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Fig. 2 | BMC Genomics

Fig. 2

From: miR-27b shapes the presynaptic transcriptome and influences neurotransmission by silencing the polycomb group protein Bmi1

Fig. 2

Sox11, Zfp90 and Bmi1 are miR-27b targets. a,b Genome-wide transcriptome analysis of miR-27b KD and CT mouse cortical neurons (DIV14). a Hierarchical clustering of differentially-expressed genes with fold-change ≥ 1.5 (FDR < 0.05). Columns represent individual experiments (KD, miR-27b knockdown; CT, miR-27b control). Rows correspond to individual genes. (See also Additional file 3: Table S3). b Top 50 most up-regulated genes in miR-27b KD neurons (n = 3, FDR < 0.006). Dark grey bars refer to candidate repressor genes. c qPCR analysis of Trib3 (the most-upregulated gene in the microarray data) and candidate repressors in miR-27b KD vs CT neurons (n = 4). Results are expressed as the KD/CT ratio. d Luciferase reporters containing the 3’UTR of candidate repressors (and a few other genes listed in (b)) were electroporated in neurons later transduced with miRZip-27b and miRZip-Scr lentiviruses. Luciferase activities were normalized to CT values (set to 1). (Trib3 and St8sia2, n = 5; Mex3a, n =6; Sox11 and Zfp90, n = 7; Sh3bp2, n = 4; Bmi1, n = 9. * p < 0.05, ** p < 0.01, *** p < 0.001, t-test). e qPCR analysis of Bmi1 expression in neurons (DIV14) transduced with a control vector or a Bmi1-expressing construct (n = 4, *** p < 0.001, t-test). f RNAi KD of Sox11 and Zfp90 in cortical neurons assessed by qPCR (n = 3, * p < 0.05, t-test). g nCounter profiling of the presynaptic transcriptome in CT and Bmi1 OE cortical neurons (n = 4, p < 0.05, t-test). 97 genes are differentially regulated. h,i nCounter analysis of the presynaptic transcriptome in Sox11- and Zfp90-silenced cortical neurons (n = 3, p < 0.05). 42 and 71 genes are differentially-expressed respectively. Error bars are SD except for C-E where they represent SEM. j,k Combinatorial intersection analysis of differentially-expressed genes in miR-27b KD, Bmi1 OE, Sox11- and Zfp90 KD neurons. j Intersections among genes repressed by Bmi1, Sox11 and Zfp90 and activated by miR-27b. k Intersections among genes repressed by miR-27b and activated by Bmi1, Sox11 and Zfp90

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