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The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues.

Lorenz P, Dietmann S, Wilhelm T, Koczan D, Autran S, Gad S, Wen G, Ding G, Li Y, Rousseau-Merck MF, Thiesen HJ - BMC Genomics (2010)

Bottom Line: Expansion of multi-C2H2 domain zinc finger (ZNF) genes, including the Krüppel-associated box (KRAB) subfamily, paralleled the evolution of tetrapodes, particularly in mammalian lineages.Six (ZNF7, ZNF34, ZNF250, ZNF251, ZNF252, ZNF517) of the seven locus members contain exons encoding KRAB domains, one (ZNF16) does not.These results are consistent with potential functions of the ZNF genes in morphogenesis and differentiation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Immunology, University of Rostock, Schillingallee 70, 18055 Rostock, Germany.

ABSTRACT

Background: Expansion of multi-C2H2 domain zinc finger (ZNF) genes, including the Krüppel-associated box (KRAB) subfamily, paralleled the evolution of tetrapodes, particularly in mammalian lineages. Advances in their cataloging and characterization suggest that the functions of the KRAB-ZNF gene family contributed to mammalian speciation.

Results: Here, we characterized the human 8q24.3 ZNF cluster on the genomic, the phylogenetic, the structural and the transcriptome level. Six (ZNF7, ZNF34, ZNF250, ZNF251, ZNF252, ZNF517) of the seven locus members contain exons encoding KRAB domains, one (ZNF16) does not. They form a paralog group in which the encoded KRAB and ZNF protein domains generally share more similarities with each other than with other members of the human ZNF superfamily. The closest relatives with respect to their DNA-binding domain were ZNF7 and ZNF251. The analysis of orthologs in therian mammalian species revealed strong conservation and purifying selection of the KRAB-A and zinc finger domains. These findings underscore structural/functional constraints during evolution. Gene losses in the murine lineage (ZNF16, ZNF34, ZNF252, ZNF517) and potential protein truncations in primates (ZNF252) illustrate ongoing speciation processes. Tissue expression profiling by quantitative real-time PCR showed similar but distinct patterns for all tested ZNF genes with the most prominent expression in fetal brain. Based on accompanying expression signatures in twenty-six other human tissues ZNF34 and ZNF250 revealed the closest expression profiles. Together, the 8q24.3 ZNF genes can be assigned to a cerebellum, a testis or a prostate/thyroid subgroup. These results are consistent with potential functions of the ZNF genes in morphogenesis and differentiation. Promoter regions of the seven 8q24.3 ZNF genes display common characteristics like missing TATA-box, CpG island-association and transcription factor binding site (TFBS) modules. Common TFBS modules partly explain the observed expression pattern similarities.

Conclusions: The ZNF genes at human 8q24.3 form a relatively old mammalian paralog group conserved in eutherian mammals for at least 130 million years. The members persisted after initial duplications by undergoing subfunctionalizations in their expression patterns and target site recognition. KRAB-ZNF mediated repression of transcription might have shaped organogenesis in mammalian ontogeny.

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Phylogenetic relationships between the human ZNF genes from 8q24.3, their murine orthologs and other human ZNF genes. The analysis relied on alignments of full nucleotide cDNA sequences (A), of whole polypeptide sequences (B), of the array of all C2H2 zinc finger domains of each protein and of the KRAB domains using the neighbor-joining method. The analysis also included Xenopus Xfin as a distant outlier and as reference group seven KRAB-ZNFs from human 19q13.2 and eight KRAB-ZNFs from other genomic locations. Numbers indicate bootstrap values in percent based on 1000 replicates. To the right of the different clades the genomic localizations of the human genes are given. Note that the two KRAB domains of presumable pseudogenes (krab A1B1, krab A2B2) within 8q24.3 as well as an artificially combined human ZNF252 KRAB domain (labeled "art") have been added; see text for more details. Since the ZNF16 ortholog cDNAs from mouse and rat do most likely not give rise to a functional protein, protein sequences were not included in the analyses. The full nucleotide and protein sequences are given in Additional files 1 and 2, respectively.
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Figure 4: Phylogenetic relationships between the human ZNF genes from 8q24.3, their murine orthologs and other human ZNF genes. The analysis relied on alignments of full nucleotide cDNA sequences (A), of whole polypeptide sequences (B), of the array of all C2H2 zinc finger domains of each protein and of the KRAB domains using the neighbor-joining method. The analysis also included Xenopus Xfin as a distant outlier and as reference group seven KRAB-ZNFs from human 19q13.2 and eight KRAB-ZNFs from other genomic locations. Numbers indicate bootstrap values in percent based on 1000 replicates. To the right of the different clades the genomic localizations of the human genes are given. Note that the two KRAB domains of presumable pseudogenes (krab A1B1, krab A2B2) within 8q24.3 as well as an artificially combined human ZNF252 KRAB domain (labeled "art") have been added; see text for more details. Since the ZNF16 ortholog cDNAs from mouse and rat do most likely not give rise to a functional protein, protein sequences were not included in the analyses. The full nucleotide and protein sequences are given in Additional files 1 and 2, respectively.

Mentions: The analysis of the 8q24.3 members revealed that, in general, the genes disperse into well separated clades/subclades with long branch lengths and often with many nodes in between (Figure 4), indicating relatively large phylogenetic distances and thus divergence times. This was the case for trees based on all four different alignments. In particular ZNF16 and ZNF252 exhibit a very distant relationship to the other 8q24.3 ZNF genes and stay closest to each other but well separated by long branches. This behavior of the 8q24.3 ZNFs is different from the members of the human ZNF locus at 19q13.2 that form a closed clade with much narrower relationships. We also did a second series of analyses with extended mammalian ortholog sequences of the human 8q24.3 ZNF genes as well as the above mentioned pseudogene sequences at our 8q.24.3 locus. The results were qualitatively similar to the one described above in that the different 8q24 ZNF genes with their respective orthologs were always clearly separated in their own clades and not intermingling, indicating significant phylogenetic distance from each other (see Additional file 4). With respect to the residual ZNF sequences on the pseudogenes named pseudo 1 and pseudo 2, the phylogenetic analysis did not indicate close relationships to any 8q24.3 ZNF gene.


The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues.

Lorenz P, Dietmann S, Wilhelm T, Koczan D, Autran S, Gad S, Wen G, Ding G, Li Y, Rousseau-Merck MF, Thiesen HJ - BMC Genomics (2010)

Phylogenetic relationships between the human ZNF genes from 8q24.3, their murine orthologs and other human ZNF genes. The analysis relied on alignments of full nucleotide cDNA sequences (A), of whole polypeptide sequences (B), of the array of all C2H2 zinc finger domains of each protein and of the KRAB domains using the neighbor-joining method. The analysis also included Xenopus Xfin as a distant outlier and as reference group seven KRAB-ZNFs from human 19q13.2 and eight KRAB-ZNFs from other genomic locations. Numbers indicate bootstrap values in percent based on 1000 replicates. To the right of the different clades the genomic localizations of the human genes are given. Note that the two KRAB domains of presumable pseudogenes (krab A1B1, krab A2B2) within 8q24.3 as well as an artificially combined human ZNF252 KRAB domain (labeled "art") have been added; see text for more details. Since the ZNF16 ortholog cDNAs from mouse and rat do most likely not give rise to a functional protein, protein sequences were not included in the analyses. The full nucleotide and protein sequences are given in Additional files 1 and 2, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2865497&req=5

Figure 4: Phylogenetic relationships between the human ZNF genes from 8q24.3, their murine orthologs and other human ZNF genes. The analysis relied on alignments of full nucleotide cDNA sequences (A), of whole polypeptide sequences (B), of the array of all C2H2 zinc finger domains of each protein and of the KRAB domains using the neighbor-joining method. The analysis also included Xenopus Xfin as a distant outlier and as reference group seven KRAB-ZNFs from human 19q13.2 and eight KRAB-ZNFs from other genomic locations. Numbers indicate bootstrap values in percent based on 1000 replicates. To the right of the different clades the genomic localizations of the human genes are given. Note that the two KRAB domains of presumable pseudogenes (krab A1B1, krab A2B2) within 8q24.3 as well as an artificially combined human ZNF252 KRAB domain (labeled "art") have been added; see text for more details. Since the ZNF16 ortholog cDNAs from mouse and rat do most likely not give rise to a functional protein, protein sequences were not included in the analyses. The full nucleotide and protein sequences are given in Additional files 1 and 2, respectively.
Mentions: The analysis of the 8q24.3 members revealed that, in general, the genes disperse into well separated clades/subclades with long branch lengths and often with many nodes in between (Figure 4), indicating relatively large phylogenetic distances and thus divergence times. This was the case for trees based on all four different alignments. In particular ZNF16 and ZNF252 exhibit a very distant relationship to the other 8q24.3 ZNF genes and stay closest to each other but well separated by long branches. This behavior of the 8q24.3 ZNFs is different from the members of the human ZNF locus at 19q13.2 that form a closed clade with much narrower relationships. We also did a second series of analyses with extended mammalian ortholog sequences of the human 8q24.3 ZNF genes as well as the above mentioned pseudogene sequences at our 8q.24.3 locus. The results were qualitatively similar to the one described above in that the different 8q24 ZNF genes with their respective orthologs were always clearly separated in their own clades and not intermingling, indicating significant phylogenetic distance from each other (see Additional file 4). With respect to the residual ZNF sequences on the pseudogenes named pseudo 1 and pseudo 2, the phylogenetic analysis did not indicate close relationships to any 8q24.3 ZNF gene.

Bottom Line: Expansion of multi-C2H2 domain zinc finger (ZNF) genes, including the Krüppel-associated box (KRAB) subfamily, paralleled the evolution of tetrapodes, particularly in mammalian lineages.Six (ZNF7, ZNF34, ZNF250, ZNF251, ZNF252, ZNF517) of the seven locus members contain exons encoding KRAB domains, one (ZNF16) does not.These results are consistent with potential functions of the ZNF genes in morphogenesis and differentiation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Immunology, University of Rostock, Schillingallee 70, 18055 Rostock, Germany.

ABSTRACT

Background: Expansion of multi-C2H2 domain zinc finger (ZNF) genes, including the Krüppel-associated box (KRAB) subfamily, paralleled the evolution of tetrapodes, particularly in mammalian lineages. Advances in their cataloging and characterization suggest that the functions of the KRAB-ZNF gene family contributed to mammalian speciation.

Results: Here, we characterized the human 8q24.3 ZNF cluster on the genomic, the phylogenetic, the structural and the transcriptome level. Six (ZNF7, ZNF34, ZNF250, ZNF251, ZNF252, ZNF517) of the seven locus members contain exons encoding KRAB domains, one (ZNF16) does not. They form a paralog group in which the encoded KRAB and ZNF protein domains generally share more similarities with each other than with other members of the human ZNF superfamily. The closest relatives with respect to their DNA-binding domain were ZNF7 and ZNF251. The analysis of orthologs in therian mammalian species revealed strong conservation and purifying selection of the KRAB-A and zinc finger domains. These findings underscore structural/functional constraints during evolution. Gene losses in the murine lineage (ZNF16, ZNF34, ZNF252, ZNF517) and potential protein truncations in primates (ZNF252) illustrate ongoing speciation processes. Tissue expression profiling by quantitative real-time PCR showed similar but distinct patterns for all tested ZNF genes with the most prominent expression in fetal brain. Based on accompanying expression signatures in twenty-six other human tissues ZNF34 and ZNF250 revealed the closest expression profiles. Together, the 8q24.3 ZNF genes can be assigned to a cerebellum, a testis or a prostate/thyroid subgroup. These results are consistent with potential functions of the ZNF genes in morphogenesis and differentiation. Promoter regions of the seven 8q24.3 ZNF genes display common characteristics like missing TATA-box, CpG island-association and transcription factor binding site (TFBS) modules. Common TFBS modules partly explain the observed expression pattern similarities.

Conclusions: The ZNF genes at human 8q24.3 form a relatively old mammalian paralog group conserved in eutherian mammals for at least 130 million years. The members persisted after initial duplications by undergoing subfunctionalizations in their expression patterns and target site recognition. KRAB-ZNF mediated repression of transcription might have shaped organogenesis in mammalian ontogeny.

Show MeSH
Related in: MedlinePlus