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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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Nervous system-expressed SET domain genes.(A) Expression patterns of closely related prdm3 and prdm16. (a–j) Lateral views (anterior to the left) of embryos at 12, 18, 24, 48 and 72 hpf. (b' and g') Ventral views of the embryos in b and g. (c'–e' and h'–j') Dorsal views of the embryos in c–e and h–j. Note the partially overlapping expression of prdm3 and prdm16. (B) Expression patterns of prdm13, prdm8a and prdm8b. (a–f) Lateral views (anterior to the left) of embryos at 24 and 48 hpf. (a'–f') Dorsal views of the embryos in a–f. Note that the expression of prdm8a is mostly restricted in hindbrain and spinal chord (c, d and c', d'), whereas that of prdm8b is restricted in olfactory placode, tegmentum, cerebellum and retina (f and f'). (C) Expression pattern of prdm12. (a and b) Lateral views (anterior to the left) of embryos at 18, 24 hpf. (a' and b') Dorsal views of the embryos in a and b. At 48 hpf, prdm12 is expressed in olfactory placode, tegmentum, cerebellum and hindbrain. (D) Expression pattern of prdm15. (a and b) Lateral views (anterior to the left) of embryos at 18, 22 hpf. (a' and b') Dorsal views of the embryos in a and b. Note that prdm15 is expressed in cranial ganglia neurons (a' and b') as well as in muscle pioneer cells and intermediate cell mass (a and b). ba, branchial arches; ce, cerebellum; cg, cranial ganglia; cnc, cranial neural crest; fb, fin buds; hb, hindbrain; icm, intermediate cell mass; mp, muscle pioneer; op, olfactory placode; pnd, pronephric duct; re, retina; sc, spinal chord; tel, telencephalon; tg, tegmentum; vd, ventral diencephalons.
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pone-0001499-g006: Nervous system-expressed SET domain genes.(A) Expression patterns of closely related prdm3 and prdm16. (a–j) Lateral views (anterior to the left) of embryos at 12, 18, 24, 48 and 72 hpf. (b' and g') Ventral views of the embryos in b and g. (c'–e' and h'–j') Dorsal views of the embryos in c–e and h–j. Note the partially overlapping expression of prdm3 and prdm16. (B) Expression patterns of prdm13, prdm8a and prdm8b. (a–f) Lateral views (anterior to the left) of embryos at 24 and 48 hpf. (a'–f') Dorsal views of the embryos in a–f. Note that the expression of prdm8a is mostly restricted in hindbrain and spinal chord (c, d and c', d'), whereas that of prdm8b is restricted in olfactory placode, tegmentum, cerebellum and retina (f and f'). (C) Expression pattern of prdm12. (a and b) Lateral views (anterior to the left) of embryos at 18, 24 hpf. (a' and b') Dorsal views of the embryos in a and b. At 48 hpf, prdm12 is expressed in olfactory placode, tegmentum, cerebellum and hindbrain. (D) Expression pattern of prdm15. (a and b) Lateral views (anterior to the left) of embryos at 18, 22 hpf. (a' and b') Dorsal views of the embryos in a and b. Note that prdm15 is expressed in cranial ganglia neurons (a' and b') as well as in muscle pioneer cells and intermediate cell mass (a and b). ba, branchial arches; ce, cerebellum; cg, cranial ganglia; cnc, cranial neural crest; fb, fin buds; hb, hindbrain; icm, intermediate cell mass; mp, muscle pioneer; op, olfactory placode; pnd, pronephric duct; re, retina; sc, spinal chord; tel, telencephalon; tg, tegmentum; vd, ventral diencephalons.

Mentions: Seven nervous system-expressed SET domain genes were identified by WISH analyses. The closely related prdm3 (GenBank accession DQ851828) and prdm16 (GenBank accession DQ851827) are expressed in a partially overlapping pattern (Figure 6A). The expression of prdm3 is first detected in telencephalon at 12 hpf (Figure 6Aa) and then extends to tegmentum, ventral diencephalons and hindbrain at 18 and 24 hpf (Figure 6Ab and c). In addition, highly specific expression of prdm3 in pronephric duct is apparent at 18 and 24 hpf (Figure 6Ab and c). At 48 and 72 hpf, prdm3 is additionally expressed in branchial arches and pectoral fin buds (Figure 6Ad and e). In contras, prdm16 is firstly detected in hindbrain rather than telencephalon (12 hpf; Figure 6Af). The fin buds-expression of prdm16 appears earlier than that of prdm3, whereas the pronephric duct-expression of prdm16 is not as specific as that of prdm3 (Figure 6Ac and h). From 24 hpf to 72 hpf, the olfactory placode-expression of prdm16 is relatively high (Figure 6Ah–j).


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)

Nervous system-expressed SET domain genes.(A) Expression patterns of closely related prdm3 and prdm16. (a–j) Lateral views (anterior to the left) of embryos at 12, 18, 24, 48 and 72 hpf. (b' and g') Ventral views of the embryos in b and g. (c'–e' and h'–j') Dorsal views of the embryos in c–e and h–j. Note the partially overlapping expression of prdm3 and prdm16. (B) Expression patterns of prdm13, prdm8a and prdm8b. (a–f) Lateral views (anterior to the left) of embryos at 24 and 48 hpf. (a'–f') Dorsal views of the embryos in a–f. Note that the expression of prdm8a is mostly restricted in hindbrain and spinal chord (c, d and c', d'), whereas that of prdm8b is restricted in olfactory placode, tegmentum, cerebellum and retina (f and f'). (C) Expression pattern of prdm12. (a and b) Lateral views (anterior to the left) of embryos at 18, 24 hpf. (a' and b') Dorsal views of the embryos in a and b. At 48 hpf, prdm12 is expressed in olfactory placode, tegmentum, cerebellum and hindbrain. (D) Expression pattern of prdm15. (a and b) Lateral views (anterior to the left) of embryos at 18, 22 hpf. (a' and b') Dorsal views of the embryos in a and b. Note that prdm15 is expressed in cranial ganglia neurons (a' and b') as well as in muscle pioneer cells and intermediate cell mass (a and b). ba, branchial arches; ce, cerebellum; cg, cranial ganglia; cnc, cranial neural crest; fb, fin buds; hb, hindbrain; icm, intermediate cell mass; mp, muscle pioneer; op, olfactory placode; pnd, pronephric duct; re, retina; sc, spinal chord; tel, telencephalon; tg, tegmentum; vd, ventral diencephalons.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2200798&req=5

pone-0001499-g006: Nervous system-expressed SET domain genes.(A) Expression patterns of closely related prdm3 and prdm16. (a–j) Lateral views (anterior to the left) of embryos at 12, 18, 24, 48 and 72 hpf. (b' and g') Ventral views of the embryos in b and g. (c'–e' and h'–j') Dorsal views of the embryos in c–e and h–j. Note the partially overlapping expression of prdm3 and prdm16. (B) Expression patterns of prdm13, prdm8a and prdm8b. (a–f) Lateral views (anterior to the left) of embryos at 24 and 48 hpf. (a'–f') Dorsal views of the embryos in a–f. Note that the expression of prdm8a is mostly restricted in hindbrain and spinal chord (c, d and c', d'), whereas that of prdm8b is restricted in olfactory placode, tegmentum, cerebellum and retina (f and f'). (C) Expression pattern of prdm12. (a and b) Lateral views (anterior to the left) of embryos at 18, 24 hpf. (a' and b') Dorsal views of the embryos in a and b. At 48 hpf, prdm12 is expressed in olfactory placode, tegmentum, cerebellum and hindbrain. (D) Expression pattern of prdm15. (a and b) Lateral views (anterior to the left) of embryos at 18, 22 hpf. (a' and b') Dorsal views of the embryos in a and b. Note that prdm15 is expressed in cranial ganglia neurons (a' and b') as well as in muscle pioneer cells and intermediate cell mass (a and b). ba, branchial arches; ce, cerebellum; cg, cranial ganglia; cnc, cranial neural crest; fb, fin buds; hb, hindbrain; icm, intermediate cell mass; mp, muscle pioneer; op, olfactory placode; pnd, pronephric duct; re, retina; sc, spinal chord; tel, telencephalon; tg, tegmentum; vd, ventral diencephalons.
Mentions: Seven nervous system-expressed SET domain genes were identified by WISH analyses. The closely related prdm3 (GenBank accession DQ851828) and prdm16 (GenBank accession DQ851827) are expressed in a partially overlapping pattern (Figure 6A). The expression of prdm3 is first detected in telencephalon at 12 hpf (Figure 6Aa) and then extends to tegmentum, ventral diencephalons and hindbrain at 18 and 24 hpf (Figure 6Ab and c). In addition, highly specific expression of prdm3 in pronephric duct is apparent at 18 and 24 hpf (Figure 6Ab and c). At 48 and 72 hpf, prdm3 is additionally expressed in branchial arches and pectoral fin buds (Figure 6Ad and e). In contras, prdm16 is firstly detected in hindbrain rather than telencephalon (12 hpf; Figure 6Af). The fin buds-expression of prdm16 appears earlier than that of prdm3, whereas the pronephric duct-expression of prdm16 is not as specific as that of prdm3 (Figure 6Ac and h). From 24 hpf to 72 hpf, the olfactory placode-expression of prdm16 is relatively high (Figure 6Ah–j).

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
Related in: MedlinePlus