Pnn/DRS protein is associated with desmosomes and colocalizes with splicing factors in nuclear speckled domains. The potential interaction of pun with RNPS1, a pre-mRNA splicing factor and a component of the exon-exon junction complex, prompted us to examine whether Pnn is involved in nuclear mRNA processing. By immunoprecipitation, we found that Pun associates preferentially with mRNAs produced by splicing in vitro. Oligonucleotide-directed RNase H digestion revealed that Pun binds to the spliced mRNAs at a position immediately upstream of the splice junction and that 5' splice site utilization determines the location of Pun in alternatively spliced mRNAs. Immunoprecipitation further showed that Pun binds to mRNAs produced from a transiently expressed reporter in vivo. Although associated with mRNPs, Pun is a nuclear-restricted protein as revealed by the heterokaryon assay. Overexpression of an amino-terminal fragment of Pun that directly interacts with RNPS1 leads to blockage of pre-mRNA splicing. However, although suppression of Pun expression shows no significant effect on splicing, it leads to some extent to nuclear accumulation of bulk poly(A)(+) RNA. Therefore, Pun may participate, via its interaction with RNPS1, in mRNA metabolism in the nucleus, including mRNA splicing and export.