From microRNAs to targets: Pathway discovery in cell fate transitions

Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Department of Urology, University of California San Francisco, San Francisco, CA, USA.
Current opinion in genetics & development (Impact Factor: 7.57). 05/2011; 21(4):498-503. DOI: 10.1016/j.gde.2011.04.011
Source: PubMed


MicroRNAs (miRNAs) are 22 nt non-coding RNAs that regulate expression of downstream targets by messenger RNA (mRNA) destabilization and translational inhibition. A large number of eukaryotic mRNAs are targeted by miRNAs, with many individual mRNAs being targeted by multiple miRNAs. Further, a single miRNA can target hundreds of mRNAs, making these small RNAs powerful regulators of cell fate decisions. Such regulation by miRNAs has been observed in the maintenance of the embryonic stem cell (ESC) cell cycle and during ESC differentiation. MiRNAs can also promote the dedifferentiation of somatic cells to induced pluripotent stem cells. During this process they target multiple downstream genes, which represent important nodes of key cellular processes. Here, we review these findings and discuss how miRNAs may be used as tools to discover novel pathways that are involved in cell fate transitions using dedifferentiation of somatic cells to induced pluripotent stem cells as a case study.

Download full-text


Available from: Robert Blelloch, Apr 23, 2015
  • Source
    • "Following export from the nucleus into the cytoplasm by exportin-5 [16], [17], the pre-miRNAs are processed by Dicer into a single-stranded mature miRNA of ∼22 nucleotides in length, which is then incorporated into the miRNA-induced silencing complex (miRISC) [18], [19]. The mature miRNA in the RISC complex can bind to target mRNAs with full or partial base complementarity and can downregulate gene expression by translational repression or mRNA cleavage [20]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Myostatin functions as a negative regulator of skeletal muscle growth by suppressing proliferation and differentiation of myoblasts. Dysfunction of the myostatin gene, either due to natural mutation or genetic manipulations such as knockout or knockdown, has been reported to increase muscle mass in mammalian species. RNA interference (RNAi) mediated by microRNAs (miRNAs) is a promising method for gene knockdown studies. In the present study, transient and stable silencing of the myostatin gene in caprine fetal fibroblasts (CFF) was evaluated using the two most effective constructs selected from four different miRNA expression constructs screened in 293FT cells. Using these two miRNA constructs, we achieved up to 84% silencing of myostatin mRNA in transiently transfected CFF cells and up to 31% silencing in stably transfected CFF cells. Moreover, off-target effects due to induction of interferon (IFN) response genes, such as interferon beta (IFN-β) and 2'-5'-oligoadenylate synthetase 2 (OAS2), were markedly fewer in stably transfected CFF cells than in transiently transfected cells. Stable expression of anti-myostatin miRNA with minimal induction of interferon shows great promise for increasing muscle mass in transgenic goats.
    Full-text · Article · Sep 2014 · PLoS ONE
  • Source
    • "MicroRNAs were discovered as small temporal RNAs that regulate developmental transitions in C. elegans. They have diverse expressive patterns and regulate a variety of areas, including embryologic development, physiology, pathophysiology, and growth, development, progression, and metastasis in cancer [15–17]. Currently, there are 2,578 (human) and 1908 (mouse) mature unique miRNAs identified (mirBase 20, June 2013), and more than half are conserved in vertebrates [18]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Both nuclear receptor subfamily 2 group F member 1 (NR2F1) and microRNAs (miRNAs) have been shown to play critical roles in the developing and functional inner ear. Based on previous studies suggesting interplay between NR2F1 and miRNAs, we investigated the coregulation between NR2F1 and miRNAs to better understand the regulatory mechanisms of inner ear development and functional maturation. Using a bioinformatic approach, we identified 11 potential miRNAs that might coregulate target genes with NR2F1 and analyzed their targets and potential roles in physiology and disease. We selected 6 miRNAs to analyze using quantitative real-time (qRT) -PCR and found that miR-140 is significantly down-regulated by 4.5-fold (P=0.004) in the inner ear of NR2F1 knockout (Nr2f1(-/-) ) mice compared to wild-type littermates but is unchanged in the brain. Based on this, we performed chromatin-immunoprecipitation followed by qRT-PCR and confirmed that NR2F1 directly binds and regulates both miR-140 and Klf9 in vivo. Furthermore, we performed luciferase reporter assay and showed that miR-140 mimic directly regulates KLF9-3'UTR, thereby establishing and validating an example coregulatory network involving NR2F1, miR-140, and Klf9. We have described and experimentally validated a novel tissue-dependent coregulatory network for NR2F1, miR-140, and Klf9 in the inner ear and we propose the existence of many such coregulatory networks important for both inner ear development and function.
    Full-text · Article · Dec 2013 · PLoS ONE
  • Source
    • "Transcriptomic analysis has shown that for each of these micronutrients changes in intake lead to altered gene expression in several biochemical pathways and networks [5] [6] [7] [8]. However, despite these known effects and the proposed role of microR- NAs (miRNA) as regulators of gene networks [9], there is little information available on whether epigenetic mechanisms involving regulation through miRNA play a role in metabolic regulation by micronutrients. However, recently zinc depletion was reported to alter blood miRNA levels [10] and miR-22 has been proposed to be a target of 1,25-dihydroxyvitamin D3 in colon cancer cells [11]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Intake of the essential micronutrient selenium (Se) has health implications. This work addressed whether some effects of Se on gene expression are exerted through microRNAs (miRNA). Human colon adenocarcinoma cells (Caco-2) were grown in Se-deficient or Se-adequate medium for 72 h. RNA was extracted and subjected to analysis of 737 miRNA using microarray technology. One hundred and forty-five miRNA were found to be expressed in Caco-2 cells. Twelve miRNA showed altered expression after Se depletion: miR-625, miR-492, miR-373*, miR-22, miR-532-5p, miR-106b, miR-30b, miR-185, miR-203, miR1308, miR-28-5p, miR-10b. These changes were validated by quantitative real-time PCR (RT-qPCR). Transcriptomic analysis showed that Se depletion altered expression of 50 genes including selenoproteins GPX1, SELW, GPX3, SEPN1, SELK, SEPSH2 and GPX4. Pathway analysis identified arachidonic acid metabolism, glutathione metabolism, oxidative stress, positive acute phase response proteins and respiration of mitochondria as Se-sensitive pathways. Bioinformatic analysis identified 13 transcripts as targets for the Se-sensitive miRNA; three were predicted to be recognised by miR-185. Silencing of miR-185 increased GPX2 and SEPSH2 expression. We propose that miR-185 plays a role in up-regulation of GPX2 and SEPHS2 expression. In the case of SEPHS2 this may contribute to maintaining selenoprotein synthesis. The data indicate that micronutrient supply can regulate the cell miRNA expression profile.
    Full-text · Article · Dec 2013 · Molecular Nutrition & Food Research
Show more