Zhang Zhenhua, Yu Zhenpeng, Chong Yujie, Liu Yao, Liu Jia, Ren Wenhua, Xu Shixia, Yang Guang
Jiangsu Key Laboratory for the Conservation and Utilization of Biodiversity in the Middle and Lower Reaches of the Yangtze River, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
BMC Biol. 2025 Jul 16;23(1):216. doi: 10.1186/s12915-025-02300-0.
Limb morphology is particularly important for animals to inhabit different environments. Limb modifications (e.g., flipper-like forelimbs and hindlimb regression) are among the most critical secondary aquatic adaptation mechanisms enabling cetaceans to fully adapt to an aquatic environment. Exploring the molecular mechanisms underlying limb evolution in cetaceans has attracted considerable attention from evolutionary biologists.
In the present study, conserved non-coding elements (CNEs) closely associated with limb development, which exhibited lineage-specific sequence divergence (nucleotide mutations and indels) in cetaceans, were identified using comparative genomics. These sequence divergences might have led to the loss of binding motifs for transcription factors involved in limb development and significant alterations in autoregulatory activity. A transgenic mouse was constructed to carry a cetacean-specific enhancer (i.e., hs1586), which exhibited a significant phenotypic difference in forelimb buds at embryonic day (E)10.5, supported by transcriptomic and epigenomic evidence. However, the phenotypic recovery after E11.5 suggested that enhancer redundancy in the mouse genome may have compensated for the effects caused by the incorporation of cetacean hs1586. This further suggests that the complex phenotypic changes of limbs in cetaceans are likely not driven by a single CNE but rather involve multiple CNEs and/or genes.
In summary, our study supports the functional role of CNE sequence divergence and the complex mechanisms underlying limb morphology changes in cetaceans.
肢体形态对于动物适应不同环境尤为重要。肢体的适应性改变（例如，鳍状前肢和后肢退化）是鲸类完全适应水生环境的最关键的二级水生适应机制之一。探索鲸类肢体进化的分子机制已引起进化生物学家的广泛关注。
在本研究中，利用比较基因组学鉴定出与肢体发育密切相关的保守非编码元件（CNE），这些元件在鲸类中表现出谱系特异性序列差异（核苷酸突变和插入缺失）。这些序列差异可能导致参与肢体发育的转录因子结合基序的丧失以及自调控活性的显著改变。构建了一只携带鲸类特异性增强子（即hs1586）的转基因小鼠，在胚胎第10.5天（E10.5）时，前肢芽表现出显著的表型差异，转录组学和表观基因组学证据支持这一结果。然而，E11.5之后的表型恢复表明，小鼠基因组中的增强子冗余可能补偿了鲸类hs1586整合所造成的影响。这进一步表明，鲸类肢体的复杂表型变化可能不是由单个CNE驱动的，而是涉及多个CNE和/或基因。
总之，我们的研究支持了CNE序列差异的功能作用以及鲸类肢体形态变化的复杂机制。
