整合 ATAC-seq 与 RNA-seq 解析斑马鱼经典与非经典成骨细胞的染色质与转录组特征，并揭示 entpd5a 调控机制
Integration of ATAC- and RNA-sequencing identifies chromatin and transcriptomic signatures in classical and non-classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation
利用新构建的转基因斑马鱼系分离经典与非经典成骨细胞，并同时开展 ATAC-seq 与 RNA-seq，分别及整合分析两类骨骼细胞的染色质动态与转录组变化。结果显示 Dlx 家族因子在经典成骨细胞调控中起重要作用，而 Hox 家族因子通过非经典成骨细胞参与脊柱骨化。研究还对 entpd5a 启动子进行了资源驱动分析，实验验证了 ATAC-seq 数据集，并提出斑马鱼骨形成过程中 entpd5a 复杂表达模式的调控机制，指出 entpd5a 位点存在时空特异性的启动子/增强子互作。
来源：eLife · doi.org
Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian cell and notochord sheath cells which serve as non-classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the indispensability of zebrafish models in vertebrate research, the genetic regulation of bone formation, as well as mechanisms of transcriptional control of entpd5a , remains largely unknown. Here, using a newly generated transgenic line, we isolate classical and non-classical osteoblasts from zebrafish embryos and performed both assay for transposase-accessible chromatin (ATAC)-seq and RNA-seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cell types. We show that although Dlx family factors are playing important roles in classical osteoblast regulation, Hox family factors are involved in governing spinal ossification via non-classical osteoblasts. We further present a resource-driven analysis of the entpd5a promoter, experimentally validating the ATAC-seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio-temporally regulated promoter/enhancer interactions taking place in the entpd5a locus.