STATISTICAL-ANALYSIS OF VERTEBRATE SEQUENCES REVEALS THAT LONG GENES ARE SCARCE IN GC-RICH ISOCHORES
STATISTICAL-ANALYSIS OF VERTEBRATE SEQUENCES REVEALS THAT LONG GENES ARE SCARCE IN GC-RICH ISOCHORES
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DOI：
10.1007/bf00163235
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发表时间：
1995-03-01
影响因子：
3.9
通讯作者：
GAUTIER, C
中科院分区：
文献类型：
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作者：
DURET, L;MOUCHIROUD, D;GAUTIER, C
我们比较了属于不同等差类别的脊椎动物基因的外显子/内含子组织，并通过它们在第三密码子位置的GC含量来预测。从GenBank上发表的序列分析中发现了两个主要特征：(1)编码长蛋白（即大于或等于500 aa）的基因在gc -贫同位异构体中的频率几乎是gc -富同位异构体的两倍；(2) GC-poor的中间序列（=内含子的总和）平均比GC-rich的同工长3倍。这些模式在人类、小鼠、大鼠、奶牛甚至鸡的基因中都可以观察到，因此可能对所有温血脊椎动物都是共同的。对非洲爪蟾序列的分析表明，同样的模式也存在于冷血脊椎动物中。可以认为，这样的结果并不能反映现实，因为序列数据库并不能代表整个基因组。然而，对GenBank的偏差分析显示，观察到的GC-rich和GC-poor等异数之间的差异并不是人为的，而且可能在很大程度上被低估了。我们研究了人类和小鼠不同等位基因内含子的微卫星和穿插重复序列的分布。该分析证实了先前的研究表明，在富含gc的同工中几乎不存在L1重复序列。微卫星和正弦信号（Alu, B1, B2）在所有等差类内含子中发现的频率大致相同。在全球范围内，重复序列的存在并不能解释GC-poor同工中内含子长度的增加。讨论了基因结构与全球基因组组织和进化的关系。
We compared the exon/intron organization of vertebrate genes belonging to different isochore classes, as predicted by their GC content at third codon position. Two main features have emerged from the analysis of sequences published in GenBank: (1) genes coding for long proteins (i.e., greater than or equal to 500 aa) are almost two times more frequent in GC-poor than in GC-rich isochores; (2) intervening sequences (=sum of introns) are on average three times longer in GC-poor than in GC-rich isochores. These patterns are observed among human, mouse, rat, cow, and even chicken genes and are therefore likely to be common to all warm-blooded vertebrates. Analysis of Xenopus sequences suggests that the same patterns exist in cold-blooded vertebrates. It could be argued that such results do not reflect the reality because sequence databases are not representative of entire genomes. However, analysis of biases in GenBank revealed that the observed discrepancies between GC-rich and GC-poor isochores are not artifactual, and are probably largely underestimated. We investigated the distribution of microsatellites and interspersed repeats in introns of human and mouse genes from different isochores. This analysis confirmed previous studies showing that L1 repeats are almost absent from GC-rich isochores. Microsatellites and SINES (Alu, B1, B2) are found at roughly equal frequencies in introns from all isochore classes. Globally, the presence of repeated sequences does not account for the increased intron length in GC-poor isochores. The relationships between gene structure and global genome organization and evolution are discussed.