Open Access Research article

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

Peter Lorenz1, Sabine Dietmann2, Thomas Wilhelm3, Dirk Koczan1, Sandra Autran4, Sophie Gad5, Gaiping Wen67, Guohui Ding8, Yixue Li8, Marie-Françoise Rousseau-Merck4 and Hans-Juergen Thiesen1*

Author Affiliations

1 Institute of Immunology, University of Rostock, Schillingallee 70, 18055 Rostock, Germany

2 Institute of Bioinformatics, GSF - Research Institute for Environment and Health, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany

3 Theoretical Systems Biology, Institute of Food Research, Norwich Research Park, Norwich NR4 7UH, UK

4 Inserm U830, Institut Curie, 26 rue d'Ulm, 75248 Paris cedex 05, France

5 Service de Génétique Oncologique, Institut Curie, 26 rue d'Ulm, 75248 Paris cedex 05 Paris, France

6 Department of Genome Analysis, Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstr 11, 07745 Jena, Germany

7 Current address: Institut für Agrar- und Ernährungswissenschaften Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 2, 06120 Halle (Saale), Germany

8 Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Yueyang Road, Shanghai 200031, PR China

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BMC Genomics 2010, 11:206  doi:10.1186/1471-2164-11-206

Published: 26 March 2010

Additional files

Additional file 1:

Nucleotide sequences. Compendium of all nucleotide sequences used for analysis.

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Additional file 2:

Amino acid sequences. Listing of all amino acid sequences used for analysis.

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Additional file 3:

Orthologs of human 8q24.3 ZNF genes at syntenic genomic regions in mouse and rat. Table summarizing accession numbers and genomic localization of the mouse and rat orthologs.

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Additional file 4:

Phylogeny of the human 8q24.3 ZNF genes and their mammalian orthologs. Extended phylogenetic trees of the human 8q24.3 ZNF genes and their mammalian orthologs that were constructed using cDNA, whole protein, zinc finger region and KRAB domain sequences.

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Additional file 5:

Calculations of synonymous and non-synonymous substitution rates. Table containing the values from the domain-wise calculations of synonymous and nonsynonymous substitution rates within an ortholog group of each 8q24.3 ZNF gene (done with the YN00 module of the PAML software package version 3.14 [106,54]).

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Additional file 6:

Zinc finger DNA-binding region comparison. "Choo & Klug plot" for the C2H2 zinc finger regions of the human 8q24.3 ZNF genes and all their orthologs. Zinc finger region alignment of the proteins in each ortholog group based on individual zinc fingers represented by residues -1, 3 and 6 that are thought to be essential in determining DNA binding specificity.

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Additional file 7:

Principal component analysis of individual zinc finger peptide sequences for functional and evolutionary conservation. List of the individual sequences and their values based on the alignment of the 8-amino acid region from positions -2 to 6 with respect to the start of the α-helix of a C2H2 zinc finger that is known to be involved in determining DNA binding specificity. Only human, mouse and rat orthologs were considered.

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Additional file 8:

Tissue expression profiling. Tables with primary data and derived relative expression values of ZNF quantitative RT-PCR and details on the gene expression assays and samples.

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Additional file 9:

Tissue expression distances inferred from ZNF gene expression. Euclidian distance between 27 human tissues based on the expression analysis of 17 human ZNF genes (7 genes from 8q24.3, 10 from other loci).

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Additional file 10:

Gene expression similarities based on tissue expression profiles. Pairwise distances between all genes based on their tissue expression profiles. Included are the seven 8q24.3 ZNF genes, ten ZNF genes from other loci, TRIM28 and twelve non-ZNF genes. Calculation: Distance = 1 - abs (Pearson correlation coefficient).

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Additional file 11:

Proximal promoter sequences of the seven human 8q24.3 locus ZNF genes. Sequences of the proximal promoter regions of the seven human 8q24.3 ZNF genes extracted by Genomatix Gene2Promoter.

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Additional file 12:

UCSC Genome Browser visualizations of the proximal promoter regions of the seven human 8q24.3 ZNF genes. Visualization along with associated features using the UCSC Genome Browser (human genome hg18). Genome Browser tracks included CpG islands, occupancy with RNA polymerase II core enzyme (Pol2) in four cell lines, occupancy with pre-initiation complex general transcription factor TAF1 and third party TSS predictions. Arrowheads in the depiction of the promoter regions indicate the direction of transcription.

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Additional file 13:

Core promoter elements in the proximal promoter regions of the seven human 8q24.3 genes. Detailed listing and sequences of core promoter elements based on Genomatix MatInspector software.

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Additional file 14:

TFBS modules occuring in at least three of the seven promoter regions of the human 8q24.3 ZNF genes. Listing of the module families, the modules, their associated individual TFBS and the respective nucleotide sequences.

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Additional file 15:

Graphical view of TFBS and TSS within the proximal promoter regions of the seven human 8q24.3 ZNF genes. Visualization of core promoter elements and those TFBS that are derived from module families that occur in at least three promoters. The symbols representing core promoter elements have ovoid shapes, those depicting TFBS from modules are rectangles. Strand orientation is reflected in the placement of the symbols above ("sense" strand) or below ("antisense" strand) the promoter DNA depiction. The width of the symbols reflects the length of the respective DNA elements.

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