CTCF and RNA polymerase II are present at the
locus on the Xi allele and CTCF interacts with the lncRNA. Allele-specific CTCF (A) and PolII-S5p (B) profiles were established based on SNP analyses of ChIP-seq results in Patski cells and in F1 mouse brain, both derived from crosses between C57BL/6 J and M. spretus. In Patski cells the Xi is from BL6 while in the brain, the Xi is from spretus X. Allele-specific sequence read counts for the Xi (blue) and the Xa (orange), and total mapped read counts (Xt) are shown in 100 bp windows. A few peaks visible in the Xt track could not be assigned to an allele due to a lack of informative SNPs. PolII-S5p peaks are present in multiple regions of Firre on the Xi, indicating alternative transcript start sites. The arrow points to a PolII-S5p peak present only on the Xa at the very 5’end of the Firre transcript in brain. Genomic coordinates are shown at the top and the position of alternative Firre transcripts, at the bottom (from UCSC). (C) CTCF-RNA interactions obtained by CLIP-seq based on re-analysis of published data . Allele-specific profiles for the Xi (blue) and Xa (orange) show differential patterns of interactions between CTCF and the lncRNA transcribed from each allele.