Three Distinct Phases of Regeneration-Specific Gene Expression in the Axolotl Blastema

The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we have performed deep RNA sequencing of the blastema over a time course. We find genes expressed in three phases with a prominent burst in oncogene expression during the first day, blastemal/limb bud genes peaking at 7 to 14 days, and markers for terminal differentiation upregulated later. We compare these expression patterns to those in a mouse digit amputation model to identify genes specific to the regenerative response. We find that limb patterning genes, SALL genes, and genes involved in the proteasome, adult stem cell, embryonic stem cell, retinoid metabolism, and WNT and NOTCH signaling are regeneration-specific. We establish the “Axolomics” Database, which provides a tool for depositing, retrieving, and searching axolotl-related “omic” information.

蝾螈具备截肢后再生肢体的卓越能力。截肢位点处的细胞会形成芽基（blastema），随后通过增殖与分化实现肢体再生。为深入解析这一再生过程，本研究对不同时间节点的芽基开展了深度RNA测序。研究发现，相关基因的表达呈现三个阶段性特征：术后首日癌基因表达出现显著爆发，芽基/肢芽基因于7至14天达到表达峰值，终末分化标志物则在后续阶段被上调。本研究将该基因表达模式与小鼠趾部截肢模型的表达谱进行比对，以此筛选出再生反应特异性基因。结果表明，肢体模式建成基因、SALL基因家族，以及参与蛋白酶体、成体干细胞、胚胎干细胞、类视黄醇代谢，以及WNT与NOTCH信号通路的相关基因均属于再生特异性基因。本研究构建了"Axolomics"数据库，该平台可提供美西钝口螈相关组学（omic）信息的提交、检索与搜索工具。

搜集汇总

背景与挑战

背景概述

该数据集通过深度RNA测序研究蝾螈肢体截肢后芽基再生过程中的基因表达动态，识别出三个不同阶段：早期癌基因表达爆发、中期芽基/肢芽基因峰值和晚期终末分化标志物上调。研究还通过比较小鼠模型，鉴定出与再生特异性相关的基因，如肢体模式基因、SALL基因以及涉及信号通路和代谢的基因。数据集包含20个样本，涵盖蝾螈和小鼠物种，专注于转录组分析，旨在为再生生物学提供重要见解。