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miRNA Profiling of Naive, Effector and Memory CD8 T Cells. PLoS ONE 2: e1020. assay was used for detecting cell viability.) B, siRNA construct for CD44 (left). siRNA-mediated silencing of CD44 was examined by Western blot probed with anti-CD44 antibody (r
- doi:10.1371/journal.pone.0002420.s010 (1.13 MB PPT
, 2007
"... microRNAs have recently emerged as master regulators of gene expression during development and cell differentiation. Although profound changes in gene expression also occur during antigen-induced T cell differentiation, the role of miRNAs in the process is not known. We compared the miRNA expression ..."
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Cited by 39 (0 self)
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microRNAs have recently emerged as master regulators of gene expression during development and cell differentiation. Although profound changes in gene expression also occur during antigen-induced T cell differentiation, the role of miRNAs in the process is not known. We compared the miRNA expression profiles between antigen-specific naïve, effector and memory CD8+ T cells using 3 different methods-small RNA cloning, miRNA microarray analysis and real-time PCR. Although many miRNAs were expressed in all the T cell subsets, the frequency of 7 miRNAs (miR-16, miR-21, miR-142-3p, miR-142-5p, miR-150, miR-15b and let-7f) alone accounted for,60 % of all miRNAs, and their expression was several fold higher than the other expressed miRNAs. Global downregulation of miRNAs (including 6/7 dominantly expressed miRNAs) was observed in effector T cells compared to naïve cells and the miRNA expression levels tended to come back up in memory T cells. However, a few miRNAs, notably miR-21 were higher in effector and memory T cells compared to naïve T cells. These results suggest that concomitant with profound changes in gene expression, miRNA profile also changes dynamically during T cell differentiation. Sequence analysis of the cloned mature miRNAs revealed an extensive degree of end polymorphism. While 39end polymorphisms dominated, heterogeneity at both ends, resembling drosha/dicer processing shift was also seen in miR-142, suggesting a possible novel mechanism to generate new miRNA and/or to diversify miRNA target selection. Overall, our results suggest that dynamic changes in the expression of miRNAs may be important for the regulation of gene expression during
Human miRNA precursors with box H/ACA snoRNA features. PLoS. Comput. Biol. 2009; 5:e1000507. [PubMed: 19763159
"... MicroRNAs (miRNAs) and small nucleolar RNAs (snoRNAs) are two classes of small non-coding regulatory RNAs, which have been much investigated in recent years. While their respective functions in the cell are distinct, they share interesting genomic similarities, and recent sequencing projects have id ..."
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Cited by 38 (6 self)
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MicroRNAs (miRNAs) and small nucleolar RNAs (snoRNAs) are two classes of small non-coding regulatory RNAs, which have been much investigated in recent years. While their respective functions in the cell are distinct, they share interesting genomic similarities, and recent sequencing projects have identified processed forms of snoRNAs that resemble miRNAs. Here, we investigate a possible evolutionary relationship between miRNAs and box H/ACA snoRNAs. A comparison of the genomic locations of reported miRNAs and snoRNAs reveals an overlap of specific members of these classes. To test the hypothesis that somemiRNAsmight have evolved from snoRNA encoding genomic regions, reportedmiRNA-encoding regions were scanned for the presence of box H/ACA snoRNA features. Twenty miRNA precursors show significant similarity to H/ACA snoRNAs as predicted by snoGPS. These include molecules predicted to target known ribosomal RNA pseudouridylation sites in vivo for which no guide snoRNA has yet been reported. The predicted folded structures of these twenty H/ACA snoRNA-like miRNA precursors reveal molecules which resemble the structures of known box H/ACA snoRNAs. The genomic regions surrounding these predicted snoRNA-like miRNAs are often similar to regions around snoRNA retroposons, including the presence of transposable elements, target site duplications and poly (A) tails. We further show that the precursors of five H/ACA snoRNA-like miRNAs (miR-151, miR-605, mir-664, miR-215 and miR-140) bind to dyskerin, a specific protein component of functional box H/ ACA small nucleolar ribonucleoprotein complexes suggesting that these molecules have retained some H/ACA snoRNA
MicroRNA 21 promotes glioma invasion by targeting matrix metalloproteinase regulators. Mol Cell Biol 28: 5369–5380
, 2008
"... Supplemental material This article cites 60 articles, 18 of which can be accessed free at: ..."
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Cited by 28 (0 self)
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Supplemental material This article cites 60 articles, 18 of which can be accessed free at:
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments
- Nucleic Acids Res
, 2009
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Antagonistic role of hnRNP A1 and KSRP in the regulation of let-7a biogenesis. Nat Struct Mol Biol. 2010; 17:1011–1018. [PubMed: 20639884
"... The pluripotency promoting proteins Lin28a and Lin28b act as posttranscriptional repressors of let-7 miRNA biogenesis in undifferentiated embryonic stem cells. The levels of mature let-7a differ substantially in cells lacking Lin28 expression, indicating the existence of additional mechanism(s) of p ..."
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Cited by 25 (2 self)
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The pluripotency promoting proteins Lin28a and Lin28b act as posttranscriptional repressors of let-7 miRNA biogenesis in undifferentiated embryonic stem cells. The levels of mature let-7a differ substantially in cells lacking Lin28 expression, indicating the existence of additional mechanism(s) of posttranscriptional regulation. Here, we present evidence supporting a role for hnRNP A1 as a negative regulator of let-7a. HnRNP A1 binds the conserved terminal loop of pri-let-7a-1 and inhibits its processing by Drosha. Levels of mature let-7a negatively correlate with hnRNP A1 levels in somatic cell lines. Furthermore, hnRNP A1 depletion increased pri-let-7a-1 processing by cell extracts, whereas its ectopic expression decreased let-7a production in vivo. Finally, hnRNP A1 binding to let-7a interferes with the binding of the KH-type splicing regulatory protein KSRP, known to promote let-7a biogenesis. We propose that hnRNP A1 and KSRP play antagonistic roles in the posttranscriptional regulation of let-7a expression.
Evidence for human microRNA-offset RNAs in small RNA sequencing data
- Bioinformatics
"... MicroRNA-offset-RNAs (moRNAs) were recently detected as highly abundant class of small RNAs in a basal chordate. Using short read sequencing data we show here that moRNAs are also produced from human microRNA precursors, albeit at quite low expression levels. The expression levels of moRNAs are unre ..."
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Cited by 22 (4 self)
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MicroRNA-offset-RNAs (moRNAs) were recently detected as highly abundant class of small RNAs in a basal chordate. Using short read sequencing data we show here that moRNAs are also produced from human microRNA precursors, albeit at quite low expression levels. The expression levels of moRNAs are unrelated to those of the associated microRNAs. Surprisingly, microRNA precursors that also show moRNAs are typically evolutionarily old, comprising more than half of the miRNA families that were present in early Bilateria, while evidence for moRNAs was found only for a relative small fraction of miRNA families of recent origin. 1
An intronic microRNA silences genes that are functionally antagonistic to its host gene. Nucleic Acids Res 36: 5232–5241. luciferase activity the Dual-Glo luciferase assay system (Promega) was performed as previously described [36]. Briefly, an appropriat
- and were cultured in Dulbecco’s Modified Eagle Medium (DMEM) high glucose (4.5 g/L)supplemented with pyruvate (10 mg/mL), penicillin/streptomycin antibiotics (20 mg/mL) and 10% fetal calf serum. The cells were maintained at 37uC and 5% CO2. Primary cultur
, 2008
"... antagonistic to its host gene ..."
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Manjunath N: Alternative processing of primary microRNA transcripts by Drosha generates 5' end variation of mature microRNA. PLoS One 2009
"... Background: It is generally believed that the miRNA processing machinery ensures the generation of a mature miRNA with a fixed sequence, particularly at its 59 end. However, we and others have recently noted that the ends of a given mature miRNA are not absolutely fixed, but subject to variation. Ne ..."
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Cited by 22 (0 self)
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Background: It is generally believed that the miRNA processing machinery ensures the generation of a mature miRNA with a fixed sequence, particularly at its 59 end. However, we and others have recently noted that the ends of a given mature miRNA are not absolutely fixed, but subject to variation. Neither the significance nor the mechanism behind the generation of such miRNA polymorphism is understood. miR-142 is an abundantly expressed miRNA in hematopoietic cells and exhibits a high frequency of 59 end polymorphism. Methodology/Principal Findings: Here we show that a shift in the Drosha processing of pri-miRNA generates multiple forms of miR-142s in vivo with differing 59 ends that might target different genes. Sequence analysis of several pre-miRNA ends cloned from T cells reveals that unlike many other pri-miRNAs that are processed into a single pre-miRNA, pri-miR-142 is processed into 3 distinct pre-miR-142s. Dicer processing studies suggest that each of the 3 pre-miR-142s is processed into a distinct double-stranded miRNA, giving rise to 4 mature miRNA variants that might regulate different target gene pools. Conclusions/Significance: Thus, alternative Drosha processing might be a novel mechanism for diversification of the miRNA target gene pool.
JB: Highly sensitive and specific microRNA expression profiling using BeadArray technology
- Nucleic Acids Res
"... We have developed a highly sensitive, specific and reproducible method for microRNA (miRNA) expression profiling, using the BeadArray TM technology. This method incorporates an enzyme-assisted specificity step, a solid-phase primer extension to distinguish between members of miRNA families. In addit ..."
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Cited by 21 (2 self)
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We have developed a highly sensitive, specific and reproducible method for microRNA (miRNA) expression profiling, using the BeadArray TM technology. This method incorporates an enzyme-assisted specificity step, a solid-phase primer extension to distinguish between members of miRNA families. In addition, a universal PCR is used to amplify all targets prior to array hybridization. Currently, assay probes are designed to simultaneously analyse 735 well-annotated human miRNAs. Using this method, highly reproducible miRNA expression profiles were generated with 100–200 ng total RNA input. Furthermore, very similar expression profiles were obtained with total RNA and enriched small RNA species (R 2 0.97). The method has a 3.5–4 log (10 5 –10 9 molecules) dynamic range and is able to detect 1.2- to 1.3-fold-differences between samples. Expression profiles generated by this method are highly comparable to those obtained with RT–PCR (R 2 = 0.85–0.90) and direct sequencing (R = 0.87–0.89). This method, in conjunction with the 96-sample array matrix should prove useful for high-throughput expression profiling of miRNAs in large numbers of tissue samples.
Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer’s disease cortex reveals altered miRNA regulation
- PLoS ONE
, 2010
"... Although microRNAs are being extensively studied for their involvement in cancer and development, little is known about their roles in Alzheimer’s disease (AD). In this study, we used microarrays for the first joint profiling and analysis of miRNAs and mRNAs expression in brain cortex from AD and ag ..."
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Although microRNAs are being extensively studied for their involvement in cancer and development, little is known about their roles in Alzheimer’s disease (AD). In this study, we used microarrays for the first joint profiling and analysis of miRNAs and mRNAs expression in brain cortex from AD and age-matched control subjects. These data provided the unique opportunity to study the relationship between miRNA and mRNA expression in normal and AD brains. Using a nonparametric analysis, we showed that the levels of many miRNAs can be either positively or negatively correlated with those of their target mRNAs. Comparative analysis with independent cancer datasets showed that such miRNA-mRNA expression correlations are not static, but rather context-dependent. Subsequently, we identified a large set of miRNA-mRNA associations that are changed in AD versus control, highlighting AD-specific changes in the miRNA regulatory system. Our results demonstrate a robust relationship between the levels of miRNAs and those of their targets in the brain. This has implications in the study of the molecular pathology of AD, as well as miRNA biology in general.
