B1 and Alu are sequence-homologous interspersed elements of unknown function 
that have expanded in the genomes of mice and humans, respectively. A minority 
of B1 and Alu sequences are expressed as small cytoplasmic RNAs. These RNAs have 
conserved a secondary structure motif also present in signal recognition 
particle (SRP) RNA despite substantial sequence divergence, whereas random B1 
and Alu sequences have not. This RNA structure has also been conserved by the 
source sequences that gave rise to successive transpositions during B1 and Alu 
evolution. In the present work small cytoplasmic B1 and Alu RNAs synthesized in 
vitro were found to bind a cellular protein by mobility shift and UV 
cross-linking analyses. The mouse and human proteins demonstrate the same 
specificity to a panel of competitor RNAs. Results using mutated B1 RNA indicate 
that a single strand loop in the conserved Alu motif is essential for binding. 
Previous work by Strub et al. (Stub, K., Moss, J. B., and Walter, P. (1991) Mol. 
Cell. Biol. 11, 3949-3959) demonstrated that the Alu-specific protein SRP 9/14 
does not footprint to this region of SRP RNA. This observation coupled with the 
failure of anti-SRP/9 antibodies to identify SRP 9/14 in the B1 RNA-protein 
complex as well as the apparent mass and other characteristics of the protein 
described here suggest that it is a novel B1-Alu RNA-binding protein. 
Conservation of primary and secondary structure by B1 and Alu small cytoplasmic 
RNAs as well as features of their specific expression and ability to interact 
with the conserved binding protein indicate that these RNAs are more homologous 
than previously appreciated.