Discovery of tissue-specific exons using comprehensive human exon microarrays.
BACKGROUND
Higher eukaryotes express a diverse population of messenger RNAs generated by alternative splicing. Large-scale methods for monitoring gene expression must adapt in order to accurately detect the transcript variation generated by this splicing.


RESULTS
We have designed a high-density oligonucleotide microarray with probesets for more than one million annotated and predicted exons in the human genome. Using these arrays and a simple algorithm that normalizes exon signal to signal from the gene as a whole, we have identified tissue-specific exons from a panel of 16 different normal adult tissues. RT-PCR validation confirms approximately 86% of the predicted tissue-enriched probesets. Pair-wise comparisons between the tissues suggest that as many as 73% of detected genes are differentially alternatively spliced. We also demonstrate how an inclusive exon microarray can be used to discover novel alternative splicing events. As examples, 17 new tissue-specific exons from 11 genes were validated by RT-PCR and sequencing.


CONCLUSIONS
In conjunction with a conceptually simple algorithm, comprehensive exon microarrays can detect tissue-specific alternative splicing events. Our data suggest significant expression outside of known exons and well annotated genes and a high frequency of alternative splicing events. In addition, we identified and validated a number of novel exons with tissue-specific splicing patterns. The tissue map data will likely serve as a valuable source of information on the regulation of alternative splicing.
Clark
Tyson A
TA
Affymetrix, Inc, Santa Clara, CA 95051, USA. tyson_clark@affymetrix.com
Schweitzer
Anthony C
AC
Chen
Tina X
TX
Staples
Michelle K
MK
Lu
Gang
G
Wang
Hui
H
Williams
Alan
A
Blume
John E
JE
D000465:Algorithms; D017398:Alternative Splicing; D001921:Brain / Q000378:metabolism; D005091:Exons; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000378:metabolism
D012333:RNA, Messenger