RNA Binding Density on X-chromosome Differing from that on 22 Autosomes in Human

To test whether X-chromosome has unique genomic characteristics, X-chromosome and 22 autosomes were compared for RNA binding density. Nucleotide sequences on the chromosomes were divided into 50kb per segment that was recoded as a set of frequency values of 7-nucleotide (7nt) strings using all possible 7nt strings (4=16384). 120 genes highly expressed in tonsil germinal center B cells were selected for calculating 7nt string frequency values of all introns (RNAs). The binding density of DNA segments and RNAs was determined by the amount of complement sequences. It was shown for the first time that gene-poor and low gene expression X-chromosome had the lowest percentage of the DNA segments that can highly bind RNAs, whereas gene-rich and high gene expression chromosome 19 had the highest percentage of the segments. On the basis of these results, it is proposed that the nonrandom properties of distribution of RNA highly binding DNA segments on the chromosomes provide strong evidence that lack of RNA highly binding segments may be a cause of X-chromosome inactivation. Key works: X-chromosome inactivation; intron RNA; DNA sequence composition; nucleotide string; Introduction Among placental mammals, the basic features of X-chromosome inactivation (XCI) are well established (BAILEY et al. 2000, OKAMOTO et al. 2000). XCI is the distinct difference between X-chromosome and autosomes. One of the two X-chromosomes of females becomes transcriptionally inactive in every cell of the early embryo and remains so in all somatic cells throughout life (COHEN and LEE 2002). This process serves to maintain the correct dosage relationship of genes between females (XX) and males (XY). As for mechanism of the X inactivation, Xist has been shown by transgenic and knockout experiments in mice to play a pivotal role in initiating X inactivation (KELLEY and KUROD 2000). The 21.4 kb chicken lysozyme (cLys) chromatin domain was inserted into X-chromosome. The gene was expressed normally from the active X, but not resistant to XCI (CHONG et al. 2002). These works seem to provide evidences that Xist gene induces XCI. If autosomal segments are attached to the X chromosome by translocation, XCI signal can spread for long distances into the autosome, (White et al 1998). However, spread into autosomal material extends less far and is less effective in gene silencing than in the X chromosome itself (White et al 1998, Rastan 1983, SOLARI et al. 2001). Thus, there is a barrier to the spreading effect of X-chromosome inactivation. The studies of gene expression in ICF female provide the examples of abnormal escape from X-chromosome inactivation in fibroblasts while Xist RNA localization is normal in these cells (HANSEN et al. 2000). Once XCI has been established, it is epigenetically inherited even if Xist is removed (BROWN and WILLARD 1994). These results argue against an independent silencing role for this RNA in somatic cells. The majority of the genome is represented by repetitive sequences and nonprotein-coding sequences (Makalowski 2001). Why so many noncoding nucleotides? Zuckerkandl proposes that