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Background  X-chromosome inactivation (XCI) is a mechanism in which one of two X chromosomes in females is randomly inactivated in order to compensate for imbalance of gene dosage between sexes. However, about 15% of genes on the inactivated X chromosome (Xi) escape from XCI. The methylation level of the promoter region of the escape gene is lower than that of the inactivated genes.  Dxz4  and/or  Firre  have critical roles for forming the three-dimensional (3D) structure of Xi. In mice, disrupting the 3D structure of Xi by deleting both  Dxz4  and  Firre  genes led to changing of the escape genes list. To estimate the impact for escape genes by X-chromosome rearrangements, including  DXZ4  and  FIRRE,  we examined the methylation status of escape gene promoters in patients with various X-chromosome rearrangements.    Results  To detect the breakpoints, we first performed array-based comparative genomic hybridization and whole-genome sequencing in four patients with X-chromosome rearrangements. Subsequently, we conducted array-based methylation analysis and reduced representation bisulfite sequencing in the four patients with X-chromosome rearrangements and controls. Of genes reported as escape genes by gene expression analysis using human hybrid cells in a previous study, 32 genes showed hypomethylation of the promoter region in both male controls and female controls. Three patients with X-chromosome rearrangements had no escape genes with abnormal methylation of the promoter region. One of four patients with the most complicated rearrangements exhibited abnormal methylation in three escape genes. Furthermore, in the patient with the deletion of the  FIRRE  gene and the duplication of  DXZ4,  most escape genes remained hypomethylated.    Conclusion  X-chromosome rearrangements are unlikely to affect the methylation status of the promoter regions of escape genes, except for a specific case with highly complex rearrangements, including the deletion of the  FIRRE  gene and the duplication of  DXZ4 .    Supplementary Information  The online version contains supplementary material available at 10.1186/s13148-021-01121-6.

Methylation status of genes escaping from X-chromosome inactivation in patients with X-chromosome rearrangements