20 developmental stages spanning the sphere stage to the early larval protruding mouth stage. Using this chromatin accessibility map, we identified 604 cell states and inferred their developmental relationships. We also identified 959,040 candidate cis-regulatory elements (cCREs) and delineated development-specific cCREs, as well as transcription factors defining diverse cell identities. Importantly, enhancer reporter assays confirmed that the majority of tested cCREs exhibited robust enhanced green fluorescent protein expression in restricted cell types or tissues. Finally, we explored gene regulatory programs that drive pigment and notochord cell differentiation. Our work provides a valuable open resource for exploring driver regulators of cell fate decisions in zebrafish embryogenesis.

DOI: 10.1038/s41556-024-01449-0

Source: https://www.nature.com/articles/s41556-024-01449-0