Exon arrays

Recently, Affymetrix also launched their exon arrays (i.e., arrays that use multiple probes to target essentially every exon of each transcript variant). This platform is the most detailed for analysis of gene expression levels, and it allows for identification of alternative splicing in addition to the standard genome-wide transcriptional analysis. 

Under the Affymetrix trademark, three hybridization assays can be found that generate three types of whole-genome arrays for expression analysis the 3 -IVT array, the gene array, and the exon array. Figure 3 illustrates the... 

The microarray consists of small DNA fragments, chemically synthesized at specific locations on a coated quartz surface. The number of locations on one array is in the range of millions. DNA is extracted and labeled from experimental samples, and then samples are hybridized on the array. Labels are monitored so that gene- and exon-level expression analysis, novel transcript discovery, genotyping, and resequencing can be carried out. 

Transcript discovery Find transcripts (genes) in genomic sequence In these experiments, arrays are made from genomic DNA sequences, rather than from complementary DNAs (cDNAs). Such studies can be used to confirm computational gene predictions and characterize alternative splicing and die boundaries of exons (DNA sequences destined to become part of die mature messenger RNA [mRNA]). 

Fig. 2. (A) Analysis of human adult skeletal (HAS) and cardiac muscle (HAC) transcripts by an oligonucleotide array representing all 363 exons of the human titin gene. Left Comparison of results obtained with HAS (top) and HAC (bottom) transcripts reveals large blocks of exons that are only positive in skeletal muscle. Right Examples of constitutively expressed exons (exon 5 and 7), cardiac specific exons (11 and 49), and skeletal muscle specific exons (156 and 210). 5MM a 50mer from exon 5 including five base-pair mismatches as a control for hybridization...

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