Identification of TBX3 and shared HAND2-TBX3 target gene in early mouse limb buds [RNA-seq]. Identification of TBX3 and shared HAND2-TBX3 target gene in early mouse limb buds [RNA-seq]

ChIP-seq is combined with RNA-seq analysis to identify the TBX3 and HAND2 target genes during mouse limb bud development. This analysis identifies the DEGs and direct transcriptional targets of HAND2 and TBX3 during the early determinative period critical to establishment of limb axis polarity and the SHH signaling center in the posterior limb bud mesenchyme. In particular, bioinformatics analysis identifies the target gene networks that are co-regulated by both TBX3 and HAND2 transcription factors in the limb bud mesenchyme. A significant fraction of the target genes identified are required for normal limb bud development and their spatio-temporal expression patterns are changed in mutant limb buds at early stages. This project was supported by SNSF Grant 310030_184734 to Rolf Zeller (project partner: Aimée Zuniga). Overall design: RNA-seq analysis of a) Hand2-deficient and b) Tbx3-deficient mouse forelimb buds

本研究将染色质免疫共沉淀测序（ChIP-seq）与RNA测序（RNA-seq）相结合，用于鉴定小鼠肢芽发育过程中TBX3与HAND2的靶基因。该分析可鉴定出在肢体轴极性建立以及肢芽后部间充质中音猬因子（SHH）信号中心形成的关键早期决定性阶段中，HAND2与TBX3的差异表达基因（DEGs）及直接转录靶标。尤为关键的是，通过生物信息学分析，本研究鉴定出了肢芽间充质中由TBX3与HAND2转录因子共同调控的靶基因调控网络。所鉴定出的靶基因中，有相当一部分对于正常肢芽发育不可或缺，且在早期突变体肢芽中，这些基因的时空表达模式发生了改变。本项目受瑞士国家科学基金会（SNSF）资助，资助编号为310030_184734，受资助人为Rolf Zeller（项目合作人：Aimée Zuniga）。实验设计：对a）HAND2缺陷型小鼠及b）TBX3缺陷型小鼠的前肢芽开展RNA-seq分析。