Relationship between gene expression and GC-content in mammals:: statistical significance and biological relevance
Relationship between gene expression and GC-content in mammals:: statistical significance and biological relevance
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DOI：
10.1093/hmg/ddi038
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发表时间：
2005-02-01
影响因子：
3.5
通讯作者：
Duret, L
中科院分区：
文献类型：
--
作者：
Sémon, M;Mouchiroud, D;Duret, L
哺乳动物染色体的特征是DNA碱基组成的大规模变化（所谓的等染色体）。与以前的研究相矛盾，Lercher et al.（2005）。摩尔Genet.，12，2411，2003）最近报道了基因表达宽度和GC含量之间的强相关性，表明可能存在有利于管家基因在富含GC的等着丝粒中集中的选择压力。我们重新评估了这个问题，在人类和小鼠的基因表达和GC含量之间的相关性，使用不同的基因表达的措施（EST，SAGE和微阵列）和GC含量的不同措施。我们发现，GC含量和表达之间的相关性是非常弱的，并可能会有所不同，根据所使用的方法来测量表达。这种弱相关性具有非常低的预测价值。Lercher等人（2003）报告的强相关性是因为他们测量了相邻基因窗口上的变量。我们在这里表明，使用基因窗口人为地增强了相关性。因此，数据不支持给定基因的表达取决于其所在区域的GC含量的说法。
Mammalian chromosomes are characterized by large-scale variations of DNA base composition (the so-called isochores). In contradiction with previous studies, Lercher et al. (Hum. Mol. Genet., 12, 2411, 2003) recently reported a strong correlation between gene expression breadth and GC-content, suggesting that there might be a selective pressure favoring the concentration of housekeeping genes in GC-rich isochores. We reassessed this issue by examining in human and mouse the correlation between gene expression and GC-content, using different measures of gene expression (EST, SAGE and microarray) and different measures of GC-content. We show that correlations between GC-content and expression are very weak, and may vary according to the method used to measure expression. Such weak correlations have a very low predictive value. The strong correlations reported by Lercher et al. (2003) are because of the fact that they measured variables over neighboring genes windows. We show here that using gene windows artificially enhances the correlation. The assertion that the expression of a given gene depends on the GC-content of the region where it is located is therefore not supported by the data.