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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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Clusters of orthologous groups (COGs) of SET domain genes from yeast to human.The relationship was determined based on combined information of “reciprocal best hit” analysis, phylogenetic analysis, and synthenic analysis. Note that, occasionally, two or more genes in one species are collectively orthologous to one gene in another species. These genes are defined as co-orthologs and incorporated into a same COG. Known histone methyltransferases (HMTases) are denoted with asterisks and their site specificities are indicated along the corresponding COGs.
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pone-0001499-g004: Clusters of orthologous groups (COGs) of SET domain genes from yeast to human.The relationship was determined based on combined information of “reciprocal best hit” analysis, phylogenetic analysis, and synthenic analysis. Note that, occasionally, two or more genes in one species are collectively orthologous to one gene in another species. These genes are defined as co-orthologs and incorporated into a same COG. Known histone methyltransferases (HMTases) are denoted with asterisks and their site specificities are indicated along the corresponding COGs.

Mentions: Besides those in vertebrates, a number of SET domain genes from invertebrate animals and fungi have been identified and functionally characterized (see Table S1 for a summary of the so far characterized SET domain proteins with specific HMTase activities). Cross-species comparison of these genes would be helpful to build a comparative framework and to bridge barriers among organism-based research communities. Particularly, determination of evolutionary relationship and identification of clusters of orthologous groups (COGs) is useful to delineate functions of the corresponding genes in different species [53]. To this end, we extracted a number of SET domain genes from human (47), Drosophila (29), C. elegans (30), S. pombe (11) and S. cerevisiae (7) through analyses of SMART database and NCBI protein database (Table S1). Among these genes, COGs were identified based on multiple approaches: 1) “reciprocal best hits” algorithm, a straightforward method for prediction of one-to-one orthologs [34]. However, lineage-specific gene duplications (and also asymmetrical evolution of paralogs sometimes) likely lead to false negatives under this method [53]. 2) Phylogenetic analysis (Figure S4) in combination with tree reconciliation, which is useful to complement the limitation of the “reciprocal best hits” method. Under this approach, the orthologous relationship is reflected by the comparison and reconciliation between the topology of a gene tree and that of the chosen species tree [53]. 3) Genomic structure comparison that relies on the assumption that the ancestral structure (exon/intron patterns) and order (syntenies) of orthologous genes are retained in the genomes of descendent species [54]. As a result, a set of COGs of SET domain genes were identified (Figure 4), which has a special reference to the functional characteristics of these genes, and may also contribute to outlining an evolutionary history of them. For example, we hereby tried to apply this result to address a question about the origins of the site specificities of SET domain HMTs through evolution (see discussion).


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)

Clusters of orthologous groups (COGs) of SET domain genes from yeast to human.The relationship was determined based on combined information of “reciprocal best hit” analysis, phylogenetic analysis, and synthenic analysis. Note that, occasionally, two or more genes in one species are collectively orthologous to one gene in another species. These genes are defined as co-orthologs and incorporated into a same COG. Known histone methyltransferases (HMTases) are denoted with asterisks and their site specificities are indicated along the corresponding COGs.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0001499-g004: Clusters of orthologous groups (COGs) of SET domain genes from yeast to human.The relationship was determined based on combined information of “reciprocal best hit” analysis, phylogenetic analysis, and synthenic analysis. Note that, occasionally, two or more genes in one species are collectively orthologous to one gene in another species. These genes are defined as co-orthologs and incorporated into a same COG. Known histone methyltransferases (HMTases) are denoted with asterisks and their site specificities are indicated along the corresponding COGs.
Mentions: Besides those in vertebrates, a number of SET domain genes from invertebrate animals and fungi have been identified and functionally characterized (see Table S1 for a summary of the so far characterized SET domain proteins with specific HMTase activities). Cross-species comparison of these genes would be helpful to build a comparative framework and to bridge barriers among organism-based research communities. Particularly, determination of evolutionary relationship and identification of clusters of orthologous groups (COGs) is useful to delineate functions of the corresponding genes in different species [53]. To this end, we extracted a number of SET domain genes from human (47), Drosophila (29), C. elegans (30), S. pombe (11) and S. cerevisiae (7) through analyses of SMART database and NCBI protein database (Table S1). Among these genes, COGs were identified based on multiple approaches: 1) “reciprocal best hits” algorithm, a straightforward method for prediction of one-to-one orthologs [34]. However, lineage-specific gene duplications (and also asymmetrical evolution of paralogs sometimes) likely lead to false negatives under this method [53]. 2) Phylogenetic analysis (Figure S4) in combination with tree reconciliation, which is useful to complement the limitation of the “reciprocal best hits” method. Under this approach, the orthologous relationship is reflected by the comparison and reconciliation between the topology of a gene tree and that of the chosen species tree [53]. 3) Genomic structure comparison that relies on the assumption that the ancestral structure (exon/intron patterns) and order (syntenies) of orthologous genes are retained in the genomes of descendent species [54]. As a result, a set of COGs of SET domain genes were identified (Figure 4), which has a special reference to the functional characteristics of these genes, and may also contribute to outlining an evolutionary history of them. For example, we hereby tried to apply this result to address a question about the origins of the site specificities of SET domain HMTs through evolution (see discussion).

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.

Show MeSH