School of Biological Sciences, Cell and Developmental Biology, University of East Anglia, Norwich Research Park, Norwich, UK.
Developmental Biology and Cancer, University College London, Great Ormond Street Hospital, Institute of Child Health, London, UK.
Nat Commun. 2021 Feb 19;12(1):1157. doi: 10.1038/s41467-021-21426-7.
Somites arising from paraxial mesoderm are a hallmark of the segmented vertebrate body plan. They form sequentially during axis extension and generate musculoskeletal cell lineages. How paraxial mesoderm becomes regionalised along the axis and how this correlates with dynamic changes of chromatin accessibility and the transcriptome remains unknown. Here, we report a spatiotemporal series of ATAC-seq and RNA-seq along the chick embryonic axis. Footprint analysis shows differential coverage of binding sites for several key transcription factors, including CDX2, LEF1 and members of HOX clusters. Associating accessible chromatin with nearby expressed genes identifies cis-regulatory elements (CRE) for TCF15 and MEOX1. We determine their spatiotemporal activity and evolutionary conservation in Xenopus and human. Epigenome silencing of endogenous CREs disrupts TCF15 and MEOX1 gene expression and recapitulates phenotypic abnormalities of anterior-posterior axis extension. Our integrated approach allows dissection of paraxial mesoderm regulatory circuits in vivo and has implications for investigating gene regulatory networks.
体节来源于轴旁中胚层，是具有分节特征的脊椎动物体轴模式的标志。它们在胚胎轴延伸过程中顺序形成，并产生肌骨骼细胞谱系。轴旁中胚层如何沿轴进行区域化，以及这与染色质可及性和转录组的动态变化如何相关仍然未知。在这里，我们报告了沿鸡胚轴的一系列时空 ATAC-seq 和 RNA-seq。足迹分析显示，包括 CDX2、LEF1 和 HOX 簇成员在内的几个关键转录因子的结合位点的覆盖情况存在差异。将可及染色质与附近表达的基因相关联，确定了 TCF15 和 MEOX1 的顺式调控元件 (CRE)。我们确定了它们在 Xenopus 和人类中的时空活性和进化保守性。内源性 CRE 的表观基因组沉默破坏了 TCF15 和 MEOX1 基因的表达，并再现了前-后轴延伸的表型异常。我们的综合方法允许在体内解析轴旁中胚层的调控回路，并对研究基因调控网络具有重要意义。
