Detection and analysis of spliced chimeric mRNAs in sequence databanks
Detection and analysis of spliced chimeric mRNAs in sequence databanks
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DOI：
10.1093/nar/gng017
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发表时间：
2003-02-15
影响因子：
14.9
通讯作者：
Alberti, S
中科院分区：
文献类型：
--
作者：
Romani, A;Guerra, E;Alberti, S
我们已经开发了一个数据库筛选程序，在Silico反式剪接检索系统（ISTRes），以确定异源，剪接的mRNA与潜在的来源于染色体易位，mRNA反式剪接和多位点转录。实现了用于筛选cDNA与基因组Blast输出的解析算法。关键的筛选标准是Blast评分大于或等于300，查询序列的匹配长度大于或等于95%，外显子-外显子边界处两个配对物的连接和一致的“有义/有义”阅读方向。通过在HGI和RefSeq数据库中成功鉴定真正的染色体易位衍生的融合转录物来验证ISTRes。针对最近鉴定的嵌合反义转录物验证了ISTRes的性能，其中它基本上没有揭示反义转录的独立证据，并且在嵌合接合处不存在外显子-外显子边界，这与人为来源一致。对UNIGENE数据库的分析显示，总共有21742个嵌合序列，相当于数据库转录本的1%。在来自RefSeq数据库的246个嵌合体中鉴定了具有异源基因剪接转录物的典型特征的新型FOP-Rho GAP和甲硫氨酰tRNA合成酶-advillin嵌合mRNA。这表明，在目前的数据库中，典型剪接嵌合体的频率约为所有杂交序列的1%。这些发现证明了ISTRes的效率和基于序列/结构的策略的整体可行性，以搜索嵌合mRNA候选人，从剪接异源转录。
We have developed a databank screening procedure, the In Silico Trans-splicing Retrieval System (ISTReS), to identify heterologous, spliced mRNAs with potential origin from chromosomal translocations, mRNA trans-splicing and multi-locus transcription. A parsing algorithm to screen cDNA versus genome Blast outputs was implemented. Key filtering criteria were Blast scores of greater than or equal to300, match lengths of greater than or equal to95% of the query sequences, junction of the two partners at exon-exon borders and concordant 'sense/sense' reading orientation. ISTReS was validated by the successful identification of bona fide chromosomal translocation-derived fusion transcripts in the HGI and RefSeq databanks. The performance of ISTReS was verified against recently identified chimeric antisense transcripts, where it revealed essentially no independent proof of antisense transcription and absence of exon-exon borders at the chimeric join, consistent with an artefactual origin. Analysis of the UNIGENE database revealed 21 742 chimeric sequences overall that correspond to similar to1% of the database transcripts. Novel FOP-Rho GAP and methionyl tRNA synthetase-advillin chimeric mRNAs with the canonical features of heterologous-genes spliced-transcripts were identified among 246 chimeras from the RefSeq databank. This suggests a frequency of canonically-spliced chimeras of similar to1% of all the hybrid sequences in current databanks. These findings demonstrate the efficiency of ISTReS and the overall feasibility of sequence/structure-based strategies to search for chimeric mRNAs candidate to derive from the splicing of heterologous transcripts.