Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes
Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes
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DOI：
10.1016/j.gene.2005.07.027
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发表时间：
2005-12-30
期刊：
影响因子：
3.5
通讯作者：
Gotoh, O
中科院分区：
文献类型：
--
作者：
Nagasaki, H;Arita, M;Gotoh, O
在基因组测序已完成或接近完成的六种真核生物（人类、小鼠、果蝇、线虫、拟南芥和水稻）中进行了可变剪接和转录起始（ASTI）的全基因组检测。通过将一批全长cDNA序列映射到相应的同源基因组序列上来收集转录异构体。对映射在同一基因位点上的异构体进行两两比较，将ASTI模式分割成最小跨度，然后将最小模式（ASTI单元）分类为独特的类型，如盒式类型或可变供体位点类型。所有这些程序在相同条件下自动执行，以便能够直接比较从不同物种获得的结果。在所有映射的位点中，经历ASTI的位点比例在哺乳动物和果蝇中最大，在植物中最小。在每个物种中发现的独特ASTI类型数量也呈现出完全相同的趋势。在进化上相近的物种，如人类和小鼠或拟南芥和水稻之间，观察到的ASTI类型的比例表示相似。另一方面，在进化上距离较远的物种，如哺乳动物和植物之间，单个ASTI类型的丰度相对顺序有很大差异。在人类和小鼠中，除保留内含子之外的可变剪接倾向于发生在蛋白质编码序列（CDS）区域内，而不是在非翻译区域（UTRs）内，而在其他四个物种中这种倾向不明显。在所有检测的物种中，可变外显子长度的差异极有可能是3的倍数，并且当可变外显子嵌入CDS内时这种趋势最为显著。这些观察结果总体上与以下观点一致：高等生物比低等生物更广泛、更复杂地利用ASTI机制，并且ASTI积极参与增强基因组上有限数量基因所产生产物的功能和结构多样性。（C）2005 Elsevier B.V.保留所有权利。
The genome-wide detection of alternative splicing and transcriptional initiation (ASTI) was conducted in six eukaryotes (human, mouse, fruit fly, nematode, cress and rice) whose genome sequencing has been completed or nearly completed. Transcriptional isoforms were collected by mapping a batch of full-length cDNA sequences onto the respective cognate genomic sequences. Isoforms mapped on the same gene locus were compared pair-wise, ASTI patterns were segmented into minimal spans, and then the minimal patterns (ASTI units) were classified into unique types, such as the cassette type or the alternative donor site. All these procedures were performed automatically under the same conditions so that the results obtained from different species could be compared directly. The fraction of loci that underwent ASTI of the total mapped loci was the largest for mammals and fruit fly, and the smallest for plants. Exactly the same trend was observed for the number of unique ASTI types found in each species. The observed fractional representations of the ASTI types were similar between evolutionarily close species, such as human and mouse or cress and rice. On the other hand, the relative orders of abundance in individual ASTI type were considerably different between evolutionarily distant species, such as between mammals and plants. In human and mouse, alternative splicing other than the retained introns tended to occur within the protein coding sequence (CDs) regions rather than within the untranslated regions (UTRs), whereas this tendency was obscure in the other four species. In all the species examined, the difference in alternative exon lengths was most likely in multiples of three, and this tendency was most prominent when the alternative exons were embedded within the CDSs. These observations are generally consistent with the idea that higher organisms utilize the ASTI mechanisms more extensively and in a more complicated manner than lower organisms, and that ASTI actively participates in the enhancement of the functional and structural diversity of products generated from a limited number of genes on a genome. (C) 2005 Elsevier B.V. All rights reserved.