Open Access Research

The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite

Andrea H Horakova1, J Mauro Calabrese2, Christine R McLaughlin1, Deanna C Tremblay1, Terry Magnuson2 and Brian P Chadwick1*

Author Affiliations

1 Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA

2 Department of Genetics, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA

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Genome Biology 2012, 13:R70  doi:10.1186/gb-2012-13-8-r70

Published: 20 August 2012

Additional files

Additional file 1:

Genomic organization and expression of the downstream tandem repeat. The pair-wise alignment and repeat content of the Ds-TR as well as expression as demonstrated by RT-PCR.

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Open Data

Additional file 2:

X chromosome tandem repeat survey. Table summarizing large tandem repeat elements along the mouse X chromosome.

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Open Data

Additional file 3:

Mouse BAC clones encompassing Dxz4. BAC clones that completely span the mouse Dxz4 tandem repeat.

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Open Data

Additional file 4:

Assessing Dxz4 for promoter activity. Assessment of mouse Dxz4 for internal promoter activity.

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Open Data

Additional file 5:

Dxz4 exon1 to tandem repeat monomer RT-PCR. The presence of primary transcript bridging exon 1 of Dxz4 into the tandem repeat.

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Open Data

Additional file 6:

CpG methylation relative to Ctcf and DNaseI hypersensitivity. The location of a Ctcf and DNaseI peak relative to CpG methylation immediately adjacent to the Ds-TR.

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Open Data

Additional file 7:

Motif alignments to Dxz4 conserved region. Alignment of the Dxz4 conserved region with DNA binding protein motifs in JASPAR.

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Open Data

Additional file 8:

Table listing all oligonucleotides used in this study.

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Open Data

Additional file 9:

Dxz4 SNP data. List of SNPs identified in proximity to the Dxz4 Ctcf site in BL6 and cast DNA that were used to assign Ctcf ChIP-Seq fragments to the BL6 or cast chromosome in Figure 5c.

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Open Data