人X染色体长臂(Xq)和短臂(Xp)基因组学比较分析

X染色体发生X染色体失活 ,但是Xp基因有 30 %表现为逃逸 ,而Xq仅不到 3%。为了研究X染色体基因失活和表达逃逸发生和维持的分子机制 ,比较了Xq和XpDNA序列的RNA模拟结合强度。X染色体的核苷酸序列被分为 5 0kb一段 ,对每一段DNA做 7碱基 (7nt)字符串组合分析 (共有 4 7=16 384种组合 ) ,记录每段 5 0kbDNA中每种 7nt字符串的频率。选择生发中心B细胞中的 12 0个高表达基因 ,计算这些基因的内含子 7nt字符串的出现频率 ,称为intron 7nt,以此作为RNAs(RNA群 ,模拟细胞中RNA在小片段的总和 )。已知一段DNA序列的 7nt频率值和intron 7nt,即可以计算该DNA段与intron 7nt的结合强度。每段 5 0kbDNA与intron 7nt的结合强度取决于该DNA段与intron 7nt互补核苷酸的频率 ,互补的核苷酸序列越多 ,结合强度就越大。DNA段与intron 7nt的模拟结合强度称为RNA结合强度 ,试图模拟该段DNA可以结合的RNA小片段的总量。之所以采用 7nt字符串组合分析是考虑到连续 7个核苷酸互补则可以形成相对稳定的结合。研究发现 :1)Xp各DNA段的RNA结合强度均值显著大于Xq (P <0 0 0 1) ;2 )Xp上高结合RNA的DNA段数目显著高于Xq (P <0 0 0 1) ;3)RNA高结合DNA段形成的簇与X染色体基因表达逃逸区关联。有证据表明 ,RNA可以通过改变染色质

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 (47=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 DNaseⅠsensitivity 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.