TY - JOUR
T1 - Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system
AU - Koyanagi, Kanako O.
AU - Hagiwara, Masato
AU - Itoh, Takeshi
AU - Gojobori, Takashi
AU - Imanishi, Tadashi
PY - 2005/7/4
Y1 - 2005/7/4
N2 - 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.
AB - 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.
KW - Co-regulated transcription
KW - Genome organization
KW - Genome rearrangement
KW - Human genome
UR - http://www.scopus.com/inward/record.url?scp=21744443068&partnerID=8YFLogxK
U2 - 10.1016/j.gene.2005.04.027
DO - 10.1016/j.gene.2005.04.027
M3 - Article
C2 - 15944140
AN - SCOPUS:21744443068
SN - 0378-1119
VL - 353
SP - 169
EP - 176
JO - GENE
JF - GENE
IS - 2
ER -