Identification and Classification of Zinc Finger Proteins Encoded in the Genome of an Ascidian

IF 2.4 4区 生物学 Q2 DEVELOPMENTAL BIOLOGY
genesis Pub Date : 2025-06-27 DOI:10.1002/dvg.70020
Natsuko Tamura, Yutaka Satou
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引用次数: 0

Abstract

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.

一种海鞘动物基因组锌指蛋白的鉴定与分类
编码c2h2型锌指(ZF)蛋白的基因是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被广泛研究。然而,由于ZF蛋白尚未在全基因组中得到很好的注释,因此尚不清楚哪些ZF蛋白可能是决定这种动物细胞命运的调节剂。因此,我们在本研究中试图对海鞘基因组中编码c2h2型ZF蛋白的所有基因进行鉴定和分类。由于ZF结构域的数量在可能的同源蛋白中经常变化,并且由于ZF结构域在许多情况下不够长,无法进行分子系统发育分析,因此我们广泛使用其他生物信息学工具对其进行分类。此外,我们发现许多海鞘ZF蛋白比它们的人类同源物含有更少的ZF结构域;这一发现可能与海鞘基因组的紧密性有关。
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来源期刊
genesis
genesis 生物-发育生物学
CiteScore
3.60
自引率
0.00%
发文量
40
审稿时长
6-12 weeks
期刊介绍: As of January 2000, Developmental Genetics was renamed and relaunched as genesis: The Journal of Genetics and Development, with a new scope and Editorial Board. The journal focuses on work that addresses the genetics of development and the fundamental mechanisms of embryological processes in animals and plants. With increased awareness of the interplay between genetics and evolutionary change, particularly during developmental processes, we encourage submission of manuscripts from all ecological niches. The expanded numbers of genomes for which sequencing is being completed will facilitate genetic and genomic examination of developmental issues, even if the model system does not fit the “classical genetic” mold. Therefore, we encourage submission of manuscripts from all species. Other areas of particular interest include: 1) the roles of epigenetics, microRNAs and environment on developmental processes; 2) genome-wide studies; 3) novel imaging techniques for the study of gene expression and cellular function; 4) comparative genetics and genomics and 5) animal models of human genetic and developmental disorders. genesis presents reviews, full research articles, short research letters, and state-of-the-art technology reports that promote an understanding of the function of genes and the roles they play in complex developmental processes.
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