Li Zhan-Jun, Song Shu-Xia, Zhai Yu, Hou Jie, Han Li-Zhi, Wang Xiu-Fang
Department of Laboratory Animal, Hebei Medical University, Shijiazhuang 050017, China.
Yi Chuan Xue Bao. 2005 Jan;32(1):1-10.
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.
在Xp上检测的基因中有30%逃避了失活，而Xq上只有不到3%的基因逃避了失活。为了研究X染色体失活和逃避的传播与维持所涉及的分子机制，对X染色体的长臂和短臂进行了RNA结合密度的比较。X染色体上的核苷酸序列被分成每段50 kb，并使用所有可能的7核苷酸（7 nt）序列（4⁷ = 16384）记录为一组7核苷酸序列的频率值。选择在扁桃体生发中心B细胞中高表达的120个基因来计算所有内含子的7核苷酸序列频率值（内含子7 nt）。内含子7 nt被视为模拟细胞中小RNA片段总和的RNA（RNA群体）。知道了DNA片段的7 nt频率值和内含子7 nt，我们就可以计算DNA片段与内含子7 nt的结合密度，即RNA结合密度。RNA结合密度由互补序列的数量决定。互补序列数量越多，RNA结合密度越高。RNA结合密度模拟了与DNA片段结合的小RNA片段的总和。首次观察到几个主要特征：（1）Xp上DNA片段的RNA结合密度平均值显著高于Xq上的（P < 0.001）；（2）与RNA高度结合的DNA片段数量在Xp上比在Xq上更多（P < 0.001）；（3）与RNA高度结合的DNA片段簇与基因逃避失活的区域相关。有人提出，RNA可激活基因，细胞中RNA与DNA的相互作用广泛，例如，RNA可增加DNA对DNase I的敏感性，细胞中有大量非蛋白质编码RNA，DNA与RNA的结合特异性远高于DNA与蛋白质的结合特异性，且与DNA相比，DNA与RNA的亲和力增加。Xp和Xq之间RNA高度结合片段分布的非随机特性，结合RNA激活基因的发现，有力地证明了RNA高度结合片段可能作为DNA信号沿染色体传播激活，反之，与RNA结合较少的DNA片段可能使基因沉默。
