Genome sequence comparative analysis of long arm and short arm of human X chromosome

30% of the genes tested on Xp escaped inactivation, whereas less than 3% of the genes on Xq escaped inactivation. To investigate the molecular mechanism involved in the propagation and maintenance of X chromosome inactivation and escape, the long arm and short arm of the X chromosome were compared for RNA binding density. Nucleotide sequences on the X chromosome were divided into 50 kb per segment that was recorded as a set of frequency values of 7-nucleotide (7 nt) strings using all possible 7 nt strings (4(7) = 16 384). 120 genes highly expressed in the tonsil germinal center B cells were selected for calculating the 7 nt string frequency values of all introns (intron 7nt). Intron 7nt was considered RNAs (RNA population) that simulated the total of small RNA fragments in cells. Knowing the 7 nt frequency values of DNA segments and the intron 7nt, we can calculate the binding density of DNA segments to the intron 7nt that was termed as RNA binding density. The RNA binding density was determined by the amount of complement sequences. The more amount of complement sequences, the more density of RNA binding. The RNA binding density simulated the total of small RNA fragments bound to the DNA segment. Several principal characteristics were observed for the first time: (1) The mean value of RNA binding density of DNA segments on Xp was significantly higher than that on Xq ( P < 0.001); (2) The numbers of DNA segments highly binding RNAs were more on Xp than on Xq (P < 0.001); (3) The clusters of RNA highly binding DNA segments were associated with regions in which genes escape inactivation. It has been suggested that RNAs activate genes and the interaction of RNA-DNA in cells are extensive, for example, RNAs increase DNase I sensitivity of DNA, there is plenty of nonprotein-coding RNAs in cells, the binding specificity of DNA-RNA is far higher than that of DNA-protein and the affinity of DNA with RNA is increased, as compared with DNA. The nonrandom properties of distribution of RNA highly binding segments between Xp and Xq, combined with the finding of RNA activating genes, provide a strong evidence that RNA highly binding segments may serve as DNA signals to propagate activation along a chromosome and vice versa, the DNA segments that less bind RNAs may silence the genes.