miR-144/451 directly represses just over 100 erythroid genes in E14.5 FL erythroblasts. (A) Fold-change (KO/WT) in protein abundance quantified by tandem mass tag labeling followed by liquid chromatography coupled with tandem mass spectrometry analysis vs mRNA abundance quantified by RNA-Seq. Each point represents a single RNA and protein (average value, 3 biological replicates for RNA-Seq and 5 for quantitative proteomics). Ago family members and known miR-451 targets (Cab39, Ywhaz, Vapa) are indicated. (B) Fold change (KO/WT) in mature mRNA levels vs mRNA stability (KO/WT exon signal divided by KO/WT intron signal). Each point indicates a single mRNA (average, 3 biological replicates). The red oval includes 131 genes (black dots) with significantly increased mRNA abundance and mRNA stability (≥0.4-fold [log 2] increase, false discovery rate [FDR] < 0.1). Positive controls Cab39, Ywhaz and Vapa are indicated by colored symbols. (C) qRT-PCR validation for mRNAs predicted by RNA stability analysis (B) to have: (1) no change in RNA level (Ago2, Hbb2), or (2) increased transcription with upregulated primary and spliced transcripts (Muc6, Vwa5a), or (3) increased mRNA stability leading to increased spliced transcript abundance without change in primary transcripts (Vapa, Ywhaz). Bar graphs show mean plus or minus SEM for data from 6 biological replicates. *P < .05; **P < .01.