INFLUENCE OF INTRON LENGTH ON ALTERNATIVE SPLICING OF CD44

Although the splicing of transcripts from most eukaryotic genes occurs in a constitutive fashion, some genes can undergo a process of altern ative splicing, This is a genetically economical process which allows a single gene to give rise to several protein isoforms by the inclusio n or exclusion of sequences into or from the mature mRNA. CD44 provide s a unique example; more than 1,000 possible isoforms can be produced by the inclusion or exclusion of a central tandem array of 10 alternat ively spliced exons, Certain alternatively spliced exons have been asc ribed specific functions; however, independent regulation of the inclu sion or skipping of each of these exons would clearly demand an extrem ely complex regulatory network. Such a network would involve the inter action of many exon-specific trans-acting factors with the pre-mRNA. T herefore, to assess whether the exons are indeed independently regulat ed, we have examined the alternative exon content of a large number of individual CD44 cDNA isoforms, This analysis shows that the downstrea m alternatively spliced exons are favored over those lying upstream an d that alternative exons are often included in blocks rather than sing ly. Using a novel in vivo alternative splicing assay, we show that int ron length has a major influence upon the alternative splicing of CD44 . We propose a kinetic model in which short introns may overcome the p oor recognition of alternatively spliced exons. These observations sug gest that for CD44, intron length has been exploited in the evolution of the genomic structure to enable tissue-specific patterns of splicin g to be maintained.