The intranuclear site of excision of each intron in Balbiani ring 3 pre-mRNA is influenced by the time remaining to transcription termination and different excision efficiencies for the various introns.

The 10.9-kb Balbiani ring 3 (BR3) gene contains 38 constitutively excised introns. Both nascent and nucleoplasmic, released BR3 gene pre-mRNA can be isolated by microdissection of the polytene salivary gland nuclei in which the gene is transcribed. Here we analyze the order of intron excision in relation to transcription and to intranuclear transport. We demonstrate that the introns are excised with an overall 5' to 3' polarity that is established during transcription and maintained during transport. In contrast, we also show that individual introns are excised at very different rates and that neighboring introns are removed in a preferred order that is not necessarily 5' to 3'. Splicing factors are, in addition, shown to associate with the nascent BR3 pre-mRNA. Our data argue that functional spliceosomes assemble rapidly as introns appear in the pre-mRNA, but that intron-specific properties influence the kinetics of spliceosome assembly and/or function, resulting in cotranscriptional excision of some introns, preferentially those located in the 5' part of the pre-mRNA, and posttranscriptional excision of other introns, preferentially those located in the 3' part of the pre-mRNA.