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 language | English (US) |
|---|---|
| Article number | e1499 |
| Journal | PLoS One |
| Volume | 3 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 30 2008 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Agricultural and Biological Sciences(all)
- Biochemistry, Genetics and Molecular Biology(all)
- Medicine(all)
Cite this
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 journal › Article
}
TY - JOUR
T1 - Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes
AU - Sun, Xiao Jian
AU - Xu, Peng Fei
AU - Zhou, Ting
AU - Hu, Ming
AU - Fu, Chun Tang
AU - Zhang, Yong
AU - Jin, Yi
AU - Chen, Yi
AU - Chen, Sai Juan
AU - Huang, Qiu Hua
AU - Liu, Ting Xiu
AU - Chen, Zhu
PY - 2008/1/30
Y1 - 2008/1/30
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=45149134029&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=45149134029&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0001499
DO - 10.1371/journal.pone.0001499
M3 - Article
C2 - 18231586
AN - SCOPUS:45149134029
VL - 3
JO - PLoS One
JF - PLoS One
SN - 1932-6203
IS - 1
M1 - e1499
ER -