The miR-26 family regulates neural differentiation-associated microRNAs and mRNAs by directly targeting REST

Our data identify the miR-26 family as a trigger of a self-amplifying system essential for neural differentiation that acts upstream REST-controlled miRs and initiate a neuronal gene expression program. Overall design: Methods:Total RNAs from two independent clones of WT and tKO26b/a1/a2 cell lines and two biological replicates and NCs (day 15) were isolated using peqGold RNA pure (PeqLab). rRNA was removed using the Ribo-Zero rRNA Removal Kit (Illumina), followed by cDNA library preparation using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). Sequence reads were aligned to the mouse genome (version mm10) using TopHat (Trapnell et al., 2012). Transcripts were quantified by Cufflinks and Cuffdiff and differential expression was determined (Trapnell et al., 2012). Small RNA cDNA libraries were generated and deep sequenced (Hafner et al., 2010). Reads were mapped against murine miR annotation database (miRBase) using Burrow-Wheeler aligner. Each miR profile was normalized to relative read frequencies (Farazi et al., 2012).