Hintermann Aurélie, Bolt Christopher C, Hawkins M Brent, Valentin Guillaume, Lopez-Delisle Lucille, Ryan Madeline M, Gitto Sandra, Barrera Gómez Paula, Mascrez Bénédicte, Mansour Thomas A, Nakamura Tetsuya, Harris Matthew P, Shubin Neil H, Duboule Denis
Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
Stowers Institute for Medical Research, Kansas City, MO, USA.
Nature. 2025 Sep 17. doi: 10.1038/s41586-025-09548-0.
The fin-to-limb transition in vertebrate evolution has been central to the study of how development underlies evolutionary change. In this context, the functional analysis of Hox gene regulation to infer evolutionary trajectories has been critical to explain the origin of new features. In tetrapods, the transcription of Hoxd genes in developing digits depends on a set of enhancers forming a large regulatory landscape. The presence of a syntenic counterpart in zebrafish, which lacks digits, suggests deep homology or shared developmental foundations underlying distal fin and limbs. However, how this regulatory program evolved has remained unresolved. We genetically evaluated the function of the zebrafish Hoxd regulatory landscapes by comparatively assessing the effects of their full deletions. We show that, unlike in mice, deletion of these regions in fish does not disrupt hoxd gene transcription during distal fin development. By contrast, we found that this deficiency leads to the loss of expression within the cloaca, a structure related by ancestry to the mammalian urogenital sinus, and that distal hox13 genes are essential for correct cloacal formation. Because Hoxd gene regulation in the mouse urogenital sinus relies on enhancers located in this same chromatin domain that controls digit development, we propose that the current regulatory landscape active in distal limbs was co-opted as a whole in tetrapods from a pre-existing cloacal regulatory machinery.
脊椎动物进化过程中的鳍到肢体的转变一直是研究发育如何构成进化变化基础的核心内容。在此背景下，通过对Hox基因调控进行功能分析以推断进化轨迹，对于解释新特征的起源至关重要。在四足动物中，发育中的指（趾）中Hoxd基因的转录依赖于一组形成大型调控区域的增强子。在缺乏指（趾）的斑马鱼中存在同线性对应物，这表明远端鳍和肢体具有深度同源性或共同的发育基础。然而，这种调控程序是如何进化的仍未得到解决。我们通过比较评估其完全缺失的影响，对斑马鱼Hoxd调控区域的功能进行了遗传学评估。我们发现，与小鼠不同，在鱼类中删除这些区域并不会破坏远端鳍发育过程中的hoxd基因转录。相比之下，我们发现这种缺陷会导致泄殖腔（一种在谱系上与哺乳动物泌尿生殖窦相关的结构）内的基因表达缺失，并且远端hox13基因对于正确的泄殖腔形成至关重要。由于小鼠泌尿生殖窦中的Hoxd基因调控依赖于位于控制指（趾）发育的同一染色质区域中的增强子，我们提出，目前在远端肢体中活跃的调控区域在四足动物中是从预先存在的泄殖腔调控机制整体上被征用的。
