Background:

Alternative splicing (AS) is a post-transcriptional process whereby the introns and exons of a single gene transcript are differentially spliced to yield multiple mature mRNAs. In eukaryotes, AS plays a central role in both protein diversity and post-transcriptional gene regulation. AS within mRNA coding regions can lead to multiple, functionally diverse, protein isoforms from a single gene transcript. AS can also act to introduce or remove regulatory elements to affect the translation, localization or degradation properties of an mRNA. The majority of human genes are thought to undergo AS and current estimates range from a conservative 60%, to as high as 88%.

AS has vast implications in human disease: the proportion of genetic mutations implicating AS has grown steadily from a first estimate of 15% of all annotated genetic disease-causing mutations a decade ago. Well-known diseases attributed to defects in AS include cystic fibrosis, thallasemia, spinal muscular atrophy, and several forms of cancer. In spite of its imposing biological relevance, tissue specific annotation of AS is only in its infancy, and very little is known about the individual functions of AS isoforms

Platform services:

To address this, we have developed the LISA, (Layered and Integrated system for Splicing Annotation), a bioinformatics and experimental platform for high-throughput RT-PCR based annotation of AS in human tissues and cell lines. The system comprises automated in silico primer and PCR experiment design, high throughput execution of PCR reactions on human total cDNA, capillary electrophoretic quantitation of amplicons, data analysis and data filtering modules.

The LISA uses publicly available mRNA and EST-based transcript compilations as a starting point for the annotation process. All proposed events are classified by type and their existence and relative abundance are assessed in each RNA source. The system also allows the detection of novel AS events, and advanced user-defined database querying.

Services offered:

• High throughput RT-PCR validation of AS events
• Tissue specific AS event validation
• Microarray validation by RT-PCR
• Tumour/normal tissue differential screening
• Novel AS event discovery
• User-defined query based screening

Contact

Further information can be obtained at RNomics@lgfus.ca or by contacting:
Roscoe Klinck, Ph.D.
Director, RNomics Platform
Laboratoire de Génomique Fonctionnelle de l'Université de Sherbrooke
CDB de Sherbrooke
3201, rue Jean-Mignault
Sherbrooke, QC, Canada J1E 4K8
Telephone: 819-820-6868 ext. 15873
Email: roscoe.klinck@usherbrooke.ca