Alternative mRNA polyadenylation can potentially affect detection of gene expression by affymetrix genechip arrays

DNA microarrays have been widely used to examine gene expression. The Affymetrix GeneChip is one of the most commonly used platforms, employing DNA probes of 25 nucleotides designed to hybridise to different regions of target mRNA. The targeted region is often biased toward the 3' end of mRNA, which can lead to biases in detection. A large number of mammalian genes can undergo alternative polyadenylation under different cellular conditions. Multiple polyadenylation sites can lead to variable transcripts with different hybridisation properties. Here, we surveyed probes on human, mouse and rat GeneChip arrays and found that the detection of a significant proportion of mRNAs can potentially be affected by alternative polyadenylation. This could lead to inaccurate interpretation of GeneChip data when the changes of expression values actually result from alternative use of polyadenylation sites.