Cell-Type-Based Analysis of MicroRNA Profiles in the Mouse Brain

SummaryMicroRNAs (miRNA) are implicated in brain development and function but the underlying mechanisms have been difficult to study in part due to the cellular heterogeneity in neural circuits. To systematically analyze miRNA expression in neurons, we have established a miRNA tagging and affinity-purification (miRAP) method that is targeted to cell types through the Cre-loxP binary system in mice. Our studies of the neocortex and cerebellum reveal the expression of a large fraction of known miRNAs with distinct profiles in glutamatergic and GABAergic neurons and subtypes of GABAergic neurons. We further detected putative novel miRNAs, tissue or cell type-specific strand selection of miRNAs, and miRNA editing. Our method thus will facilitate a systematic analysis of miRNA expression and regulation in specific neuron types in the context of neuronal development, physiology, plasticity, pathology, and disease models, and is generally applicable to other cell types and tissues.

► We established a “novel” miRNA tagging and affinity-purification method (miRAP)
► miRAP enables cell type specific miRNA profiling from complex tissues in mice
► We revealed distinct miRNA profiles in neuron types of cortex and cerebellum
► We detected putative “novel” miRNAs and miRNA editing by deep sequencing