{"title":"Identification and Classification of Zinc Finger Proteins Encoded in the Genome of an Ascidian","authors":"Natsuko Tamura, Yutaka Satou","doi":"10.1002/dvg.70020","DOIUrl":null,"url":null,"abstract":"<div>\n \n <p>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.</p>\n </div>","PeriodicalId":12718,"journal":{"name":"genesis","volume":"63 4","pages":""},"PeriodicalIF":2.4000,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"genesis","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/dvg.70020","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"DEVELOPMENTAL BIOLOGY","Score":null,"Total":0}
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.
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.