The X chromosome is enriched in AT-rich motifs in mouse. (A) The mouse X chromosome (red symbols) is uniquely enriched in a subset of 6-mers as compared with each autosome. A total of 427 6-mers were initially defined as those present in introns of the X-linked Clcn4 loci in five species (M. spretus, rat, human, cow, dog), but absent in the autosomal locus in M. musculus (Supplemental Table S4). The frequencies per kilobase of genomic DNA for a subset 120 6-mers on the X and autosomes are shown for the repeat-masked mouse genome (6-mers were ordered by decreasing frequency per kilobase on the X). (B) The frequencies per kilobase for a subset of 120 6-mers on genes that escape X inactivation (black) show an intermediate enrichment, as compared with the X chromosome (red) and autosomes (yellow). Each point represents the frequency per kilobase for each 6-mer. (C) The relative X to autosome frequency per kilobase for each 6-mer increases with the AT content. Frequency ratios between the X and autosomes are shown as a function of the AT content of the 6-mers (expressed as a fraction of the six nucleotides). Analysis shown for the repeat-masked mouse genome (see Supplemental Figs. S4, S5 for other species). (D) AT-rich sequence motif logos for 6-mers enriched at least 1.2-fold on the X in the unmasked genome (left), and the repeat masked genome (right).
