Rowsell Joanna, da Silva Camargo Renata, Langdon William B, Stalteri Maria A, Harrison Andrew P
Departments of Biological and Mathematical Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
J Integr Bioinform. 2010 Mar 25;7(3):460. doi: 10.2390/biecoll-jib-2010-137.
A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras.
We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression Omnibus. We show that for six probe sets, a unique probe mapping to a transcript produced by one of the adjacent genes can be used to identify the expression patterns of readthrough transcripts. Furthermore, unique probes mapping to an intergenic exon present only in the MASK-BP3 chimera can be used directly to study the expression levels of this transcript.
We have attempted to implement a new method for identifying tandem chimerism. In this analysis unambiguous probes are needed to measure run-off transcription and probes that map to intergenic exons are particularly valuable for identifying the expression of chimeras.
嵌合转录本是一种单一RNA序列，由两个相邻基因转录产生。最近的研究估计，至少4%的串联人类基因对可能形成嵌合转录本。Affymetrix基因芯片数据用于研究数万个基因的表达模式，这些微阵列中使用的探针序列可能会映射到外来RNA序列，如嵌合体。
我们研究了人类嵌合体，并使用从基因表达综合数据库获得的大量Affymetrix微阵列数据调查了它们的表达模式。我们表明，对于六个探针集，一个映射到由相邻基因之一产生的转录本的独特探针可用于识别通读转录本的表达模式。此外，映射到仅存在于MASK-BP3嵌合体中的基因间外显子的独特探针可直接用于研究该转录本的表达水平。
我们尝试实施一种识别串联嵌合现象的新方法。在该分析中，需要明确的探针来测量延伸转录，而映射到基因间外显子的探针对于识别嵌合体的表达特别有价值。
