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首页> 外文期刊>BMC Genomics >Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6
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Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6

机译：通过从牛染色体6的确定区域挖掘基因组DNA发现新的转录本

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Background Linkage analyses strongly suggest a number of QTL for production, health and conformation traits in the middle part of bovine chromosome 6 (BTA6). The identification of the molecular background underlying the genetic variation at the QTL and subsequent functional studies require a well-annotated gene sequence map of the critical QTL intervals. To complete the sequence map of the defined subchromosomal regions on BTA6 poorly covered with comparative gene information, we focused on targeted isolation of transcribed sequences from bovine bacterial artificial chromosome (BAC) clones mapped to the QTL intervals. Results Using the method of exon trapping, 92 unique exon trapping sequences (ETS) were discovered in a chromosomal region of poor gene coverage. Sequence identity to the current NCBI sequence assembly for BTA6 was detected for 91% of unique ETS. Comparative sequence similarity search revealed that 11% of the isolated ETS displayed high similarity to genomic sequences located on the syntenic chromosomes of the human and mouse reference genome assemblies. Nearly a third of the ETS identified similar equivalent sequences in genomic sequence scaffolds from the alternative Celera-based sequence assembly of the human genome. Screening gene, EST, and protein databases detected 17% of ETS with identity to known transcribed sequences. Expression analysis of a subset of the ETS showed that most ETS (84%) displayed a distinctive expression pattern in a multi-tissue panel of a lactating cow verifying their existence in the bovine transcriptome. Conclusion The results of our study demonstrate that the exon trapping method based on region-specific BAC clones is very useful for targeted screening for novel transcripts located within a defined chromosomal region being deficiently endowed with annotated gene information. The majority of identified ETS represents unknown noncoding sequences in intergenic regions on BTA6 displaying a distinctive tissue-specific expression profile. However, their definite regulatory function has to be analyzed in further studies. The novel transcripts will add new sequence information to annotate a complete bovine genome sequence assembly, contribute to establish a detailed transcription map for targeted BTA6 regions and will also be helpful to dissect of the molecular and regulatory background of the QTL detected on BTA6.
机译：背景连锁分析强烈建议在牛染色体6（BTA6）的中部产生一些有关生产，健康和构象特征的QTL。鉴定QTL遗传变异基础的分子背景和随后的功能研究需要关键QTL间隔的注解基因序列图。为了完成BTA6上定义的亚染色体区域的序列图，该序列很难被比较基因信息覆盖，我们集中于从定位到QTL间隔的牛细菌人工染色体（BAC）克隆中有针对性地分离转录序列。结果采用外显子诱捕方法，在基因覆盖率较差的染色体区域发现了92个独特的外显子诱捕序列（ETS）。对于91％的独特ETS，检测到与BTA6当前NCBI序列装配的序列同一性。比较序列相似性搜索显示11％的分离的ETS与位于人和小鼠参考基因组组装体同系染色体上的基因组序列显示出高度相似性。从人类基因组的另一种基于Celera的序列装配中，近三分之一的ETS在基因组序列支架中鉴定出相似的等效序列。筛选基因，EST和蛋白质数据库可检测到17％的ETS，且与已知的转录序列相同。 ETS子集的表达分析表明，大多数ETS（84％）在泌乳母牛的多组织面板中显示出独特的表达模式，验证了它们在牛转录组中的存在。结论我们的研究结果表明，基于区域特异性BAC克隆的外显子诱集方法对于靶向筛选在已知基因信息不足的限定染色体区域内的新型转录本的靶向筛选非常有用。大部分鉴定出的ETS代表BTA6基因间区域中未知的非编码序列，显示出独特的组织特异性表达谱。但是，它们的确定的调节功能必须在进一步的研究中进行分析。新的转录本将增加新的序列信息，以注释完整的牛基因组序列装配，有助于建立针对靶BTA6区域的详细转录图，还将有助于剖析在BTA6上检测到的QTL的分子和调控背景。

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