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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.

Show MeSH
Somite/muscle-expressed SET domain genes and their evolutionary relationships.The phylogenetic relationships of the genes were indicated with the trees constructed based on the SET domains of the encoded proteins and rooted with zebrafish Smyd4 and Prdm14 proteins as outgroups, respectively. Lateral views (anterior to the left) of embryos at 16–18 hpf (a, d, g, j and m), 22–24 hpf (b, e, h, k and n) and 48 hpf (c, f, i, l and o) are presented. (a', d', g', j' and m') Dorsal views of the embryos in a, d, g, j and m. (A) Zebrafish smyd1a, smyd1b, smyd2a and smyd2b genes show somite/muscle-specific expression patterns and form a close paralog group with the smyd3 gene (double asterisks), which shows a ubiquitous expression pattern (a–c). Note the relatively low expressions of smyd1a at early stage (18 hpf; g) and smyd2a and smyd2b at late stage (48 hpf; l and o). (B) Expression patterns of the second paralog group. prdm1a is specifically expressed in anterior somites and adaxial cells at 18 hpf (g and g') and 24 hpf (h). Besides, it is also expressed in hatching gland (g), branchial arch, fin fold (g, g' and h), fin buds, cloaca (h and i) and retina (i). prdm1b (asterisk) is highly expressed in somites at 24 hpf (e) and in retina at 48 hpf (f). prdm1c (double asterisks) is ubiquitously expressed (a–c). prdm4 is highly expressed in somites and retina (k and l). prdm15 is expressed in muscle pioneer cells (m, m' and n). ac, adaxial cells; ba, branchial arch; cl, cloaca; fb, fin buds; ff, fin fold; hg, hatching gland; mp, muscle pioneer; re, retina; s, somite.
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pone-0001499-g005: Somite/muscle-expressed SET domain genes and their evolutionary relationships.The phylogenetic relationships of the genes were indicated with the trees constructed based on the SET domains of the encoded proteins and rooted with zebrafish Smyd4 and Prdm14 proteins as outgroups, respectively. Lateral views (anterior to the left) of embryos at 16–18 hpf (a, d, g, j and m), 22–24 hpf (b, e, h, k and n) and 48 hpf (c, f, i, l and o) are presented. (a', d', g', j' and m') Dorsal views of the embryos in a, d, g, j and m. (A) Zebrafish smyd1a, smyd1b, smyd2a and smyd2b genes show somite/muscle-specific expression patterns and form a close paralog group with the smyd3 gene (double asterisks), which shows a ubiquitous expression pattern (a–c). Note the relatively low expressions of smyd1a at early stage (18 hpf; g) and smyd2a and smyd2b at late stage (48 hpf; l and o). (B) Expression patterns of the second paralog group. prdm1a is specifically expressed in anterior somites and adaxial cells at 18 hpf (g and g') and 24 hpf (h). Besides, it is also expressed in hatching gland (g), branchial arch, fin fold (g, g' and h), fin buds, cloaca (h and i) and retina (i). prdm1b (asterisk) is highly expressed in somites at 24 hpf (e) and in retina at 48 hpf (f). prdm1c (double asterisks) is ubiquitously expressed (a–c). prdm4 is highly expressed in somites and retina (k and l). prdm15 is expressed in muscle pioneer cells (m, m' and n). ac, adaxial cells; ba, branchial arch; cl, cloaca; fb, fin buds; ff, fin fold; hg, hatching gland; mp, muscle pioneer; re, retina; s, somite.

Mentions: In this study, eight somite/muslce-expressed SET domain genes were identified to be significantly expressed in somites and muscles at certain stages (Figure 5A and B, right). By merging the information of their evolutionary relationships, these genes were clustered into two groups, which subsequently distribute into subfamilies IX and X, respectively (Figure 5A and B, left). To a degree, their relationships suggest that these genes were evolved from two ancestral genes, both of which may be related with somite/muscle development of the ancestral species.


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)

Somite/muscle-expressed SET domain genes and their evolutionary relationships.The phylogenetic relationships of the genes were indicated with the trees constructed based on the SET domains of the encoded proteins and rooted with zebrafish Smyd4 and Prdm14 proteins as outgroups, respectively. Lateral views (anterior to the left) of embryos at 16–18 hpf (a, d, g, j and m), 22–24 hpf (b, e, h, k and n) and 48 hpf (c, f, i, l and o) are presented. (a', d', g', j' and m') Dorsal views of the embryos in a, d, g, j and m. (A) Zebrafish smyd1a, smyd1b, smyd2a and smyd2b genes show somite/muscle-specific expression patterns and form a close paralog group with the smyd3 gene (double asterisks), which shows a ubiquitous expression pattern (a–c). Note the relatively low expressions of smyd1a at early stage (18 hpf; g) and smyd2a and smyd2b at late stage (48 hpf; l and o). (B) Expression patterns of the second paralog group. prdm1a is specifically expressed in anterior somites and adaxial cells at 18 hpf (g and g') and 24 hpf (h). Besides, it is also expressed in hatching gland (g), branchial arch, fin fold (g, g' and h), fin buds, cloaca (h and i) and retina (i). prdm1b (asterisk) is highly expressed in somites at 24 hpf (e) and in retina at 48 hpf (f). prdm1c (double asterisks) is ubiquitously expressed (a–c). prdm4 is highly expressed in somites and retina (k and l). prdm15 is expressed in muscle pioneer cells (m, m' and n). ac, adaxial cells; ba, branchial arch; cl, cloaca; fb, fin buds; ff, fin fold; hg, hatching gland; mp, muscle pioneer; re, retina; s, somite.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0001499-g005: Somite/muscle-expressed SET domain genes and their evolutionary relationships.The phylogenetic relationships of the genes were indicated with the trees constructed based on the SET domains of the encoded proteins and rooted with zebrafish Smyd4 and Prdm14 proteins as outgroups, respectively. Lateral views (anterior to the left) of embryos at 16–18 hpf (a, d, g, j and m), 22–24 hpf (b, e, h, k and n) and 48 hpf (c, f, i, l and o) are presented. (a', d', g', j' and m') Dorsal views of the embryos in a, d, g, j and m. (A) Zebrafish smyd1a, smyd1b, smyd2a and smyd2b genes show somite/muscle-specific expression patterns and form a close paralog group with the smyd3 gene (double asterisks), which shows a ubiquitous expression pattern (a–c). Note the relatively low expressions of smyd1a at early stage (18 hpf; g) and smyd2a and smyd2b at late stage (48 hpf; l and o). (B) Expression patterns of the second paralog group. prdm1a is specifically expressed in anterior somites and adaxial cells at 18 hpf (g and g') and 24 hpf (h). Besides, it is also expressed in hatching gland (g), branchial arch, fin fold (g, g' and h), fin buds, cloaca (h and i) and retina (i). prdm1b (asterisk) is highly expressed in somites at 24 hpf (e) and in retina at 48 hpf (f). prdm1c (double asterisks) is ubiquitously expressed (a–c). prdm4 is highly expressed in somites and retina (k and l). prdm15 is expressed in muscle pioneer cells (m, m' and n). ac, adaxial cells; ba, branchial arch; cl, cloaca; fb, fin buds; ff, fin fold; hg, hatching gland; mp, muscle pioneer; re, retina; s, somite.
Mentions: In this study, eight somite/muslce-expressed SET domain genes were identified to be significantly expressed in somites and muscles at certain stages (Figure 5A and B, right). By merging the information of their evolutionary relationships, these genes were clustered into two groups, which subsequently distribute into subfamilies IX and X, respectively (Figure 5A and B, left). To a degree, their relationships suggest that these genes were evolved from two ancestral genes, both of which may be related with somite/muscle development of the ancestral species.

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