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

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.