Koyanagi Kanako O, Hagiwara Masato, Itoh Takeshi, Gojobori Takashi, Imanishi Tadashi
Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido 060-0814, Japan.
Gene. 2005 Jul 4;353(2):169-76. doi: 10.1016/j.gene.2005.04.027.
Arrangement of genes in the human genome was not considered to be ordered like those of prokaryotes, as in many cases genes appeared to be randomly distributed across the genome. However, by focusing on the closely located adjacent gene pairs, it was recently suggested that the bidirectional pairs were enriched in the human genome and these pairs tended to be coexpressed by sharing promoter sequences. We compared this biased organization found in the human genome with those in the genomes of nine other eukaryotes to reveal when and how the biased organization had evolved using a total of 122,945 adjacent gene pairs. As a result, we found that the biased organization was found only in mammals, and not in other eukaryotes. Interestingly, we found that many of these genes in the bidirectional arrangement were not mammalian specific genes but conserved among various animals. Further analyses revealed that the bidirectional arrangement of these pairs had arisen by utilizing already-existing genes in the lineage leading to mammals recently, no earlier than the vertebrate-ascidian divergence. Since the novel bidirectional arrangement could result in novel co-regulated transcription, our results here provide evidence that shows how a transcriptional regulation system has evolved through changes in the genome organization, especially in the lineage leading to humans.
人类基因组中的基因排列并不像原核生物那样有序，因为在许多情况下，基因似乎是随机分布在整个基因组中的。然而，通过关注紧密相邻的基因对，最近有人提出双向基因对在人类基因组中富集，并且这些基因对倾向于通过共享启动子序列而共表达。我们将在人类基因组中发现的这种偏向性组织与其他九种真核生物基因组中的情况进行了比较，使用总共122,945对相邻基因对来揭示这种偏向性组织是何时以及如何进化的。结果，我们发现这种偏向性组织仅在哺乳动物中存在，而在其他真核生物中不存在。有趣的是，我们发现这些双向排列中的许多基因并非哺乳动物特有的基因，而是在各种动物中保守的。进一步的分析表明，这些基因对的双向排列是通过利用导致哺乳动物的谱系中已经存在的基因而产生的，最近不早于脊椎动物-海鞘分歧。由于这种新的双向排列可能导致新的共同调控转录，我们在此的结果提供了证据，表明转录调控系统是如何通过基因组组织的变化，特别是在导致人类的谱系中，而进化的。
