Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation - PubMed (original) (raw)

Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation

Lorenzo F Sempere et al. Genome Biol. 2004.

Abstract

Background: The microRNAs (miRNAs) are an extensive class of small noncoding RNAs (18 to 25 nucleotides) with probable roles in the regulation of gene expression. In Caenorhabditis elegans, lin-4 and let-7 miRNAs control the timing of fate specification of neuronal and hypodermal cells during larval development. lin-4, let-7 and other miRNA genes are conserved in mammals, and their potential functions in mammalian development are under active study.

Results: In order to identify mammalian miRNAs that might function in development, we characterized the expression of 119 previously reported miRNAs in adult organs from mouse and human using northern blot analysis. Of these, 30 miRNAs were specifically expressed or greatly enriched in a particular organ (brain, lung, liver or skeletal muscle). This suggests organ- or tissue-specific functions for miRNAs. To test if any of the 66 brain-expressed miRNAs were present in neurons, embryonal carcinoma cells were treated with all-trans-retinoic acid to promote neuronal differentiation. A total of 19 brain-expressed miRNAs (including lin-4 and let-7 orthologs) were coordinately upregulated in both human and mouse embryonal carcinoma cells during neuronal differentiation. The mammalian ortholog of C. elegans lin-28, which is downregulated by lin-4 in worms via 3' untranslated region binding, was also repressed during neuronal differentiation of mammalian embryonal carcinoma cells. Mammalian lin-28 messenger RNAs contain conserved predicted binding sites in their 3' untranslated regions for neuron-expressed miR-125b (a lin-4 ortholog), let-7a, and miR-218.

Conclusions: The identification of a subset of brain-expressed miRNAs whose expression behavior is conserved in both mouse and human differentiating neurons implicates these miRNAs in mammalian neuronal development or function.

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Figures

Figure 1

Figure 1

The miRNA expression in mammalian organs and carcinoma cells. Mouse and human organs analyzed by northern blotting were brain (B), liver (Li), heart (H), skeletal muscle (M), lung (Lu), kidney (K), and spleen (S). P19 and NT2/D1 were treated with RA at time 0, cells were harvested and total RNA extracted at the indicated times (days). The miRNA levels detected by northern blot hybridization are represented as fold change of radioactive signal over background, as described in Materials and methods. The intensity of the yellow scale corresponds to the intensity of miRNA expression; black indicates no signal was detected over background, either by quantification or by visual inspection of the phosphoimager image. White indicates cases that were not tested. The stringency of hybridization was not sufficient to distinguish single nucleotide mismatches; very similar expression profiles were observed for members of closely related miRNA families, and so these profiles may reflect a composite of expression profiles from each member.

Figure 2

Figure 2

The miRNA expression profiles in mammalian organs. (a) Distribution of all expressed miRNAs in mouse organs (center), miRNAs expressed only in a particular organ (right), and miRNA enriched in a particular organ at least two-fold over other organs (left). Note that mouse brain-specific miRNAs were detected at higher levels than mouse lung-specific miRNAs. Indeed, four of the seven brain-specific miRNA radioactive signals were detected at least two-fold over background. (b) Northern blots of representative miRNAs with similar expression patterns in organs of mouse and human. (c) Clustering of expressed miRNAs by their similar expression profiles in mouse (Mm) and human (Hs) brain (B), liver (Li), heart (H), skeletal muscle (M), lung (Lu), kidney (K), and spleen (S). Note that some mouse lung-specific miRNAs (miR-19a, miR -130, miR -213) are also expressed in other human organs. Colored bars to the right of miRNA names refer to the corresponding color-coded classes in the right hand pie chart in (a): brain-specific (red), brain-enriched (purple), or lung-specific (light grey).

Figure 3

Figure 3

Genomic organization and correlated expression of clustered miRNAs. (a) In some miRNA clusters, all members of the cluster can be expressed in a highly correlated pattern; (b,c) for other clusters, the expression of different cluster members can vary in level or pattern. In some cases, entire clusters, or individual cluster members, have been cloned in human or mouse cDNA libraries, or detected by northern blot hybridization (dotted lines). Some miRNAs are associated with aberrant cytological locations (parenthesis). Chromosomal location of miRNAs is given by their cytological coordinates or BAC clone. Expression profiles are shown for mouse and human brain (B), liver (Li), heart (H), skeletal muscle (M), lung (Lu), kidney (K), and spleen (S).

Figure 4

Figure 4

The miRNA expression profiles in EC cells differentiating in response to RA. (a) Sets of miRNAs expressed in P19 and NT2/D1 cells treated with RA. All RA-induced miRNAs in P19 and NT2/D1 cells are also expressed in the brain (Figures 1, 2). Numbers in overlapping areas indicate the amount of miRNAs that belong to intersecting sets. (b) Clustering of the 19 miRNAs induced by RA-treatment in both P19 and NT2/D1 cells by their similar expression profile in mouse (Mm) and human (Hs) brain (B), liver (Li), heart (H), muscle (M), lung (Lu), kidney (K) and spleen (S). Colored bars to the right of miRNA names indicate miRNA expression classes in reference to the pie chart on the left: brain-specific (red), brain-enriched (purple), or brain-nonenriched (grey). (c) Northern blots of representative RA-induced miRNAs, constitutively expressed miRNAs (miR-92), and nonexpressed miRNAs (miR-1d) in P19 and NT2/D1 cells treated with RA.

Figure 5

Figure 5

LIN-28: a potential miRNA target in P19 and NT2/D1 cells. (a) Western blot of LIN-28 protein in P19 and NT2/D1 cells treated with RA at day 0. Actin is shown as loading control for protein concentration. (b) Depiction of 3' UTR of mouse Lin-28 mRNA, colored blocks indicated strong sequence homology with human Lin-28 3' UTR. Colored bars indicate predicted miRNA sites on Lin-28 3' UTR conserved blocks. Insets of block 2 and block 3 show predicted RNA-RNA interaction of Lin-28 3' UTR and RA-induced let-7a, miR-125b, and miR-218.

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References

    1. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. Identification of novel genes coding for small expressed RNAs. Science. 2001;294:853–858. doi: 10.1126/science.1064921. - DOI - PubMed
    1. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T. Identification of tissue-specific microRNAs from mouse. Curr Biol. 2002;12:735–739. doi: 10.1016/S0960-9822(02)00809-6. - DOI - PubMed
    1. Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T. New microRNAs from mouse and human. RNA. 2003;9:175–179. doi: 10.1261/rna.2146903. - DOI - PMC - PubMed
    1. Lai EC, Tomancak P, Williams RW, Rubin GM. Computational identification of Drosophila microRNA genes. Genome Biol. 2003;4:R42. doi: 10.1186/gb-2003-4-7-r42. - DOI - PMC - PubMed
    1. Lau NC, Lim LP, Weinstein EG, Bartel DP. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science. 2001;294:858–862. doi: 10.1126/science.1065062. - DOI - PubMed

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