Comparative analysis of cis-encoded antisense RNAs in eukaryotes
Comparative analysis of cis-encoded antisense RNAs in eukaryotes
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DOI：
10.1016/j.gene.2006.12.005
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发表时间：
2007-05-01
期刊：
影响因子：
3.5
通讯作者：
Tomita, Masaru
中科院分区：
文献类型：
--
作者：
Numata, Koji;Okada, Yuki;Tomita, Masaru
最近的大规模转录组学分析已经确定了许多内源性编码的顺式反义rna，这些rna被认为在不同的细胞过程中发挥重要作用，尽管尚未在多物种之间进行全面的比较研究。为了研究不同物种之间可能与正反义调控相关的保守基因组特征，我们对5种模式真核生物（智人、小家鼠、果蝇、拟南芥和水稻唾液）中大约1000-2000对顺式编码的反义RNA进行了比较分析。与外显子-内含子结构相关的重叠模式分析表明，除了水稻外，共享转录本3‘部分的配对数量大于共享5’部分的配对数量。此外，人类和小鼠之间大多数保守性良好的义-反义对都表现出3'-重叠，这表明涉及这些区域的调控机制可能在义-反义转录中很重要。利用基因本体进行功能分类发现，与非外显子重叠组相比，动物中与催化活性、核苷酸结合、DNA代谢和线粒体相关的基因优先分布在外显子重叠组的正反义基因中。尽管在人和小鼠中分别发现了大量的正反义对，但保守对的数量极少（占总数的6.6%）。尽管大多数保守的义-反义对的两个基因都具有编码蛋白质的潜力，但近一半的非保守对包含一个非编码RNA，这表明非编码义-反义RNA可能在物种特异性调控途径中起作用。(c) 2006 Elsevier B.V.版权所有
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 saliva). 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. (c) 2006 Elsevier B.V. All rights reserved.