One class of heterogeneous nuclear ribonucleoproteins (hnRNPs), AUF1/hnRNP D, 
consists of four isoform proteins (p45, p42, p40, and p37) which are generated 
by alternative splicing. The present study was therefore undertaken to clarify 
any isoform-specific differences in terms of their functions and 
nucleocytoplasmic localization. All isoforms primarily localized in the nucleus. 
However, heterokaryon analysis and a study using RNA polymerase II inhibitor 
revealed that p40/p37 exhibited a continuous shuttling between the nucleus and 
cytoplasm. Constant nuclear retention activity was mapped to the 
p45/p42-specific sequence at the C-terminal region, which is retained by 
alternative splicing. Using this domain as a probe, we performed a yeast 
two-hybrid screening and we found that scaffold attachment factor B (SAF-B), a 
nuclear matrix-associated protein, exhibits protein-protein interaction to this 
region. Colocalization of p45/p42 and SAF-B was observed as a speckle in the 
nucleus. Interestingly, p45/p42 isoforms appeared to act as a negative regulator 
in gene expression by forming a complex with SAF-B. Thus, the present study 
revealed that the isoform-specific functions of AUF1/hnRNP D are defined by 
intracellular shuttling capacity.