Cell-type-based analysis of microRNA profiles in the mouse brain

Abstract

MicroRNAs (miRNA) are implicated in brain development and function but the underlying mechanisms have been difficult to study in part due to the cellular heterogeneity in neural circuits. To systematically analyze miRNA expression in neurons, we have established a miRNA tagging and affinity-purification (miRAP) method that is targeted to cell types through the Cre-loxP binary system in mice. Our studies of the neocortex and cerebellum reveal the expression of a large fraction of known miRNAs with distinct profiles in glutamatergic and GABAergic neurons and subtypes of GABAergic neurons. We further detected putative novel miRNAs, tissue or cell type-specific strand selection of miRNAs, and miRNA editing. Our method thus will facilitate a systematic analysis of miRNA expression and regulation in specific neuron types in the context of neuronal development, physiology, plasticity, pathology, and disease models, and is generally applicable to other cell types and tissues.

Figure 1

The miRAP methodology. (A) The scheme of miRNA tagging and Affinity Purification (miRAP). tAGO2 (a GFP-MYC-AGO2 fusion protein) expression is activated by Cre recombinase in certain cell types in mouse brain. Using MYC antibody, miRNAs in Cre⁺ cells are co-precipitated with tAGO2. Using AGO2 antibody, miRNAs in all cells of the tissue are co-precipitated with AGO2 or tAGO2. RNAs prepared from immunoprecipitation (IP) product is subjected to deep sequencing or miRNA Taqman PCR. (B) Cre-loxP binary system to achieve cell type specific delivery of tAGO2. (C)Western analysis of tAGO2 expression and immunoprecipitation. (D) Autoradiogram of ³²P-labelled RNA purified from tAgo2 brain lysate by immunoprecipitation. RNAs ranging between 20–30nt were observed, corresponding to the size of miRNAs. (see also Sppl Figure 1)

Figure 2

Cell type specific tAgo2 expression in the neocortex and cerebellum activated by Cre drivers. Cre driver lines used are marked at top of each panel. tAgo2 expression was detected by GFP immunostaining. Pia of cortex is outlined. In the Camk2α -Cre line which labels pyramidal cells, GAD2 antibody was used due to the lack of appropriate Camk2α antibody; the lack of co-localization with GAD2 indicates tAgo2 expression in pyramidal neurons (also see sppl Figure 2 which demonstrates neuronal expression). In cortical GABA neuron drivers (Gad2, Pv, Sst), GFP⁺ cells colocalized with corresponding cell type markers. In the L7-cre line, Purkinje cells were identified by their characteristic morphology and position. Note the prominent GFP signal in Purkinje dendrites. tAGO2 is predominantly localized in cell somata but not the nucleus, surrounded by LaminB (red) which labels nuclear envelop. Scale bar: 100μm in low magnification images, 20μm in high magnification images, 10μm in LaminB image. (see also Sppl Figure 2)

Figure 3

Relative miRNA expression profiles and hierarchical clustering of samples. Relative expression profiles of mature miRNAs were constructed as follows: the raw reads counts of each miRNA are first normalized to the total number of reads that were mapped to all of the known mature miRNAs and miRNA* species, then log2 transformed, and mean centered. Inset: Hieratical clustering of miRNA expression of all the libraries. (see also Sppl Table 2)

Figure 4

miRNA expression profiling in neocortical neurons. (A) A simple schematic of neocortical neurons included in this study. The two major neuron types, glutamatergic projection neurons and GABAergic interneurons are targeted by Camk2α-cre and Gad2-cre lines, respectively. PV and SST interneurons are two non-overlapping subtypes of GABAergic neurons targeted by Pv-Cre and Sst-Cre, respectively. (B–C) Normalized expression values of miRNAs are plotted for Camk2α vs. Gad2 samples, and PV vs SST samples. The middle diagonal line represents equal expression, and lines to each side represent 2-fold enrichment in either cell population. The labels of axes are log 2 scaled. miRNAs with fold changes equal or larger than 2 and P values lower than 0.001 are represented in red. (D–E) miRNA Taqman PCR validation of deep sequencing. All readings were normalized to miRNA-124 using the ΔΔCt method. Deep sequencing reads number were log2 transformed and then normalized to miRNA-124. (D) The value of Camk2α sample was compared to Gad2 sample. Values above 0 represent higher expression in Gad2 than Camk2α, and vice versa. n=3 for deep sequencing; n=4 for Taqman PCR. (E) The value of PV sample was compared to SST sample. Values above 0 represent higher expression in SST than PV, and vice versa. n=2 for deep sequencing; n=4 for Taqman PCR. (F) miR-133b and miR-187 expression in four neocortical neuron types. The cell type specific data was normalized to data of neocortex homogenates in each case. Value above 0 indicates higher expression than neocortex sample, and vice versa. (G) Comparison between RNAs purified from FACS sorting and miRAP using Taqman PCR in Camk2α neurons. n=4.Error bar: standard deviation. (see also Sppl Figure 3)

Figure 5

Correlation among miRNA gene expression, genomic organization, and sequence similarity. (A) Correlation of the expression and genomic distance of miRNA genes. Each miRNA gene was paired with every other miRNA gene lying in the same orientation on the same chromosome. For each pair, the distance between the two loci was ranked, and the correlation coefficient for their expression was plotted according this rank (grey circle). The red line indicates the relationship between the rank and actual genomic distance. 50-point moving average of correlation coefficients was calculated. The difference of each moving average and the next was plotted according to the rank (black diamond). The blue line indicates the first point where this value deviates abruptly from the previous ones, i.e. where the average correlation coefficient beyond certain genomic distance changes abruptly. (B) Correlation of expression among miRNA genes within a family (intra-family) and those that do not belong to the same family (inter-family). miRNA genes within the same family tend to have higher correlation coefficient than those that belong to different families. The relative frequency counts (density) on Y axis are arbitrarily defined so that the sum of area in all bins is equal to 1. (see also Sppl Figure 4 and Sppl Table 3–6)

Figure 6

Secondary structures and northern blot validation of two candidate novel miRNAs, miR-N3 and miR-N16. miR-124 was included as positive control. Red region: mature miRNA; yellow region: loop; purple region: miRNA*. * :signals corresponding to putative mature miRNA. ^ : signals corresponding to putative miRNA precursor. (see also Sppl Figure 6 and Sppl Table 7)