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

Sun XJ, Xu PF, Zhou T, Hu M, Fu CT, Zhang Y, Jin Y, Chen Y, Chen SJ, Huang QH, Liu TX, Chen Z - PLoS ONE (2008)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

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 ranging 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.

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Evolutionary conservation of zebrafish and human SET domain genes.(A) Phylogenetic analysis. Unrooted neighbor-joining tree was constructed based on the alignment of the amino acid sequences of the SET domains of 47 human proteins (red) and 58 predicted zebrafish proteins (blue). Bootstrap percentages computed from 1000 replicates are shown along the internal braches. The major branches (bootstrap support ≥ 65%; labeled with black circles) define 10 subfamilies of the genes, which are denoted with light blue vertical bars. The single brackets followed by numbers denote zebrafish gene pairs that have been found corresponding to single human genes. Note that zebrafish likely lacks an ortholog of human SUV39H2 gene (single asterisk) and that human PRDM7 and PRDM9 genes (double asterisks) are co-orthologous to a single zebrafish gene named prdm9. Abbreviations: Hs, Homo sapiens; Dr, Denio rerio. (B) One-to-one identities and similarities between the SET domains of zebrafish proteins and their human counterparts. The identities and similarities on SET domains were calculated with FASTA program (http://fasta.bioch.virginia.edu/fasta_www2) and represented with blue and purple bars, respectively.
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pone-0001499-g001: Evolutionary conservation of zebrafish and human SET domain genes.(A) Phylogenetic analysis. Unrooted neighbor-joining tree was constructed based on the alignment of the amino acid sequences of the SET domains of 47 human proteins (red) and 58 predicted zebrafish proteins (blue). Bootstrap percentages computed from 1000 replicates are shown along the internal braches. The major branches (bootstrap support ≥ 65%; labeled with black circles) define 10 subfamilies of the genes, which are denoted with light blue vertical bars. The single brackets followed by numbers denote zebrafish gene pairs that have been found corresponding to single human genes. Note that zebrafish likely lacks an ortholog of human SUV39H2 gene (single asterisk) and that human PRDM7 and PRDM9 genes (double asterisks) are co-orthologous to a single zebrafish gene named prdm9. Abbreviations: Hs, Homo sapiens; Dr, Denio rerio. (B) One-to-one identities and similarities between the SET domains of zebrafish proteins and their human counterparts. The identities and similarities on SET domains were calculated with FASTA program (http://fasta.bioch.virginia.edu/fasta_www2) and represented with blue and purple bars, respectively.

Mentions: The evolutionary relationships among the zebrafish and human SET domain genes were examined by phylogenetic analysis. As shown by the neighbor-joining tree that was constructed based on the alignment of the amino acid sequences of the SET domains of the encoded proteins [41] (Figure 1A), it is generally observed that a zebrafish SET domain gene and a human SET domain gene form a monophyletic branch (occasionally, two zebrafish genes are clustered together with a single human gene and thereby act as potential “zebrafish lineage-specific paralogs”, which will be elucidated below), suggesting reciprocal orthologous relationships between them. Considering zebrafish as a lower vertebrate organism, this phylogenetic analysis indicates a good conservation of SET domain genes through vertebrate evolution. Furthermore, according to this tree, the vertebrate SET domains are divided into 10 subfamilies (≥65% bootstrap support; if the cut-off bootstrap value is set higher than 80%, the subfamily I can be further divided into 3 groups). When using different methods (e.g. Minimum Evolution and Maximum Parsimony methods) to construct the trees [41], similar results were consistently reproduced.


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

Sun XJ, Xu PF, Zhou T, Hu M, Fu CT, Zhang Y, Jin Y, Chen Y, Chen SJ, Huang QH, Liu TX, Chen Z - PLoS ONE (2008)

Evolutionary conservation of zebrafish and human SET domain genes.(A) Phylogenetic analysis. Unrooted neighbor-joining tree was constructed based on the alignment of the amino acid sequences of the SET domains of 47 human proteins (red) and 58 predicted zebrafish proteins (blue). Bootstrap percentages computed from 1000 replicates are shown along the internal braches. The major branches (bootstrap support ≥ 65%; labeled with black circles) define 10 subfamilies of the genes, which are denoted with light blue vertical bars. The single brackets followed by numbers denote zebrafish gene pairs that have been found corresponding to single human genes. Note that zebrafish likely lacks an ortholog of human SUV39H2 gene (single asterisk) and that human PRDM7 and PRDM9 genes (double asterisks) are co-orthologous to a single zebrafish gene named prdm9. Abbreviations: Hs, Homo sapiens; Dr, Denio rerio. (B) One-to-one identities and similarities between the SET domains of zebrafish proteins and their human counterparts. The identities and similarities on SET domains were calculated with FASTA program (http://fasta.bioch.virginia.edu/fasta_www2) and represented with blue and purple bars, respectively.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2200798&req=5

pone-0001499-g001: Evolutionary conservation of zebrafish and human SET domain genes.(A) Phylogenetic analysis. Unrooted neighbor-joining tree was constructed based on the alignment of the amino acid sequences of the SET domains of 47 human proteins (red) and 58 predicted zebrafish proteins (blue). Bootstrap percentages computed from 1000 replicates are shown along the internal braches. The major branches (bootstrap support ≥ 65%; labeled with black circles) define 10 subfamilies of the genes, which are denoted with light blue vertical bars. The single brackets followed by numbers denote zebrafish gene pairs that have been found corresponding to single human genes. Note that zebrafish likely lacks an ortholog of human SUV39H2 gene (single asterisk) and that human PRDM7 and PRDM9 genes (double asterisks) are co-orthologous to a single zebrafish gene named prdm9. Abbreviations: Hs, Homo sapiens; Dr, Denio rerio. (B) One-to-one identities and similarities between the SET domains of zebrafish proteins and their human counterparts. The identities and similarities on SET domains were calculated with FASTA program (http://fasta.bioch.virginia.edu/fasta_www2) and represented with blue and purple bars, respectively.
Mentions: The evolutionary relationships among the zebrafish and human SET domain genes were examined by phylogenetic analysis. As shown by the neighbor-joining tree that was constructed based on the alignment of the amino acid sequences of the SET domains of the encoded proteins [41] (Figure 1A), it is generally observed that a zebrafish SET domain gene and a human SET domain gene form a monophyletic branch (occasionally, two zebrafish genes are clustered together with a single human gene and thereby act as potential “zebrafish lineage-specific paralogs”, which will be elucidated below), suggesting reciprocal orthologous relationships between them. Considering zebrafish as a lower vertebrate organism, this phylogenetic analysis indicates a good conservation of SET domain genes through vertebrate evolution. Furthermore, according to this tree, the vertebrate SET domains are divided into 10 subfamilies (≥65% bootstrap support; if the cut-off bootstrap value is set higher than 80%, the subfamily I can be further divided into 3 groups). When using different methods (e.g. Minimum Evolution and Maximum Parsimony methods) to construct the trees [41], similar results were consistently reproduced.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

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 ranging 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.

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