CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families
CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families
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DOI：
10.1016/s0378-1119(98)00474-0
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发表时间：
1998-12-11
期刊：
影响因子：
3.5
通讯作者：
Bernardi, G
中科院分区：
文献类型：
--
作者：
Jabbari, K;Bernardi, G
对946个大于50kb、代表约118Mb DNA的人类DNA序列进行了计算机分析，得出了以下观察结果。(I)CpG水平与等位基因和编码序列的GC水平之间存在正相关，正如先前的结果所预期的那样。(Ii)假基因的CpG水平和GC水平之间的相关性特征是CpG值较低(在可比的GC水平上)，并且与编码序列的相关性相比斜率较低；这一发现表明CpG二联体发生了广泛的甲基化，随后是脱氨基，导致CpG进一步短缺。(3)在人类长序列中，CpG岛的频率随着GC的增加而增加，并且几乎平行于基因频率。(4)Alu序列的频率也随着GC的增加而增加，但在H2等温线上达到最大值，与以前的实验数据一致。(V)5mC/CpG比率(即可用位点上的甲基化水平)随等物质GC水平的增加而降低。这种下降在很小程度上是由于富含GC的等值线中(未甲基化的)CpG岛的增加，并且尽管富含GC的等值线中强甲基化的Alu序列增加，但这种下降还是发生的；这强调了位于富含GC的等值线中的单拷贝序列的相对甲基化(5mC/CpG)比位于贫GC的等值线中的单拷贝序列的相对甲基化程度要低得多。(6)AlU岛和CpG岛的CpG水平与其所在长层序的GC水平呈正相关。(Vii)Alus岛和CpG岛的CpG水平都随着GC水平的升高而增加。(C)1998 Elsevier Science B.V.保留所有权利。
A computer analysis of 946 human DNA sequences larger than 50 kb and representing about 118 Mb of DNA has led to the following observations. (i) Positive correlations hold between CpG levels and the GC levels of isochores and coding sequences, as expected from previous results. (ii) The correlation between CpG levels and the GC levels of pseudogenes is characterized by lower CpG values (at comparable GC levels) and by a lower slope compared with the correlation with coding sequences; this finding suggests that an extensive methylation followed by deamination has taken place on CpG doublets from inactive genes leading to a further CpG shortage. (iii) The frequency of CpG islands in long human sequences increases with increasing GC and almost parallels gene frequency. (iv) The frequency of Alu sequences also increases with increasing GC, but attains a maximum in H2 isochores, in agreement with previous experimental data. (v) The ratio 5mC/CpG (namely, the methylation level over available sites) decreases with increasing GC levels of isochores. This decrease is due only to a small extent to the increase of (unmethylated) CpG islands in GC-rich isochores, and takes place in spite of the increase of strongly methylated Alu sequences in GC-rich isochores; this stresses the much lower relative methylation (5mC/CpG) of single-copy sequences located in GC-rich isochores relative to those located in GC-poor isochores. (vi) CpG levels of Alus and CpG islands are positively correlated with the GC levels of the long sequences in which they are located. (vii) The CpG levels of both Alus and CpG islands increase with their GC levels. (C) 1998 Elsevier Science B.V. All rights reserved.