Tamura Natsuko, Satou Yutaka
Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan.
Genesis. 2025 Aug;63(4):e70020. doi: 10.1002/dvg.70020.
Genes encoding C2H2-type zinc finger (ZF) proteins constitute one of the largest gene families in animal genomes. Many C2H2-type ZF domains are used for DNA-binding, and others are used for protein-protein interactions and RNA-binding. In ascidian embryos, a gene regulatory network controlling cell fate decision has been studied extensively. However, because ZF proteins have not been well annotated genome-widely, it has not been clear which ZF proteins are possible regulators for cell fate decision in this animal. Therefore, we tried to identify and classify all genes encoding C2H2-type ZF proteins in the genome of an ascidian in the present study. Because the number of ZF domains often varies among possible orthologous proteins, and because ZF domains are not long enough for molecular phylogenetic analyses in many cases, we extensively utilized other bioinformatics tools for their classification. In addition, we found that many ascidian ZF proteins contain fewer ZF domains than their human orthologs; this finding might be related to the compactness of the ascidian genome.
编码C2H2型锌指（ZF）蛋白的基因构成了动物基因组中最大的基因家族之一。许多C2H2型ZF结构域用于DNA结合，其他的则用于蛋白质-蛋白质相互作用和RNA结合。在海鞘胚胎中，一个控制细胞命运决定的基因调控网络已得到广泛研究。然而，由于ZF蛋白尚未在全基因组范围内得到很好的注释，目前尚不清楚哪些ZF蛋白可能是这种动物细胞命运决定的调节因子。因此，在本研究中，我们试图识别并分类海鞘基因组中所有编码C2H2型ZF蛋白的基因。由于ZF结构域的数量在可能的直系同源蛋白中常常不同，并且在许多情况下ZF结构域不够长，无法进行分子系统发育分析，我们广泛利用其他生物信息学工具对它们进行分类。此外，我们发现许多海鞘ZF蛋白含有的ZF结构域比其人类直系同源蛋白少；这一发现可能与海鞘基因组的紧凑性有关。
