Deep Sequencing Reveals Novel MicroRNAs and Regulation of MicroRNA Expression during Cell Senescence

Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America.
PLoS ONE (Impact Factor: 3.23). 05/2011; 6(5):e20509. DOI: 10.1371/journal.pone.0020509
Source: PubMed


In cell senescence, cultured cells cease proliferating and acquire aberrant gene expression patterns. MicroRNAs (miRNAs) modulate gene expression through translational repression or mRNA degradation and have been implicated in senescence. We used deep sequencing to carry out a comprehensive survey of miRNA expression and involvement in cell senescence. Informatic analysis of small RNA sequence datasets from young and senescent IMR90 human fibroblasts identifies many miRNAs that are regulated (either up or down) with cell senescence. Comparison with mRNA expression profiles reveals potential mRNA targets of these senescence-regulated miRNAs. The target mRNAs are enriched for genes involved in biological processes associated with cell senescence. This result greatly extends existing information on the role of miRNAs in cell senescence and is consistent with miRNAs having a causal role in the process.

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Available from: David I K Martin, Oct 06, 2015
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    • "The SA-miRNAs control cell transition , mainly through the G 1 /S checkpoint during cell cycle progression by targeting the components of cell cycle including cyclin-dependent kinases (CDKs) and cyclin-dependent kinase inhibitors (CDKIs) [16]. Despite the reported discrepancies between the upregulation and downregulation of miRNAs during aging and cellular senescence, such as miR-34a [17] [18], study of the modulatory effect of dietary compound on miRNAs may aid in the understanding of how SA-miRNAs can be regulated in favour of slowing down aging process or reducing aging phenotypes. Modulation of miRNAs by dietary and pharmacological agents has been reported recently [19]. "
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    ABSTRACT: Emerging evidences highlight the implication of microRNAs as a posttranscriptional regulator in aging. Several senescence-associated microRNAs (SA-miRNAs) are found to be differentially expressed during cellular senescence. However, the role of dietary compounds on SA-miRNAs remains elusive. This study aimed to elucidate the modulatory role of tocotrienol-rich fraction (TRF) on SA-miRNAs (miR-20a, miR-24, miR-34a, miR-106a, and miR-449a) and established target genes of miR-34a (CCND1, CDK4, and SIRT1) during replicative senescence of human diploid fibroblasts (HDFs). Primary cultures of HDFs at young and senescent were incubated with TRF at 0.5 mg/mL. Taqman microRNA assay showed significant upregulation of miR-24 and miR-34a and downregulation of miR-20a and miR-449a in senescent HDFs (P < 0.05). TRF reduced miR-34a expression in senescent HDFs and increased miR-20a expression in young HDFs and increased miR-449a expression in both young and senescent HDFs. Our results also demonstrated that ectopic expression of miR-34a reduced the expression of CDK4 significantly (P < 0.05). TRF inhibited miR-34a expression thus relieved its inhibition on CDK4 gene expression. No significant change was observed on the expression of CCND1, SIRT1, and miR-34a upstream transcriptional regulator, TP53. In conclusion tocotrienol-rich fraction prevented cellular senescence of human diploid fibroblasts via modulation of SA-miRNAs and target genes expression.
    Oxidative medicine and cellular longevity 07/2014; 2014(2):725929. DOI:10.1155/2014/725929 · 3.36 Impact Factor
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    • "Furthermore, epigenetically, microRNAs (miRNA) could influence many basic cellular and pathological processes by regulating gene expression post-transcriptionally through binding to complementary sequences in the 3′ untranslated region (3′ UTR) of target mRNAs [16]. And recent studies showed that miRNAs participated in regulation of aging and a variety of age-associated pathways [17]. "
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    ABSTRACT: The functional deficiencies of bone marrow-derived mesenchymal stem cells (MSCs) may contribute to the aging process and age-related diseases, such as osteoporosis. Although it has been reported that microRNAs (miRNAs) played an important role in mechanisms of gene regulation of aging, and their expression profiles in MSCs osteogenic differentiation were established in recent years, but it is still elusive for the dynamic patterns of miRNAs in aging process. Importantly, the miRNAs in aged bone tissue had not been yet reported so far. Here, we combined high through-put sequencing with computational techniques to detect miRNAs dynamics in MSCs and bone tissue of age-related osteoporosis. Among the detected miRNAs, 59 identified miRNAs in MSCs and 159 in bone showed significantly differential expressions. And more importantly, there existed 8 up-regulated and 30 down-regulated miRNAs in both MSCs and bone during the aging process, with the majority having a trend of down-regulation. Furthermore, after target prediction and KEGG pathway analysis, we found that their targeted genes were significantly enriched in pathways in cancer, which are complex genetic networks, comprise of a number of age-related pathways. These results strongly suggest that these analyzed miRNAs may be negatively involved in age-related osteoporosis, given that most of them showed a decreased expression, which could lay a good foundation for further functional analysis of these miRNAs in age-related osteoporosis.
    PLoS ONE 08/2013; 8(8):e71895. DOI:10.1371/journal.pone.0071895 · 3.23 Impact Factor
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    • "Increasing evidence has confirmed that miRNAs act as novel cellular senescence regulators [26,27]. However, there is little information regarding the potential involvement of miRNAs in regulating the cellular senescence of the corneal endothelium. "
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    ABSTRACT: To identify critical microRNAs (miRNAs) that play important roles in regulating the aging of corneal endothelial cells in mice aged 10-13 weeks and 2 years. We collected the corneal endothelia from 30 mice aged 10-13 weeks and 30 mice aged 2 years. The samples were pooled into six groups (Y1, Y2, Y3 and S1, S2, S3). Each group comprised corneal endothelia from 10 mice, and these six groups were used for a genome-wide miRNA microarray study. The expression levels of eight selected miRNAs were further validated independently by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Target genes were predicted using a computational approach due to their base-pairing rules between miRNA and messenger RNA target sites. The locations of binding sequences were within the target's 3' untranslated regions (UTR), and the conservation of target binding sequences occurred within related genomes. Additional gene ontology and signaling pathway analyses were performed using bioinformatics tools. Twenty-seven miRNAs (7 upregulated and 20 downregulated) were found to be differentially expressed (fold change >2, p value <0.05) in the corneal endothelia of adult and old mice. The qRT-PCR results confirmed the differential expression of eight miRNAs between the corneal endothelia of adult and old mice. A computational approach demonstrated that the target genes of the differentially expressed miRNAs might be involved in several signaling pathways, including the glutamatergic synapse pathway (p=0.000313), the phosphatidylinositol signaling pathway (p=0.00197), the neurotrophin signaling pathway (p=0.00687), the transforming growth factor-beta signaling pathway (p=0.0143), and oxidative phosphorylation (p=0.0223). Our study identified miRNAs that are differentially expressed in the corneal endothelium during aging for the first time. We also identified fluctuations in the expression of these specific miRNAs that may be related to age-specific changes. Understanding miRNA expression and interactions in tissues such as the cornea may aid in the understanding of the basic and pathophysiological processes of age-related ocular pathologies.
    Molecular vision 08/2013; 19:1815-25. · 1.99 Impact Factor
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