Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment
Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment
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DOI：
10.1038/sj.onc.1207362
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发表时间：
2004-04-15
期刊：
影响因子：
8
通讯作者：
Hu, GX
中科院分区：
文献类型：
--
作者：
Hui, LJ;Zhang, X;Hu, GX
已经发表了几个数据库，通过将表达序列标签(EST)与基因组序列比对来分析外显子连锁关系来预测mRNAs的选择性剪接；然而，很少有人致力于研究癌症和选择性剪接之间的关系。我们开发了一个程序，选择性剪接装配器(ASA)，通过全基因组EST比对来寻找人类基因转录本的剪接变体。使用ASA，我们构建了Biosino选择性剪接数据库(BASD)，该数据库从参考序列数据库(RefSeq)预测参考序列的剪接变体，并以图形和文本的形式呈现它们。至少一个剪接位点上与参考序列不同的EST簇被算作剪接变体。在筛选的4322个基因中，3490个(81%)至少有一个可供选择的剪接变体。为了发现与癌症相关的变异，从UniLib数据库中提取了EST序列的组织来源，并对相同组织类型的EST进行了计数。将其作为基因表达水平的指标。利用Fisher‘s Exact检验，确定了可供选择的剪接变体，其中EST计数在癌组织和相应的正常组织之间存在显著差异。据预测，26812个变异体中有2149个变异体，或在Bonferroni校正后的383个变异体可能与肿瘤相关。通过逆转录-聚合酶链式反应，13个新的选择性剪接变异体中的11个和9个变异体中的8个在肝细胞癌和肺癌中被证实具有组织特异性。文中还讨论了选择性剪接在癌症中的可能作用。
Several databases have been published to predict alternative splicing of mRNAs by analysing the exon linkage relationship by alignment of expressed sequence tags (ESTs) to the genome sequence; however, little effort has been made to investigate the relationship between cancers and alternative splicing. We developed a program, Alternative Splicing Assembler (ASA), to look for splicing variants of human gene transcripts by genome-wide ESTs alignment. Using ASA, we constructed the biosino alternative splicing database (BASD), which predicted splicing variants for reference sequences from the reference sequence database (RefSeq) and presented them in both graph and text formats. EST clusters that differ from the reference sequences in at least one splicing site were counted as splicing variants. Of 4322 genes screened, 3490 (81%) were observed with at least one alternative splicing variants. To discover the variants associated with cancers, tissue sources of EST sequences were extracted from the UniLib database and ESTs from the same tissue type were counted. These were regarded as the indicators for gene expression level. Using Fisher's exact test, alternative splicing variants, of which EST counts were significantly different between cancer tissues and their counterpart normal tissues, were identified. It was predicted that 2149 variants, or 383 variants after Bonferroni correction, of 26 812 variants were likely tumor-associated. By reverse transcription-PCR, 11 of 13 novel alternative splicing variants and eight of nine variants' tissue specificity were confirmed in hepatocelluar carcinoma and in lung cancer. The possible involvement of alternative splicing in cancer is discussed.