The long noncoding RNA Malat1 regulates CD8(+) T cell differentiation by mediating epigenetic repression

Kanbar et al. show that the long noncoding RNA Malat1 impacts the differentiation of effector and memory CD8(+) T cell subsets by virtue of preferential epigenetic repression of memory-associated genes in terminal effector cells through an interaction with Ezh2. During an immune response to microbial infection, CD8(+) T cells give rise to short-lived effector cells and memory cells that provide sustained protection. Although the transcriptional programs regulating CD8(+) T cell differentiation have been extensively characterized, the role of long noncoding RNAs (lncRNAs) in this process remains poorly understood. Using a functional genetic knockdown screen, we identified the lncRNA Malat1 as a regulator of terminal effector cells and the terminal effector memory (t-T-EM) circulating memory subset. Evaluation of chromatin-enriched lncRNAs revealed that Malat1 grouped with trans lncRNAs that exhibit increased RNA interactions at gene promoters and gene bodies. Moreover, we observed that Malat1 was associated with increased H3K27me3 deposition at a number of memory cell-associated genes through a direct interaction with Ezh2, thereby promoting terminal effector and t-T-EM cell differentiation. Our findings suggest an important functional role of Malat1 in regulating CD8(+) T cell differentiation and broaden the knowledge base of lncRNAs in CD8(+) T cell biology.