Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.
Nat Commun. 2021 Nov 23;12(1):6790. doi: 10.1038/s41467-021-27159-x.
Lineage commitment and differentiation is driven by the concerted action of master transcriptional regulators at their target chromatin sites. Multiple efforts have characterized the key transcription factors (TFs) that determine the various hematopoietic lineages. However, the temporal interactions between individual TFs and their chromatin targets during differentiation and how these interactions dictate lineage commitment remains poorly understood. Here we perform dense, daily, temporal profiling of chromatin accessibility (DNase I-seq) and gene expression changes (total RNA-seq) along ex vivo human erythropoiesis to comprehensively define developmentally regulated DNase I hypersensitive sites (DHSs) and transcripts. We link both distal DHSs to their target gene promoters and individual TFs to their target DHSs, revealing that the regulatory landscape is organized in distinct sequential regulatory modules that regulate lineage restriction and maturation. Finally, direct comparison of transcriptional dynamics (bulk and single-cell) and lineage potential between erythropoiesis and megakaryopoiesis uncovers differential fate commitment dynamics between the two lineages as they exit the stem and progenitor stage. Collectively, these data provide insights into the temporally regulated synergy of the cis- and the trans-regulatory components underlying hematopoietic lineage commitment and differentiation.
谱系的确定和分化是由主转录调控因子在其靶染色质位点上的协同作用驱动的。已经有多项研究对决定各种造血谱系的关键转录因子（TFs）进行了描述。然而，在分化过程中单个 TF 与其染色质靶标之间的时间相互作用以及这些相互作用如何决定谱系的确定仍然知之甚少。在这里，我们对体外人类红细胞生成过程中的染色质可及性（DNase I-seq）和基因表达变化（总 RNA-seq）进行了密集、每日、定时的分析，以全面定义发育调控的 DNase I 超敏位点（DHSs）和转录本。我们将远端 DHSs 与其靶基因启动子以及单个 TF 与其靶 DHSs 联系起来，揭示了调控景观组织在不同的顺序调控模块中，这些模块调节谱系限制和成熟。最后，对红细胞生成和巨核细胞生成中的转录动力学（批量和单细胞）和谱系潜力进行直接比较，揭示了两个谱系在离开干细胞和祖细胞阶段时之间不同的命运确定动力学。总的来说，这些数据为造血谱系确定和分化的顺式和反式调控成分的时间调节协同作用提供了深入了解。
