Dynamic regulation of miRNA expression in ordered stages of cellular development

Neilson, Joel R.; Zheng, Grace X. Y.; Burge, Christopher B.; Sharp, Phillip A.

doi:10.1101/gad.1522907

Cited by 427 publications

(425 citation statements)

References 50 publications

(60 reference statements)

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“…As we have only measured miRNAs that are known so far, we cannot exclude that there are additional highly expressed unknown miRNAs that would raise the overall number of miRNAs per CD34+ cell. Interestingly, comparable miRNAs levels were reported by Neilson et al (2007) for cells representing different stages of T-lymphocyte development. Furthermore, it was demonstrated that global miRNA abundance is higher at high cell densities in diverse animal cell lines (Hwang et al 2009), so that the cell-cell contact in tissues could also lead to an increased overall miRNA expression.…”

Section: Discussionmentioning

confidence: 48%

Absolute quantification of microRNAs by using a universal reference

Bissels¹,

Wild²,

Tomiuk³

et al. 2009

RNA

174

132

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MicroRNAs (miRNAs) are a species of small RNAs ;21-23-nucleotides long that have been shown to play an important role in many different cellular, developmental, and physiological processes. Accordingly, numerous PCR-, sequencing-, or hybridization-based methods have been established to identify and quantify miRNAs. Their short length results in a high dynamic range of melting temperatures and therefore impedes a proper selection of detection probes or optimized PCR primers. While miRNA microarrays allow for massive parallel and accurate relative measurement of all known miRNAs, they have so far been less useful as an assay for absolute quantification. Here, we present a microarray-based approach for global and absolute quantification of miRNAs. The method relies on the parallel hybridization of the sample of interest labeled with Cy5 and a universal reference of 954 synthetic miRNAs in equimolar concentrations that are labeled with Cy3 on a microarray slide containing probes for all human, mouse, rat, and viral miRNAs (miRBase 12.0). Each single miRNA is quantified with respect to the universal reference canceling biases related to sequence, labeling, or hybridization. We demonstrate the accuracy of the method by various spike-in experiments. Furthermore, we quantified miRNA copy numbers in liver samples and CD34(+)/ CD133(À) hematopoietic progenitor cells.

show abstract

Section: Discussionmentioning

confidence: 48%

Absolute quantification of microRNAs by using a universal reference

Bissels¹,

Wild²,

Tomiuk³

et al. 2009

RNA

174

132

View full text Add to dashboard Cite

show abstract

“…It has been shown that miRNAs expressed at low levels (< 100 copies per cell) did not significantly repress target-containing transcripts [42], since target encounter occurs by mass action and modestly expressed miRNAs have a low probability to meet target-containing transcripts. Previous measurements of miRNAs in liver samples revealed that let-7a, miR-16, miR-20, miR-21, and miR-22 were present at 700, 3 890, 130, 4 450, and 310 copies per cell, respectively [43], while miR-181a was expressed at 810 copies per cell in DP thymocytes [44] and miR-223 and miR-451 were 828 and 1 972 copies per cell in CD34(+)/CD133(−) cells [45]. It has been widely demonstrated that miRNAs expressed at these concentrations are biologically active [46][47][48][49].…”

Section: Ago2-associated Mature Mir168a In Mvs Is the Functional Formmentioning

confidence: 99%

Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA

et al. 2011

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Our previous studies have demonstrated that stable microRNAs (miRNAs) in mammalian serum and plasma are actively secreted from tissues and cells and can serve as a novel class of biomarkers for diseases, and act as signaling molecules in intercellular communication. Here, we report the surprising finding that exogenous plant miRNAs are present in the sera and tissues of various animals and that these exogenous plant miRNAs are primarily acquired orally, through food intake. MIR168a is abundant in rice and is one of the most highly enriched exogenous plant miRNAs in the sera of Chinese subjects. Functional studies in vitro and in vivo demonstrated that MIR168a could bind to the human/mouse low-density lipoprotein receptor adapter protein 1 (LDLRAP1) mRNA, inhibit LDLRAP1 expression in liver, and consequently decrease LDL removal from mouse plasma. These findings demonstrate that exogenous plant miRNAs in food can regulate the expression of target genes in mammals.

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“…Thus, sponges show direct effects on natural and endogenous targets, and can be used to validate target predictions. To test some predicted targets that had not yet been experimentally validated, we used a luciferase reporter regulated by a large fragment of the CD69 3′ UTR 17 or by the E2F5 UTR. As predicted by the TargetScan 4.0 and miRanda algorithms, respectively, these UTRs are each regulated by a single miR-20 site 18,19 .…”

Section: Validation Of Predicted Microrna Targetsmentioning

confidence: 99%

MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells

2007

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MicroRNAs are predicted to regulate thousands of mammalian genes, but relatively few targets have been experimentally validated and few microRNA loss-of-function phenotypes have been assigned. As an alternative to chemically modified antisense oligonucleotides, we developed microRNA inhibitors that can be expressed in cells, as RNAs produced from transgenes. Termed 'microRNA sponges', these competitive inhibitors are transcripts expressed from strong promoters, containing multiple, tandem binding sites to a microRNA of interest. When vectors encoding these sponges are transiently transfected into cultured cells, sponges derepress microRNA targets at least as strongly as chemically modified antisense oligonucleotides. They specifically inhibit microRNAs with a complementary heptameric seed, such that a single sponge can be used to block an entire microRNA seed family. RNA polymerase II promoter (Pol II)-driven sponges contain a fluorescence reporter gene for identification and sorting of spongetreated cells. We envision the use of stably expressed sponges in animal models of disease and development.MicroRNAs are 20-24-nucleotide RNAs derived from hairpin precursors. Through pairing with partially complementary sites in 3′ untranslated regions (UTRs), they mediate posttranscriptional silencing of a predicted 30% of protein-coding genes in mammals 1 . MicroRNAs have been implicated in critical processes including differentiation, apoptosis, proliferation, and the maintenance of cell and tissue identity; furthermore, their misexpression has been linked to cancer and other diseases [2][3][4][5][6][7] . But relatively few micro-RNA-target interactions have been experimentally validated in cell culture or in mouse models, and the functions of most microRNAs remain to be discovered. Creating genetic knockouts to determine the function of microRNA families is difficult, as individual microRNAs expressed from multiple genomic loci may repress a common set of targets containing a complementary seed sequence. Thus, a method for inhibiting these functional classes of paralogous micro-RNAs in vivo is needed. Presently, loss-of-function phenotypes are induced by means of chemically modified antisense oligonucleotides-2′ O-methyl, locked nucleic acid (LNA) and others-which are presumed to pair with and block mature microRNAs through extensive sequence complementarity [8][9][10] . Typically, oligonucleotide

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Dynamic regulation of miRNA expression in ordered stages of cellular development

Cited by 427 publications

References 50 publications

Absolute quantification of microRNAs by using a universal reference

Absolute quantification of microRNAs by using a universal reference

Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA

MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells

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