Microarray profiling reveals broad and differential effects of RBM3 on miRNA expression

MicroRNAs (miRNAs) are a family of short, noncoding RNAs that regulate translation of mRNAs by mechanisms involving the binding of complementary sequences. The influence of miRNAs on the proteome and cellular events is extensive as they regulate an estimated 60% of the transcriptome and play key roles in differentiation, plasticity, circadian rhythm, immunity, and disease. The post-transcriptional biogenesis of most miRNAs involves a sequential cleavage process mediated by RNase III family enzymes. Primary transcripts (pri-miRNAs) are first cleaved by Drosha in the nucleus to yield ~70nt hairpin precursors (pre-miRNAs). These intermediates are transported to the cytoplasm where ~22mer dsRNAs are excised by Dicer. Typically, one strand of the dsRNAs is inserted as a mature miRNA into the RNA-induced silencing complex (RISC), which contains members of the Argonaute (Ago) protein family that contribute to translational regulation. Recent studies indicate that some RNA-binding proteins (RNA-BPs) can regulate discrete processing steps, differentially blocking or promoting the formation of specific miRNAs to control cellular proliferation and differentiation. Elegant examples of this mechanism include the attenuation of let-7 biogenesis in embryonic stem cells by the pluripotency factor LIN28, and the selective enhancement of miR-18a biogenesis from a polycistronic transcript by hnRNPA1. Mature miRNA expression profiles in B104 cells were measured after siRNA-mediated knockdown of RBM3 in the B104 neuronal cell line. Mock treated B104 cells were used as a control. Experiments were replicated in duplicates.