A microarray configuration to quantify expression levels and relative abundance of splice variants.
Over the past decade, alternative RNA splicing has raised a great interest appearing to be of high importance in the generation of expression diversity. This regulatory process plays a critical role in the normal development and its impact on the initiation and development of human disorders as well as on the pharmacological properties of drugs is increasingly being recognized. Only few studies describe specific alternative splicing expression profiling. Microarray strategies have been conceived to address alternative splicing events but with very few experimental data related to their abilities to provide true quantification values. We have developed a specific microarray configuration relying on a few, well optimized probes per splice event. Basically, five probes of 24mer are used to fully characterize a splice event. These probes are of two types, exon probes and junction probes, and are either specific to a splice event or not. The performances of such a 'splice array' were validated on synthetic model systems and on complex biological materials. The results indicate that DNA chips based on this design combining exon and junction derived probes enable the detection and, absolute and relative quantification of splice variants. In addition, this strategy is compatible with all the microarrays that use oligonucleotide probes.
Fehlbaum
Pascale
P
ExonHit Therapeutics, 63/65 boulevard Masséna, 75013 Paris, France.
Guihal
Caroline
C
Bracco
Laurent
L
Cochet
Olivier
O
D017398:Alternative Splicing; D002460:Cell Line; D005091:Exons; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D007438:Introns; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000737:chemistry; D020033:Protein Isoforms / Q000032:analysis / Q000235:genetics
D015345:Oligonucleotide Probes; D020033:Protein Isoforms