An efficient framework to decipher microRNA regulatory programs in functionally divergent naïve T cell subsets [RNAseq_mir29cre]

Naïve CD8+ T cells are heterogenous, with subsets exhibiting divergent kinetics and functions post-activation. MicroRNAs (miRNAs) are post-transcriptional regulators, and certain miRNAs contribute to specification of different naïve T cell subsets. However, the microRNA regulatory circuits mediating functional specialization of naïve subsets have not been identified. In this work, we profiled microRNA expression in diverse subsets of naïve CD8+ T cells, revealing significant differences in their microRNA expression landscapes. We developed a novel framework, miR-Inf, to decipher microRNA regulatory programs. MiR-Inf has two key components: (i) an efficient method for estimating gene decay rates from the RNA seq profiles to better capture microRNA regulatory effects, and (ii) identification of functional microRNA targets by integrating decay rate data and microRNA expression data. We applied this framework to identify consequential miRNAs in naïve CD8+ T cell subsets and predicted their context-specific targets. Our analyses revealed that miR-29, a microRNA known to be important in CD8+ T cells, likely functions by modulating transcripts encoding epigenetic factors. Collectively, our data and framework defined microRNA regulatory circuits across diverse naïve CD8+ T cell subsets.