We have investigated the fate of the RNA components of small ribonucleoprotein particles in apoptotic cells. We show that the cytoplasmic Ro ribonucleoprotein-associated Y RNAs are specifically and rapidly degraded during apoptosis via a caspase-dependent mechanism. This is the first study describing the selective degradation of a specific class of small structural RNA molecules in apoptotic cells. Cleavage and subsequent truncation of Y RNAs was observed upon exposure of cells to a variety of apoptotic stimuli and were found to be inhibited by Bcl-2, zinc, and several caspase inhibitors. These results indicate that apoptotic degradation of Y RNAs is dependent on caspase activation, which suggests that the nucleolytic activity responsible for hY RNA degradation is activated downstream of the caspase cascade. The Y RNA degradation products remain bound by the Ro60 protein and in part also by the La protein, the only two proteins known to be stably associated with intact Ro ribonucleoprotein particles. The size of the Y RNA degradation products is consistent with the protection from degradation of the most highly conserved region of the Y RNAs by the bound Ro60 and La proteins. Our results indicate that the rapid abrogation of the yet unknown function of Y RNAs might be an early step in the systemic deactivation of the dying cell.Apoptosis is a form of cell death characterized by distinct morphological and biochemical alterations. Morphologically, apoptotic cells are characterized by chromatin condensation, cell shrinkage, fragmentation of the nucleus, and partition of cytoplasm and nucleus into membrane bound-vesicles (apoptotic bodies) (1). During the last 5 years, many of the molecules that participate in the biochemical pathway mediating apoptosis have been identified. A major role in this pathway is played by caspases, cysteine proteases with aspartic acid substrate specificity (2). Proteins cleaved by caspases appear to be structural proteins essential for maintaining nuclear and cytoplasmic architecture and enzymes essential for repair of damaged cell components (reviewed in Ref.3). A prominent nuclear event during apoptosis is internucleosomal cleavage of DNA, recognized as a "DNA ladder" on conventional agarose gel electrophoresis (4). The endonuclease activity responsible for apoptotic degradation of chromosomal DNA has recently been identified (5). The activity depends on two interacting proteins, one of which contains the endonuclease activity (caspase-activated deoxyribonuclease (CAD) 1 ), which is retained in the cytoplasm in an inactive form due to its association with the second protein (inhibitor of CAD). Caspase activation in apoptotic cells leads to cleavage of the inhibitor of CAD, thereby releasing active CAD resulting in DNA fragmentation in the nuclei (5, 6).Much less is known about cleavage and degradation of RNA in apoptotic cells. An increased rate of mRNA turnover has been suggested (7, 8) as well as mitochondrial 16 S ribosomal RNA degradation (9), but no nuclease associated with specif...