Novel Roles for Ribonucleic Acids in Programmed Cell Death

Abstract

Apoptosis is a tightly coordinated program to shut down and dismantle a cell, characterized by mitochondrial outer membrane permeabilization (MOMP), caspase activation to cleave hundreds of proteins, DNA fragmentation, and blocked translation. Little is known about the fate of RNA as cells die, even though apoptosis has been intensively studied for decades. Here I show that mRNAs, but not noncoding RNAs (ncRNAs), are rapidly and globally degraded during apoptosis. The decay occurs in many cell types responding to diverse apoptotic stimuli. mRNA decay is triggered early in apoptosis, preceding membrane lipid scrambling, genomic DNA fragmentation and modifications to translation initiation factors that might cause translational arrest. mRNA decay depends on MOMP and is amplified by effector caspase activity. 3' truncated mRNA decay intermediates with nontemplated uridylate-rich tails are generated during apoptosis and degraded by the 3' to 5' exonuclease DIS3L2. Knockdown of DIS3L2 reduces apoptotic mRNA decay and partially rescues cell death. I propose that global mRNA decay is a new hallmark of apoptosis caused by the concerted action of several nucleases. I also report a new role for RNA and DNA in directing cytotoxic leukocyte proteases to their substrates. When cytotoxic lymphocytes recognize and attack infected or cancerous cells, they deliver the granzyme (Gzm) serine proteases into the target cell. The Gzms cleave diverse protein substrates to orchestrate cell death. RNA binding proteins are highly enriched in unbiased proteomic screens of Gzm protein substrates. I hypothesized that the Gzms are guided to nucleic acid binding protein targets via direct binding to RNA or DNA. Using fluorescence polarization, I show that the Gzms and related leukocyte proteases bind to RNA and DNA with low nanomolar affinity. Nucleic acid binding by the Gzms facilitates their cleavage of RNA and DNA binding proteins, and guides them into target cell nuclei and onto neutrophil extracellular traps. Nucleic acid binding provides an elegant mechanism to confer protease substrate specificity for cleavage of nucleic acid-binding proteins that play essential roles in cellular gene expression and cell proliferation.