Fig. 6

Transcriptional dysregulation of genes on the X and Y chromosomes correlates with methylation changes. a Volcano plot showing log fold change (FC) in transcription as measured by HT12 array versus FDR-corrected significance values: genes with > 2FC and FDR < 0.05 are highlighted in red. b Numbers of dysregulated genes at different FDR thresholds for the different KD lines. c Genes common to more than one KD line at FDR < 0.05; total numbers in each cell line are indicated in brackets. d Ontology enrichment output from DAVID for the genes common to all KD lines. e RT-PCR analysis of the three MAGE genes on X and a member of the TSPY gene family on Y highlighted in DAVID analysis (C). ACTB is a loading control; −ve, negative control lacking cDNA. A 100-bp ladder is shown at left with the 200-bp band indicated by an arrowhead. f Transcription levels of indicated MAGE genes from the HT12 array or by qPCR. Error bars are 95% CI for the array, SEM for qPCR; fold change was significant (p < 0.05) in all cases. g Median β values on 450K array for probes at MAGE promoters were decreased, though failed to reach significance. h Gene body methylation was increased in transcriptionally upregulated genes