Fig. 2.

HuR regulates the polysomal positioning of functionally related mRNAs in the developing neocortex. (A) KEGG and GO bioinformatics analyses indicate that, among mRNAs stable in total levels with HuR-cKO, those altered in 40S–60S–80S and polysomal fractions are functionally related transcripts. Venn diagrams present the number of mRNAs within each functional group (e.g., regulation of transcription) that differ in either 40S–60S–80S or polysomal fractions at E13 (Left) and P0 (Right) in HuR-cKO. Developmental-stage-dependent changes in each functional group are shown as a comparison between E13 and P0. Each Venn circle sums to the total number of mRNAs that undergo changes in abundance; the changes for each functional group are highlighted as subsets of WT and HuR-cKO. (B) The mRNA candidates revealed by RNAseq were confirmed with qRT-PCR of WT (filled bars) and HuR-cKO (open bars). Fractions corresponding to the nontranslating free, 40S/60S, and 80S vs. translating light and heavy polysomes are highlighted. (C) Quantification and statistical analysis of the nontranslating and translating fractions are shown comparing WT and HuR-cKO (n = 4 cortices in two fractionations; qRT-PCRs were performed in duplicate for each fraction). Statistical significance between WT and cKO for each category with t test is indicated in red text in Right (P < 0.05). (D) Bioinformatic analysis of the number of neocortical layer-specific mRNAs increased or decreased by HuR-cKO in the 40S–60S–80S and polysome at E13 and P0, showing a particularly strong effect on layer-2/3 and -5 polysome mRNAs at both ages.