Evolution of Conserved Non-Coding Sequences Within the Vertebrate Hox Clusters Through the Two-Round Whole Genome Duplications Revealed by Phylogenetic Footprinting Analysis
As a result of two-round whole genome duplications, four or more paralogous Hox clusters exist in vertebrate genomes. The paralogous genes in the Hox clusters show similar expression patterns, implying shared regulatory mechanisms for expression of these genes. Previous studies partly revealed the expression mechanisms of Hox genes. However, cis-regulatory elements that control these paralogous gene expression are still poorly understood. Toward solving this problem, the authors searched conserved non-coding sequences (CNSs), which are candidates of cis-regulatory elements. When comparing orthologous Hox clusters of 19 vertebrate species, 208 intergenic conserved regions were found. The authors then searched for CNSs that were conserved not only between orthologous clusters but also among the four paralogous Hox clusters. The authors found three regions that are conserved among all the four clusters and eight regions that are conserved between intergenic regions of two paralogous Hox clusters. In total, 28 CNSs were identified in the paralogous Hox clusters, and nine of them were newly found in this study. One of these novel regions bears a RARE motif. These CNSs are candidates for gene expression regulatory regions among paralogous Hox clusters. The authors also compared vertebrate CNSs with amphioxus CNSs within the Hox cluster, and found that two CNSs in the HoxA and HoxB clusters retain homology with amphioxus CNSs through the two-round whole genome duplications.
KeywordsHox cluster Two-round whole genome duplications Conserved non-coding sequences Phylogenetic footprinting Retinoic acid response element Amphioxus
The authors thank Drs. Kiyoshi Ezawa, Hiroki Kokubo, Kazuho Ikeo, Toshihiko Shiroishi, and Hiroyuki Sasaki for their many helpful discussions, suggestions, and comments. The authors appreciate English polishing by Ms Rumiko Suzuki, Ms Mahoko Takahashi, and Mr. Tim Jinam. This study was supported partly by The Graduate University for Advanced Studies (Sokendai) to M.M. and by Grant-in-Aid for scientific research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan to N.S.
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