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Abstract：
Abnormal expression of the transcriptional regulator and hedgehog (Hh) signaling pathway effector Gli3 is known to trigger congenital disease, most frequently affecting the central nervous system (CNS) and the limbs. Accurate delineation of the genomic cis-regulatory landscape controlling Gli3 transcription during embryonic development is critical for the interpretation of noncoding variants associated with congenital defects. Here, we employed a comparative genomic analysis on fish species with a slow rate of molecular evolution to identify seven previously unknown conserved noncoding elements (CNEs) in Gli3 intronic intervals (CNE15-21). Transgenic assays in zebrafish revealed that most of these elements drive activities in Gli3 expressing tissues, predominantly the fins, CNS, and the heart. Intersection of these CNEs with human disease associated SNPs identified CNE15 as a putative mammalian craniofacial enhancer, with conserved activity in vertebrates and potentially affected by mutation associated with human craniofacial morphology. Finally, comparative functional dissection of an appendage-specific CNE conserved in slowly evolving fish (elephant shark), but not in teleost (CNE14/hs1586) indicates co-option of limb specificity from other tissues prior to the divergence of amniotes and lobe-finned fish. These results uncover a novel subset of intronic Gli3 enhancers that arose in the common ancestor of gnathostomes and whose sequence components were likely gradually modified in other species during the process of evolutionary diversification.
摘要：
转录调节因子和hedgehog（Hh）信号通路效应子Gli3的异常表达已知会引发先天性疾病，最常影响中枢神经系统（CNS）和四肢。在胚胎发育过程中控制Gli3转录的基因组顺式调节景观的准确描绘对于解释与先天性缺陷相关的非编码变体至关重要。在这里，我们对分子进化速率缓慢的鱼类进行了比较基因组分析，以鉴定Gli3内含子间隔（CNE15-21）中七个先前未知的保守非编码元件（CNE）。斑马鱼的转基因实验表明，这些元素中的大多数驱动Gli3表达组织的活性，主要是鳍，CNS,还有心脏.这些CNE与人类疾病相关SNP的交叉将CNE15鉴定为推定的哺乳动物颅面增强剂，在脊椎动物中具有保守的活性，并可能受到与人类颅面形态相关的突变的影响。最后,在缓慢进化的鱼类（象鲨）中保守的附属物特异性CNE的比较功能解剖，但在硬骨鱼（CNE14/hs1586）中没有表明在羊膜和叶翅鱼分化之前，其他组织对肢体特异性的共同选择。这些结果揭示了内含子Gli3增强子的一个新子集，该子集出现在颌骨的共同祖先中，并且在进化多样化的过程中，其序列成分可能在其他物种中逐渐被修饰。本文受版权保护。保留所有权利。
