A53
In 100 sequences associated with alternatively spliced forms of estrogen receptor alpha in breast cancer
David Ross Sibson, Bryony Lloyd, Dan Kim
University of Liverpool, Liverpool, UK
Background
To investigate the contribution of alternatively spliced estrogen receptor alpha isoforms in breast cancer hormone therapy, we have cloned PCR products between the first and final exons. Exon 7 skipping occurred in up to 50% of transcripts followed by skipping of exons 3 and 4 at a few percentage each. Their coding sequences allow for the possibility that each of these isoforms has functional significance. Breast cancer cell lines had characteristic ratios of the isoforms that were not significantly affected by hormone treatment and therefore may reflect key states of the breast cancer cells. Alternative splicing of Caspase 2 to pro and anti apoptic forms is regulated by PTB acting at an In100 sequence. An In100 sequence has been reported in estrogen receptor alpha. We therefore analysed the global distribution of In100 sequences in relation to global alternative splicing and estrogen receptor alpha.
Method
A database of cassette exons with or without In100 elements and constitutive exons was prepared in relation to confirmed alternative splicing and EST data. BioProspector was used to identify the top 3 motifs downstream of alternatively spliced exons. A Markov Background model from the constitutive data was used to enrich for alternative splicing-associated motifs.
Results
Cell cycle control was the most over represented gene ontology term for the In100 alternatively spliced associated introns. Introns 4 and 5 but not 7 of estrogen receptor alpha had In100 motifs. The In100 of intron 4 had reduced pyrimidine usage compared to intron 5.
Conclusion
In100 sequences provide a possible explanation for some of the alternative splicing observed in estrogen receptor alpha and more generally may provide a means of classifying the behaviour of cancers.
