Numata Koji, Okada Yuki, Saito Rintaro, Kiyosawa Hidenori, Kanai Akio, Tomita Masaru
Graduate School of Media and Governance, Bioinformatics Program, Keio University, Fujisawa, 252-8520, Japan.
Gene. 2007 May 1;392(1-2):134-41. doi: 10.1016/j.gene.2006.12.005. Epub 2006 Dec 13.
Recent large-scale transcriptomic analyses have identified numerous endogenously encoded cis-antisense RNAs that are thought to play important roles in diverse cellular processes although comprehensive comparative studies among multiple species have yet to be performed. To investigate conserved genomic features across various species that may be related to sense-antisense regulation, we performed comparative analysis of approximately 1000-2000 cis-encoded antisense RNA pairs from five model eukaryotes (Homo sapiens, Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, and Oryza sativa). Analysis of overlapping patterns relative to the exon-intron structure revealed that the number of pairs sharing the 3' part of the transcripts was larger than that of the 5'-sharing pairs except in rice. Moreover, most of the well-conserved sense-antisense pairs between human and mouse exhibited 3'-overlaps, suggesting that regulatory mechanisms involving these regions may be important in sense-antisense transcription. Functional classification using Gene Ontology revealed that genes related to catalytic activity, nucleotide binding, DNA metabolism, and mitochondria were preferentially distributed within the set of exon-overlapping sense-antisense genes compared to the non-exon-overlapping group in animals. Despite the numerous sense-antisense pairs identified in human and mouse individually, the number of conserved pairs was extremely small (6.6% of the entire set). Whereas both genes of most of the conserved sense-antisense pairs had protein-coding potential, nearly half of the non-conserved pairs included a non-coding RNA, suggesting that non-coding sense-antisense RNAs may function in species-specific regulatory pathways.
最近的大规模转录组分析已经鉴定出许多内源性编码的顺式反义RNA，尽管尚未在多个物种之间进行全面的比较研究，但这些RNA被认为在多种细胞过程中发挥重要作用。为了研究可能与正义-反义调控相关的不同物种间保守的基因组特征，我们对来自五种模式真核生物（智人、小家鼠、黑腹果蝇、拟南芥和水稻）的大约1000-2000个顺式编码反义RNA对进行了比较分析。相对于外显子-内含子结构的重叠模式分析表明，除水稻外，共享转录本3'部分的RNA对数量多于共享5'部分的RNA对。此外，人类和小鼠之间大多数保守的正义-反义RNA对表现出3'重叠，这表明涉及这些区域的调控机制在正义-反义转录中可能很重要。使用基因本体进行的功能分类显示，与非外显子重叠组相比，动物中外显子重叠的正义-反义基因集中优先分布着与催化活性、核苷酸结合、DNA代谢和线粒体相关的基因。尽管在人类和小鼠中分别鉴定出了大量的正义-反义RNA对，但保守的RNA对数量极少（占整个集合的6.6%）。大多数保守的正义-反义RNA对的两个基因都具有蛋白质编码潜力，而近一半的非保守RNA对包含一个非编码RNA，这表明非编码正义-反义RNA可能在物种特异性调控途径中发挥作用。
