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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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Genomic organization of the human ZNF cluster at chromosomal region 8q24.3 and its syntenic regions in mouse and rat. A. FISH of ZNF gene PAC clones on combed DNA. Orientation is given by indicating the centromeric (centr) and telomeric (tel) directions. Numbers on the depicted DNA indicate sizes within the piece of combed DNA. B. Map of the sequenced individual PAC clones at the 8q24.3-8qter locus (open bars) and their alignment/assembly within the whole contig (genomic assemblies with respective GenBank accessions shown as grey bars). Range, size and chromosomal position of the whole contig is reflected in the depicted chromosomal region on top. The ZNF gene models (see Table 1, Figure 2 and text) are indicated as colored boxes encompassing the sequence stretch from first to last exon. Genomic regions syntenic to human 8q24.3 in mouse and rat are depicted at the bottom. Same coloring designates orthologs. The three human genes depicted in black lack orthologs in mouse and rat (exception: presumable KRAB-B remnant of ZNF252 ortholog in rat, see text). Isolated, often degenerate sequences for KRAB-A ("pin" with square head), KRAB-B ("pin" with round head) and C2H2 zinc fingers (open rectangle with label "pseudo") are displayed at their respective position. Two other well characterized genes (RPL8, COMMD5) in the region are shown by striped boxes. The coding strand of each element is indicated by positioning above or below the depicted chromosomal region. Based on genome assemblies UCSC hg18 (human), mm9 (mouse) and rn4 (rat).
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Figure 1: Genomic organization of the human ZNF cluster at chromosomal region 8q24.3 and its syntenic regions in mouse and rat. A. FISH of ZNF gene PAC clones on combed DNA. Orientation is given by indicating the centromeric (centr) and telomeric (tel) directions. Numbers on the depicted DNA indicate sizes within the piece of combed DNA. B. Map of the sequenced individual PAC clones at the 8q24.3-8qter locus (open bars) and their alignment/assembly within the whole contig (genomic assemblies with respective GenBank accessions shown as grey bars). Range, size and chromosomal position of the whole contig is reflected in the depicted chromosomal region on top. The ZNF gene models (see Table 1, Figure 2 and text) are indicated as colored boxes encompassing the sequence stretch from first to last exon. Genomic regions syntenic to human 8q24.3 in mouse and rat are depicted at the bottom. Same coloring designates orthologs. The three human genes depicted in black lack orthologs in mouse and rat (exception: presumable KRAB-B remnant of ZNF252 ortholog in rat, see text). Isolated, often degenerate sequences for KRAB-A ("pin" with square head), KRAB-B ("pin" with round head) and C2H2 zinc fingers (open rectangle with label "pseudo") are displayed at their respective position. Two other well characterized genes (RPL8, COMMD5) in the region are shown by striped boxes. The coding strand of each element is indicated by positioning above or below the depicted chromosomal region. Based on genome assemblies UCSC hg18 (human), mm9 (mouse) and rn4 (rat).

Mentions: The ZNF cluster was initially determined by chromosome mapping of sixteen different ZNF PAC clones to genomic locus 8q24.3 of which thirteen were specific for this locus [44] whereas three clones showed signals of comparable intensities on other chromosomes as well. Fluorescence in situ hybridization (FISH) on interphasic nuclei and molecular combing techniques allowed to approximate the size and the organization of the 8q24.3 ZNF cluster. A first approach on interphasic nuclei was employed to select the closer co-localizing PAC clones from the more distant mapping ones. Two Pac clones, RP5-1109M23 and RP4-698E23 were clearly delimiting the borders of the cluster. FISH on combed DNA, performed with two series of three PAC clones, confirmed the close proximity of the ZNF PAC clones all along the cluster and allowed to estimate an approximate size for each probe taking into account a 10% variability for the resolution. Overall alignment lengths of 209 kb and 383 kb were obtained for RP5-1124C13/RP1-291P5/RP4-718C10 and RP5-1109M23/RP4-626A24/RP4-698E23, respectively (Figure 1A).


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)

Genomic organization of the human ZNF cluster at chromosomal region 8q24.3 and its syntenic regions in mouse and rat. A. FISH of ZNF gene PAC clones on combed DNA. Orientation is given by indicating the centromeric (centr) and telomeric (tel) directions. Numbers on the depicted DNA indicate sizes within the piece of combed DNA. B. Map of the sequenced individual PAC clones at the 8q24.3-8qter locus (open bars) and their alignment/assembly within the whole contig (genomic assemblies with respective GenBank accessions shown as grey bars). Range, size and chromosomal position of the whole contig is reflected in the depicted chromosomal region on top. The ZNF gene models (see Table 1, Figure 2 and text) are indicated as colored boxes encompassing the sequence stretch from first to last exon. Genomic regions syntenic to human 8q24.3 in mouse and rat are depicted at the bottom. Same coloring designates orthologs. The three human genes depicted in black lack orthologs in mouse and rat (exception: presumable KRAB-B remnant of ZNF252 ortholog in rat, see text). Isolated, often degenerate sequences for KRAB-A ("pin" with square head), KRAB-B ("pin" with round head) and C2H2 zinc fingers (open rectangle with label "pseudo") are displayed at their respective position. Two other well characterized genes (RPL8, COMMD5) in the region are shown by striped boxes. The coding strand of each element is indicated by positioning above or below the depicted chromosomal region. Based on genome assemblies UCSC hg18 (human), mm9 (mouse) and rn4 (rat).
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2865497&req=5

Figure 1: Genomic organization of the human ZNF cluster at chromosomal region 8q24.3 and its syntenic regions in mouse and rat. A. FISH of ZNF gene PAC clones on combed DNA. Orientation is given by indicating the centromeric (centr) and telomeric (tel) directions. Numbers on the depicted DNA indicate sizes within the piece of combed DNA. B. Map of the sequenced individual PAC clones at the 8q24.3-8qter locus (open bars) and their alignment/assembly within the whole contig (genomic assemblies with respective GenBank accessions shown as grey bars). Range, size and chromosomal position of the whole contig is reflected in the depicted chromosomal region on top. The ZNF gene models (see Table 1, Figure 2 and text) are indicated as colored boxes encompassing the sequence stretch from first to last exon. Genomic regions syntenic to human 8q24.3 in mouse and rat are depicted at the bottom. Same coloring designates orthologs. The three human genes depicted in black lack orthologs in mouse and rat (exception: presumable KRAB-B remnant of ZNF252 ortholog in rat, see text). Isolated, often degenerate sequences for KRAB-A ("pin" with square head), KRAB-B ("pin" with round head) and C2H2 zinc fingers (open rectangle with label "pseudo") are displayed at their respective position. Two other well characterized genes (RPL8, COMMD5) in the region are shown by striped boxes. The coding strand of each element is indicated by positioning above or below the depicted chromosomal region. Based on genome assemblies UCSC hg18 (human), mm9 (mouse) and rn4 (rat).
Mentions: The ZNF cluster was initially determined by chromosome mapping of sixteen different ZNF PAC clones to genomic locus 8q24.3 of which thirteen were specific for this locus [44] whereas three clones showed signals of comparable intensities on other chromosomes as well. Fluorescence in situ hybridization (FISH) on interphasic nuclei and molecular combing techniques allowed to approximate the size and the organization of the 8q24.3 ZNF cluster. A first approach on interphasic nuclei was employed to select the closer co-localizing PAC clones from the more distant mapping ones. Two Pac clones, RP5-1109M23 and RP4-698E23 were clearly delimiting the borders of the cluster. FISH on combed DNA, performed with two series of three PAC clones, confirmed the close proximity of the ZNF PAC clones all along the cluster and allowed to estimate an approximate size for each probe taking into account a 10% variability for the resolution. Overall alignment lengths of 209 kb and 383 kb were obtained for RP5-1124C13/RP1-291P5/RP4-718C10 and RP5-1109M23/RP4-626A24/RP4-698E23, respectively (Figure 1A).

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