Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.
BACKGROUND
Genes in the CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues. They have been known to play important roles in RNA processing as RNA-binding proteins in animals. To date, few plant CCCH proteins have been studied functionally.


RESULTS
In this study, a comprehensive computational analysis identified 68 and 67 CCCH family genes in Arabidopsis and rice, respectively. A complete overview of this gene family in Arabidopsis was presented, including the gene structures, phylogeny, protein motifs, and chromosome locations. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. These results revealed that the CCCH families in Arabidopsis and rice were divided into 11 and 8 subfamilies, respectively. The gene duplication contributed to the expansion of the CCCH gene family in Arabidopsis genome. Expression studies indicated that CCCH proteins exhibit a variety of expression patterns, suggesting diverse functions. Finally, evolutionary analysis showed that one subfamily is higher plant specific. The expression profile indicated that most members of this subfamily are regulated by abiotic or biotic stresses, suggesting that they could have an effective role in stress tolerance.


CONCLUSIONS
Our comparative genomics analysis of CCCH genes and encoded proteins in two model plant species provides the first step towards the functional dissection of this emerging family of potential RNA-binding proteins.
Wang
Dong
D
State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China. ideal.sam@gmail.com
Guo
Yinghui
Y
Wu
Changai
C
Yang
Guodong
G
Li
Yingying
Y
Zheng
Chengchao
C
D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D032461:Chromosomes, Plant / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D017343:Genes, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D005810:Multigene Family; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment / Q000706:statistics & numerical data; D017386:Sequence Homology, Amino Acid; D012984:Software; D013045:Species Specificity; D016335:Zinc Fingers / Q000235:genetics*
D029681:Arabidopsis Proteins; D017931:DNA Primers; D010940:Plant Proteins; D018749:RNA, Plant; D016601:RNA-Binding Proteins