Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips.
BACKGROUND
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.


RESULTS
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.


CONCLUSIONS
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.
Rowsell
Joanna
J
Departments of Biological and Mathematical Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
da Silva Camargo
Renata
R
Langdon
William B
WB
Stalteri
Maria A
MA
Harrison
Andrew P
AP
D015342:DNA Probes / Q000378:metabolism; D003625:Data Collection; D005091:Exons / Q000235:genetics; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics*; D014158:Transcription, Genetic
D015342:DNA Probes; D012333:RNA, Messenger