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Open Access Research article

The SWI/SNF protein ATRX co-regulates pseudoautosomal genes that have translocated to autosomes in the mouse genome

Michael A Levy14, Andrew D Fernandes12, Deanna C Tremblay14, Claudia Seah34 and Nathalie G Bérubé134*

Author Affiliations

1 Department of Biochemistry, University of Western Ontario, London, N6A 4L6, Canada

2 Applied Mathematics, University of Western Ontario, London, N6A 4L6, Canada

3 Paediatrics, University of Western Ontario, London, N6A 4L6, Canada

4 Children's Health Research Institute, Lawson Health Research Institute, 800 Commissioners Road East, London, N6C 2V5, Canada

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BMC Genomics 2008, 9:468  doi:10.1186/1471-2164-9-468

Published: 8 October 2008

Additional files

Additional file 1:

Summary of microarray results. cRNA was generated from total forebrain RNA from three pairs of littermate-matched ATRX-null and wild type forebrain tissue and hybridized to an Affymetrix Mouse Genome 430 2.0 Array. Data was analyzed using GeneSpring. Probe sets were filtered by fold change (1.5 and 2 fold at E13.5 and P0.5) and confidence, P < 0.05, and duplicate genes were removed. (A) Venn diagrams to categorize probe sets according to developmental timepoint and fold change in expression levels. (B) Hierarchical clustering of differentially expressed probe sets. Approximately two-thirds of the misregulated genes are upregulated. Ancestral PAR genes are consistently downregulated at both timepoints and are indicated by blue text. Probe sets were filtered by 1.5 fold or 2 fold change, P < 0.05, at either E13.5 or P0.5. Normalized expression levels are displayed.

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Additional file 2:

Significantly misregulated GO categories. GeneSpring was used to identify significantly overrepresented GO categories. Probe sets were filtered by 1.5 fold change, P < 0.05 and categorized as either up or downregulated. When there were multiple probe sets for a gene, duplicates were removed. P < 0.001 was used as the significance cutoff.

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Additional file 3:

Amino acid alignment of a small portion of ARSD/E between multiple species. Sequences were aligned using T-Coffee 5.56 [47] using default parameters, edited using JalView [46] and shaded using Boxshade [51]. Mouse ARSD/E has highest identity to rat ARSE (65%). Accession numbers are ARSE: chicken [GenBank:XP_416856], cow [GenBank:ABS45001], dog [GenBank:NP_001041587], horse [GenBank:XP_001495573], macaque [GenBank:Q60HH5], human [GenBank:CAA58556], platypus [GenBank:XP_001514429], opossum [GenBank:XP_001362844], pufferfish [GenBank:CAG09268], rat [GenBank:CAI84983]. ARSD: dog [GenBank:XP_548838], horse [GenBank:XP_001495553], human [GenBank:CAA58555], macaque [GenBank:XP_001092405], opossum, [GenBank:XP_001362931], platypus [GenBank:XP_001507106], chicken [GenBank:XP_416855], zebrafish [GenBank:XP_700386]. Mouse Arsd/e translated from [GenBank:BE457721].

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Additional file 4:

Comparisons of Ars family members. The transcript identified as a putative mouse Arse ortholog is more similar to rat Arse then to any other Ars family members. Pairwise percent identities were calculated using Jalview [46]. Accession numbers are: Arse [GenBank:BE45772], Arsa [GenBank:NM_009713], Arsb [GenBank:NM_009712.3], Arsc/Sts [GenBank:NM_009293.1], Arsg [GenBank:NM_028710.2], Arsi [GenBank:NM_001038499.1], Arsj [GenBank:NM_173451.2], Arsk [GenBank:NM_029847.4], rat Arse [GenBank:NM_001047885.1], rat Arsc/Sts [GenBank:NM_012661.1].

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Additional file 5:

Amino acid alignment of the N terminal of ASMTL between multiple species. Sequences were aligned using T-Coffee 5.56 [47] using default parameters, edited using JalView [46] and shaded using Boxshade [51]. The putative mouse ASMTL aligns within the N terminal MAF domain and is most similar to rat ASMTL (54% identity) which also contains only the MAF domain. Accession numbers are: human [GenBank:XP_001133965], orangutan [GenBank:CAH90398], chimpanzee [XP_001137696], cow [GenBank:AAI03000], dog [GenBank:XP_851655], frog [GenBank:NP_001085814], chicken [GenBank:XP_001231914], zebrafish [GenBank:NP_998676], platypus [GenBank:XP_001506357], mouse [GenBank:NP_081215].

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Additional file 6:

Conditions for quantitative real-time PCR. Primer sequences and annealing temperatures used for quantitative real-time PCR confirmation of downregulated ancestral PAR genes.

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