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Open Access Research

DNA binding specificities of the long zinc-finger recombination protein PRDM9

Timothy Billings1, Emil D Parvanov2, Christopher L Baker1, Michael Walker1, Kenneth Paigen1* and Petko M Petkov1*

Author Affiliations

1 Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA

2 National Centre for Biomolecular Research and Department of Biology, Masaryk University, Brno 625 00, Czech Republic

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Genome Biology 2013, 14:R35  doi:10.1186/gb-2013-14-4-r35

Published: 24 April 2013

Additional files

Additional file 1:

Figure S1. Escherichia coli-expressed PRDM9 protein variants retain their H3K4 trimethylation activity. The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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Additional file 2:

Figure S2. The PRDM9Dom2 binding site of Pbx1. The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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Additional file 3:

Figure S3. The PRDM9Cst binding site of Hlx1. The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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Additional file 4:

Figure S4. The PRDM9Cst binding site of Esrrg-1. The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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Additional file 5:

Figure S5. Alignment of the three PRDM9Cst binding sites. The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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Additional file 6:

Table S1. Persikov algorithm predictions for 200 bp regions surrounding binding sites. The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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Additional file 7:

Table S2. Position-weighted matrix based on the results of the electrophoretic mobility shift assay (EMSA). The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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Open Data

Additional file 8:

Figure S6. Nucleotide substitution analysis of Hlx1. The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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Additional file 9:

Table S3. Binding changes at each position along the Hlx1 binding site caused by a mutated nucleotide. The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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Additional file 10:

Figure S7. Effect of Mg2+ on PRDM9-DNA binding. The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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Additional file 11:

Additional experimental procedures: oligos used for analysis of binding. The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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Additional file 12:

Sequences of Prdm9Dom2 and Prdm9Cst cDNA cloned in pBAD/HisB. The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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Additional file 13:

Figure S8. PRDM9 binds to its targets in an allele-specific manner. The Additional material contains maps of all hotspots studied in this paper, their sequences, additional figures and tables highlighting specific points in the paper, and the sequences of the oligos used for mapping.

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