Epigenetic regulation of miR-184 by MBD1 governs neural stem cell proliferation and differentiation

Abstract

Methyl-CpG binding protein 1 (MBD1) regulates gene expression via a DNA methylation-mediated epigenetic mechanism. We have previously demonstrated that MBD1 deficiency impairs adult neural stem/progenitor cell (aNSC) differentiation and neurogenesis, but the underlying mechanism was unclear. Here, we show that MBD1 regulates the expression of several microRNAs in aNSCs and, specifically, that miR-184 is directly repressed by MBD1. High levels of miR-184 promoted proliferation but inhibited differentiation of aNSCs, whereas inhibition of miR-184 rescued the phenotypes associated with MBD1 deficiency. We further found that miR-184 regulates the expression of Numblike (Numbl), a known regulator of brain development, by binding to the 3'-UTR of Numbl mRNA and affecting its translation. Expression of exogenous Numbl could rescue the aNSC defects that result from either miR-184 overexpression or MBD1 deficiency. Therefore, MBD1, miR-184, and Numbl form a regulatory network that helps control the balance between proliferation and differentiation of aNSCs.

Figure 1. Loss of MBD1 leads to increased proliferation and reduced differentiation of aNSCs

(A) Adult NSCs cultured under proliferating conditions expressed the neural progenitor markers Nestin (cytoplasmic, green) and Sox2 (nuclear, red). (B) Western blotting showing the expression of MBD1 [2 different isoforms (Zhao et al., 2003)] in WT aNSCs and the absence of MBD1 in Mbd1 KO aNSCs. β-actin was used as an internal control. (C) Both Mbd1 KO and WT aNSCs cultured under proliferating conditions incorporated bromodeoxyuridine (BrdU) in cell proliferation analyses (BrdU in red, DAPI in blue). (D) Quantitative analysis showing that a higher percentage of Mbd1 KO aNSCs incorporated BrdU compared with WT control cells (n = 3). (E, F, G) Mbd1 KO aNSCs differentiated into fewer TuJ1-positive (E, red; F, n = 4) neurons and GFAP-positive astrocytes (E, green; G, n = 4) (DAPI in blue). (H, I, J) Quantitative analyses showing that, under differentiation conditions, Mbd1 KO aNSCs exhibited reduced neuronal differentiation capacity, as assessed by decreased mRNA levels of neuronal specific NeuroD1 (H, n = 4) and Tuj1 (I, n = 4) and reduced promoter activity of transfected NeuroD1-promoter driven firefly luciferase (NeuroD1-Luc) construct (J, n = 3). (K, L) Quantitative analyses showing that Mbd1 KO aNSCs exhibited reduced astrocyte differentiation capacity, as assessed by decreased GFAP mRNA levels (K, n = 4) and reduced GFAP-promoter activity (L, n = 3). *, p < 0.05; **, p < 0.01.

Figure 2. Altered miRNA expression in Mbd1 KO aNSCs

(A) Heatmap of miRNAs that show significant changes (> 1.7 × fold) in expression levels in proliferating Mbd1 KO aNSCs compared with WT aNSCs, with increased expression showing in red and decreased expression showing in green. (B) The expression of miR-184 was increased in Mbd1 KO proliferating aNSCs. Real-time PCR analyses were performed using independently isolated aNSCs (n = 6). (C) Acute knockdown of MBD1 resulted in increased miR-184 expression in aNSCs (n = 3). (D) Overexpression of MBD1 in aNSCs led to reduced miR-184 expression (n = 4). (E) Upper panel shows a schematic drawing of the 7-kilobase (kb) regions proximal to the miR-184 gene on chromosome 9qE3 that were assayed in ChIP experiments. The relative CpG-rich sequences are indicated. Lower panel shows the enrichment of MBD1 protein at genomic sequence 4 kb upstream and 1 kb downstream of the miR-184 locus in WT aNSCs, as assessed by MBD1-specific chromatin immunoprecipitation (ChIP). ChIP with IgG in WT aNSCs and ChIP of MBD1 antibody in Mbd1 KO aNSCs were used as negative controls. Relative enrichment of MBD1 in either WT or KO aNSCs was calculated relative to IgG-only nonspecific control in the same cells (n = 4). Quantities were calculated from an input DNA-generated standard curve. Two-way ANOVA, Bonferroni post-test. (F) Fluorescence in situ hybridization (FISH) analyses showing expression of miR-184 in the subventricular zone (top panels) and the dentate gyrus (bottom panels) of WT and Mbd1 KO mice (Green: miRNA probe signal). White arrows point to the aNSC-containing germinal zone located at the lateral wall of the lateral ventricles. An increase in staining intensity for miR-184 was observed in Mbd1 KO brains. miR-1 probe was used as a negative control for FISH. Scale bars = 40 μm. LV, lateral ventricle. g, granule cells of the dentate gyrus. h, hilar region of the dentate gyrus. *, p < 0.05; **, p < 0.01. (Also see Figures S1, S2, S3, S4, and S5 and Table S1).

Figure 3. miR-184 modulates the proliferation and differentiation of adult NSCs in vitro

(A) RNA transfected aNSCs differentiated into neurons (Tuj1, red) and astrocytes (GFAP, green; DAPI, blue). (B, C) Transfection with miR-184 RNA led to reduced neuronal (B, n = 3) and astrocyte (C, n = 3) differentiation, compared with control nonspecific miR (miR-C). On the other hand, transfection with specific inhibitor to miR-184 (anti-miR-184) led to increased neuronal (B) and astrocyte (C) differentiation, compared with anti-miR control (Anti-C). (D, E) Similar results as B and C were obtained by using real-time PCR analyses for mRNA levels of neuronal-specific Tuj1 (D, n = 4) and astrocyte marker GFAP (E, n = 4). (F, G) We then used lentivirus expressing a small hairpin of miR-184 (F) to infect aNSCs. This lentiviral vector also expressed GFP under the CMV promoter, allowing us to track infected cells (G, green). Neuronal and glial differentiation was assessed using Tuj1 (red) and GFAP (white) staining and quantification. (H, I) Adult NSCs infected by the lentivirus expressing sh-miR-184 differentiated into fewer neurons (H, n = 5) and fewer astrocytes (I, n = 5) compared with aNSCs infected with lentivirus expressing a nonspecific shRNA (sh-Control). (J) Proliferation of miR-184- or anti-miR-184-transfected aNSCs was analyzed using BrdU pulse labeling. BrdU, red; DAPI, blue. (K) miR-184–transfected aNSCs had increased BrdU incorporation relative to miR-C-transfected cells (n = 3). Anti-miR-184–treated aNSCs, on the other hand, displayed reduced BrdU incorporation relative to Anti-C-transfected aNSCs (n = 3). (L) Lentivirus-shRNA-miR-184–infected aNSCs had increased BrdU incorporation relative to sh-Control lentivirus-infected aNSCs (n = 4). *, p < 0.05; **, p < 0.01. Scale bars = 40 μm. (Also see Figure S6).

Figure 4. miR-184 modulates the proliferation and differentiation of adult NSCs in vivo

(A) Retroviral vector used for in vivo miRNA expression. miRNA was expressed as a short hairpin under U6 RNA Polymerase III promoter, while GFP was expressed under a chicken actin (CAG) promoter. (B) Experimental timeline for in vivo analyses. (C) Retroviruses expressing sh-miR-184 and control shRNA were grafted into contralateral sides of the same animals. (D) A representative image of immunohistological analysis of virus-infected cells in the subgranular zone of the dentate gyrus. Orange arrow points to a cell that was positive for GFP (green), BrdU (white), and DCX (red), indicating that this viral-infected cell proliferated and then differentiated into neurons. Scale bar = 20 μm. g, granule cells layer. h, hilar region. m, molecular layer. (E) Sh-miR-184 virus-infected cells proliferated more compared with control virus-infected cells (n = 4). Right panel shows a representative 3D Z-stack image used for quantification of BrdU⁺GFP⁺ DCX^- cells. (F) Sh-miR-184–infected cells differentiated into fewer DCX+ early neurons when compared with control virus-infected cells (n = 4). Right panel shows a representative confocal 3D Z-stack image used for quantification of DCX⁺GFP⁺BrdU^- cells. DCX, red; GFP, green; BrdU, white. *, p < 0.05; **, p < 0.01.

Figure 5. Numblike (Numbl) is a functional target of miR-184

(A) A miR-184 target site was found in the Numbl 3′-untranslated region (3′-UTR) as predicted by miRanda software. The Mutant Numbl 3′-UTR used in C is shown. (B) Numbl-3′-UTR–dependent expression of a Renilla luciferase (R-luc) was suppressed by miR-184 and increased by anti-miR-184 in aNSCs. (C) miR-184-mediated suppression of R-luc-Numbl-3-′UTR was dependent on the miR-184 target site, because that mutation of the miR-184 target site in the Numbl-3′-UTR abolished the repression by miR-184 and the enhancement by anti-miR-184 (n = 3). For B and C, R-luc-Numbl-3′-UTR expression was normalized to control firefly luciferase (fLuc) activities. (D, E) Overexpression of miR-184 in WT aNSCs led to reduced endogenous Numbl mRNA (D, real-time PCR, n = 3) and protein (E, representative western blot) expression. (F, G) Mbd1 KO aNSCs exhibited reduced expression levels of both Numbl mRNA (D, real-time PCR, n = 4) and protein (E, representative western blot) expression. (H, I) Transfection of anti-miR-184 into Mbd1 KO aNSCs could restore Numbl protein expression to levels similar to those in WT aNSCs (n = 3). *, p < 0.05; **, p < 0.01; ***, p < 0.001. (Also see Table S2)

Figure 6. Numbl rescues the aNSC deficits associated with miR-184 overexpression

(A) Overexpression of Numbl in WT aNSCs using lentivirus resulted in reduced proliferation of aNSCs as assessed by BrdU pulse labeling (n = 3). (B) Acute knockdown of Numbl using lentivirus expressing Numbl siRNA led to increased aNSC proliferation of aNSCs (n = 3). (C) Expression of Numbl could suppress increased proliferation of aNSCs caused by overexpression of miR-184 (n = 3). The Numbl expression vector containing Numbl 3′-UTR (Numbl+3′-UTR) was not as effective in rescuing the proliferation effect of miR-184. (D) Overexpression of Numbl in WT aNSCs resulted in increased neuronal differentiation as assessed by Tuj1 mRNA levels (n = 3) and NeuroD1 promoter activities (n = 3). (E) Acute knockdown of Numbl in WT aNSCs resulted in reduced neuronal differentiation as assessed by Tuj1 mRNA levels (n = 3) and NeuroD1 promoter activities (n = 5). (F and G) Expression of Numbl could rescue the decreased neuronal differentiation of aNSCs caused by overexpression of miR-184 as assessed by both mRNA levels of NeuroD1 (F left, n = 3) and Tuj1 (F right, n = 3) and NeuroD1 promoter activities (G, n = 6). The Numbl expression vector containing Numbl 3′-UTR (Numbl+3′-UTR) was not as effective at rescuing the differentiation effect of miR-184 overexpression (G, hatched bar). *, p < 0.05; **, p < 0.01, ***, p < 0.001.

Figure 7. Numbl rescues the aNSC deficits associated with MBD1 deficiency

(A-B) Exogenous MBD1 expressed by a recombinant lentivirus could restore the Numbl expression levels in Mbd1 KO aNSCs to levels seen in the WT aNSCs (n = 3). (C) Exogenous Numbl could rescue proliferation deficits exhibited by Mbd1 KO aNSCs (n = 3). (D, E) Exogenous Numbl could rescue neuronal differentiation deficits exhibited by Mbd1 KO aNSCs as assessed by both Tuj1 and NeuroD1 mRNA expression in differentiating cells (n = 4). *, p < 0.05; **, p < 0.01. (Also see Figure S7). (F) Model for the MBD1, miR-184, and Numbl molecular network in modulating adult neurogenesis.