The mouse hinge region binds CTCF and associates with the nucleolus. a Allelic profiles of CTCF and PolII binding in F1 brain and Patski cells are shown for the Xi (blue) and Xa (orange) at the minisatellite Ds-TR, its adjacent promoter region, and at Dxz4. The Ds-TR promoter binds CTCF on the Xa and Xi. No reads were mapped within the minisatellite Ds-TR or at Dxz4 due to low mappability. Different y-axis scales were used for the Xi and Xa in order to show the significant peaks on the Xi, given that there are about threefold more reads at the Ds-TR promoter peak region on the Xa compared with the Xi. b ChIP-chip analysis for CTCF and nucleophosmin in female (FL) and male liver (ML). CTCF binds at the Ds-TR promoter region in female and male liver, and at Dxz4 in female but not male liver. Nucleophosmin binds to Ds-TR, its promoter, and Dxz4 in female liver, while in male liver lower binding is present at Ds-TR. c Enrichment in DNA sequences representing nucleolus-associated domains measured by quantitative PCR in the nucleolus-associated fraction (naDNA) versus genomic DNA (gDNA) is seen at the minisatellite Ds-TR, its promoter and at Dxz4 in Patski cells. The positions of quantitative PCR amplicons used to measure enrichment at these three regions are indicated in (b). Enrichment at control autosomal and X-linked genes is shown. Two primer pairs for different regions of the 18S ribosomal RNA gene known to be associated with the nucleolus serve as positive controls. The dashed line indicates no enrichment (naDNA/gDNA ratio of 1). d Quantitative PCR analysis of chromatin immunoprecipitation (ChIP) for nucleophosmin confirms high enrichment at Ds-TR and adjacent promoter. Error bars indicate s.e.m.