Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells

Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America.
PLoS ONE (Impact Factor: 3.23). 07/2008; 3(7). DOI: 10.1371/journal.pone.0002548
Source: PubMed Central


MicroRNAs (miRNAs: a class of short non-coding RNAs) are emerging as important agents of post transcriptional gene regulation and integral components of gene networks. MiRNAs have been strongly linked to stem cells, which have a remarkable dual role in development. They can either continuously replenish themselves (self-renewal), or differentiate into cells that execute a limited number of specific actions (pluripotence).

Methodology/Principal Findings
In order to identify novel miRNAs from narrow windows of development we carried out an in silico search for micro-conserved elements (MCE) in adult tissue progenitor transcript sequences. A plethora of previously unknown miRNA candidates were revealed including 545 small RNAs that are enriched in embryonic stem (ES) cells over adult cells. Approximately 20% of these novel candidates are down-regulated in ES (Dicer−/−) ES cells that are impaired in miRNA maturation. The ES-enriched miRNA candidates exhibit distinct and opposite expression trends from mmu-mirs (an abundant class in adult tissues) during retinoic acid (RA)-induced ES cell differentiation. Significant perturbation of trends is found in both miRNAs and novel candidates in ES (GCNF−/−) cells, which display loss of repression of pluripotence genes upon differentiation.

Combining expression profile information with miRNA target prediction, we identified miRNA-mRNA pairs that correlate with ES cell pluripotence and differentiation. Perturbation of these pairs in the ES (GCNF−/−) mutant suggests a role for miRNAs in the core regulatory networks underlying ES cell self-renewal, pluripotence and differentiation.

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Available from: Austin Cooney, Oct 09, 2015
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    • "However, our study has identified cfa-miR-214 as an RA pathway associated miRNA in canine spermatogenesis. In support of our findings, there is another study showed up-regulation of miR-214 in RA-induced differentiated ES cells [30]. "
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    ABSTRACT: Spermatogenesis is a multistep synchronized process. Diploid spermatogonia differentiate into haploid spermatozoa following mitosis, meiosis and spermiogenesis. Division and differentiation of male germ cells is achieved through the sequential expression of several genes. Numerous mRNAs in the differentiating germ cells undergo post-transcriptional and translational regulation. MiRNAs are powerful negative regulators of mRNA transcription, stability, and translation and recognize their mRNA targets through base-pairing. Retinoic acid (RA) signaling is essential for spermatogenesis and testicular function. Testicular RA level is critical for RA signal transduction. This study investigated the miRNAs modulation in an RA- induced testicular environment following the administration of all-trans RA (2 µM) and CYP26B1- inhibitor (1 µM) compared to control. Eighty four canine mature miRNAs were analyzed and their expression signatures were distinguished using real-time PCR based array technology. Of the miRNAs analyzed, miRNA families such as miR-200 (cfa-miR-200a, cfa-miR-200b and cfa-miR-200c), Mirlet-7 (cfa-let-7a, cfa-let-7b, cfa-let-7c, cfa-let-7g and cfa-let-7f), miR-125 (cfa-miR-125a and cfa-miR-125b), miR-146 (cfa-miR-146a and cfa-miR-146b), miR-34 (cfa-miR-34a, cfa-miR-34b and cfa-miR-34c), miR-23 (cfa-miR-23a and cfa-miR-23b), cfa-miR-184, cfa-miR-214 and cfa-miR-141 were significantly up-regulated with testicular RA intervention via administration of CYP26B1 inhibitor and all-trans-RA and species of miRNA such as cfa-miR-19a, cfa-miR-29b, cfa-miR-29c, cfa-miR-101 and cfa-miR-137 were significantly down-regulated. This study explored information regarding chromosome distribution, human orthologous sequences and the interaction of target genes of miRNA families significantly distinguished in this study using prediction algorithms. This study importantly identified dysregulated miRNA species resulting from RA-induced spermatogenesis. The present contribution serves as a useful resource for further elucidation of the regulatory role of individual miRNA in RA synchronized canine spermatogenesis.
    PLoS ONE 06/2014; 9(6):e99433. DOI:10.1371/journal.pone.0099433 · 3.23 Impact Factor
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    • "We were interested in investigating the effect of microRNAs in stem cell fate and self-renewal. The cellular response to crucial microRNAs is of particular importance, especially when the fate of pluripotent genes has shown to be regulated by these minuscule elements.[1][24][41][42] In this study, we looked upon the effect of certain microRNAs on self-renewal factors such as Oct4, Sox2, Klf4, cMyc and lin28 which play an essential role in stem cell maintenance and propagation.[1][8][10][11][43] "
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    ABSTRACT: MicroRNAs are endogenous non-coding RNAs with important regulatory and cell fate functions. Many studies have shown that several microRNAs are obviously up-regulated during stem cell differentiation. The question rises here is weather inhibiting differentiation will affect the stemness and self renewal status of stem cells. miRCURY ™LNA microRNA inhibitor (anti-miR-145 and anti-let7g) are a sequence-specific and chemically modified oligonucleotide that specifically target and knockdown miR-145 and let7g miRNA molecules. Unrestricted somatic stem cells (USSCs) were isolated from umbilical cord blood and treated with LNAs. The effect of anti-miRNA transfection was assessed by quantitative real-time PCR. Real-time PCR showed that LNA was efficiently introduced into the cells and reduced miR145 and Let7g expression levels to 40% and 10% in relation to corresponding scramble control, respectively. Gene expression analysis as to self renewal and expansion showed more than 3.5 fold up regulation in Oct4 in cells treated with mir145 inhibition. Similarly a significant up to 2.5 fold up-regulation in Oct4 and cMyc expression was observed in samples treated with anti-let7g. Suppression in differentiation inducing microRNAs (miR-145 and let7g) can enhance the self renewal and stemness status of USSCs at transcriptional level.
    10/2011; 13(10):726-34.
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    • "Northern blotting to confirm novel miRNA tgu-miR-2954-3p was performed by modifying the protocol of [97]. 2 μg of total RNA was heated at 65°C for 5 min with 2X loading dye (Ambion), quenched on ice, and loaded on a 15% TBE Urea gel (Invitrogen). Total RNA was separated by electrophoresis at 200V for 50 min. "
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    ABSTRACT: In an important model for neuroscience, songbirds learn to discriminate songs they hear during tape-recorded playbacks, as demonstrated by song-specific habituation of both behavioral and neurogenomic responses in the auditory forebrain. We hypothesized that microRNAs (miRNAs or miRs) may participate in the changing pattern of gene expression induced by song exposure. To test this, we used massively parallel Illumina sequencing to analyse small RNAs from auditory forebrain of adult zebra finches exposed to tape-recorded birdsong or silence. In the auditory forebrain, we identified 121 known miRNAs conserved in other vertebrates. We also identified 34 novel miRNAs that do not align to human or chicken genomes. Five conserved miRNAs showed significant and consistent changes in copy number after song exposure across three biological replications of the song-silence comparison, with two increasing (tgu-miR-25, tgu-miR-192) and three decreasing (tgu-miR-92, tgu-miR-124, tgu-miR-129-5p). We also detected a locus on the Z sex chromosome that produces three different novel miRNAs, with supporting evidence from Northern blot and TaqMan qPCR assays for differential expression in males and females and in response to song playbacks. One of these, tgu-miR-2954-3p, is predicted (by TargetScan) to regulate eight song-responsive mRNAs that all have functions in cellular proliferation and neuronal differentiation. The experience of hearing another bird singing alters the profile of miRNAs in the auditory forebrain of zebra finches. The response involves both known conserved miRNAs and novel miRNAs described so far only in the zebra finch, including a novel sex-linked, song-responsive miRNA. These results indicate that miRNAs are likely to contribute to the unique behavioural biology of learned song communication in songbirds.
    BMC Genomics 05/2011; 12(1):277. DOI:10.1186/1471-2164-12-277 · 3.99 Impact Factor
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