Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes

Xiao Jian Sun, Peng Fei Xu, Ting Zhou, Ming Hu, Chun Tang Fu, Yong Zhang, Yi Jin, Yi Chen, Sai Juan Chen, Qiu Hua Huang, Ting Xiu Liu, Zhu Chen

Research output: Contribution to journalArticle

77 Citations (Scopus)

Abstract

SET domain-containing proteins represent an evolutionarily conserved family of epigenetic regulators, which are responsible for most histone lysine methylation. Since some of these genes have been revealed to be essential for embryonic development, we propose that the zebrafish, a vertebrate model organism possessing many advantages for developmental studies, can be utilized to study the biological functions of these genes and the related epigenetic mechanisms during early development. To this end, we have performed a genome-wide survey of zebrafish SET domain genes. 58 genes total have been identified. Although gene duplication events give rise to several lineage-specific paralogs, clear reciprocal orthologous relationship reveals high conservation between zebrafish and human SET domain genes. These data were further subject to an evolutionary analysis ranginq from yeast to human, leading to the identification of putative clusters of orthologous groups (COGs) of this gene family. By means of whole-mount mRNA in situ hybridization strategy, we have also carried out a developmental expression mapping of these genes. A group of maternal SET domain genes, which are implicated in the programming of histone modification states in early development, have been identified and predicted to be responsible for all known sites of SET domain-mediated histone methylation. Furthermore, some genes show specific expression patterns in certain tissues at certain stages, suggesting the involvement of epigenetic mechanisms in the development of these systems. These results provide a global view of zebrafish SET domain histone methyltransferases in evolutionary and developmental dimensions and pave the way for using zebrafish to systematically study the roles of these genes during development.

Original languageEnglish (US)
Article numbere1499
JournalPLoS One
Volume3
Issue number1
DOIs
StatePublished - Jan 30 2008
Externally publishedYes

Fingerprint

Zebrafish
Danio rerio
Genes
Genome
genome
histones
genes
Epigenomics
epigenetics
Histones
methylation
Methylation
early development
Histone Code
Surveys and Questionnaires
Gene Duplication
Chromosome Mapping
methyltransferases
gene duplication
in situ hybridization

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Sun, X. J., Xu, P. F., Zhou, T., Hu, M., Fu, C. T., Zhang, Y., ... Chen, Z. (2008). Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. PLoS One, 3(1), [e1499]. https://doi.org/10.1371/journal.pone.0001499

Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. / Sun, Xiao Jian; Xu, Peng Fei; Zhou, Ting; Hu, Ming; Fu, Chun Tang; Zhang, Yong; Jin, Yi; Chen, Yi; Chen, Sai Juan; Huang, Qiu Hua; Liu, Ting Xiu; Chen, Zhu.

In: PLoS One, Vol. 3, No. 1, e1499, 30.01.2008.

Research output: Contribution to journalArticle

Sun, XJ, Xu, PF, Zhou, T, Hu, M, Fu, CT, Zhang, Y, Jin, Y, Chen, Y, Chen, SJ, Huang, QH, Liu, TX & Chen, Z 2008, 'Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes', PLoS One, vol. 3, no. 1, e1499. https://doi.org/10.1371/journal.pone.0001499
Sun, Xiao Jian ; Xu, Peng Fei ; Zhou, Ting ; Hu, Ming ; Fu, Chun Tang ; Zhang, Yong ; Jin, Yi ; Chen, Yi ; Chen, Sai Juan ; Huang, Qiu Hua ; Liu, Ting Xiu ; Chen, Zhu. / Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. In: PLoS One. 2008 ; Vol. 3, No. 1.
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