A Novel Method to Detect Functional MicroRNA Targets

Vatolin, Sergei; Navaratne, Kapila; Weil, Robert J.

doi:10.1016/j.jmb.2006.02.063

Cited by 53 publications

(22 citation statements)

References 56 publications

(55 reference statements)

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“…Purified hybrid 3'-cDNA-miRNA-5' molecules are used in a second round of reverse transcription and sequenced (Vatolin et al, 2006). However, this method is prone to artifacts stemming from the variability of miRNA:target mRNA base pairing, which would result in highly variable efficiency of reverse transcription priming.…”

Section: Mirna Extensionmentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFS3

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This report is the outcome of an EFSA procurement aiming at investigating and summarising the state of knowledge on (I) the mode-of-action of dsRNA and miRNA pathways, (II) the potential for nontarget gene regulation by dsRNA-derived siRNAs or miRNAs, (III) the determination of siRNA pools in plant tissues and the importance of individual siRNAs for silencing. The report is based on a comprehensive and systematic literature search, starting with the identification and retrieval of~190,000 publications related to the research area and further filtered down with keywords to produce focused collections used for subsequent screening of titles and abstracts. The report is comprised of an (I) Introduction to the field of small RNAs, (II) a Data and Methodologies section containing strategies used for literature search and study selection, and (III) the Results of the literature review organized according to the three main procurement tasks. The outcome of the first task reviews dsRNA and miRNA pathways in mammals (including humans), birds, fish, arthropods, annelids, molluscs, nematodes, and plants. Eight taxon-dedicated chapters are based on~1,400 cumulative references chosen from~10,000 inspected titles and abstracts. We review conserved and divergent aspects of small RNA pathways and dsRNA responses in animals and plants including structure and function of key proteins as well as four basic mechanisms: genome-encoded posttranscriptional regulations (miRNA), degradation of RNAs by short interfering RNA pools generated from long dsRNA (RNAi), transcriptional silencing, and sequence-independent responses to dsRNA. The outcome of the second task focuses on base pairing between small RNAs and their target RNAs and predictability of biological effects of small RNAs in animals and plants. The outcome of the last task reviews methodology, siRNA pools, and movement of small RNAs in plants. Potential transfer of small RNAs between species and circulating miRNAs in mammals is described in the final chapter.

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Section: Mirna Extensionmentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFS3

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“…The pri-miRNA is cleaved by the Drosha ribonuclease III enzyme to generate an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is exported into the cytoplasm by the transporter exportin 5 [4]. Subsequently, it is further cleaved by the Dicer ribonuclease to produce the mature miRNA and antisense miRNA star (miRNA*) products [5]. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which most commonly results in translational inhibition or destabilization of the target mRNAs [6,7].…”

Section: Introductionmentioning

confidence: 99%

MicroRNA-451 suppresses tumor cell growth by down-regulating IL6R gene expression

Liu

Wang

et al. 2014

Cancer Epidemiology

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“…The method essentially gives no information on miRNA-target combinations. Another method for detecting miRNA-mRNA complexes was proposed by Vatolin et al (2006), in which cytoplasmic extract was reacted with reverse transcriptases to indicate that an endogenous miRNA can be a primer for cDNA synthesis on a target mRNA template. The cDNA fragment was ligated to an adapter oligonucleotide at the 59 terminus and amplified by polymerase chain reaction (PCR) with a primer from the adapter and a genespecific primer corresponding to the target mRNA.…”

Section: Introductionmentioning

confidence: 99%

A novel biochemical method to identify target genes of individual microRNAs: Identification of a new Caenorhabditis elegans let-7 target

Andachi¹

2008

RNA

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MicroRNAs (miRNAs) are roughly 22-nucleotide regulatory RNAs that play important roles in many developmental and physiological processes. Animal miRNAs down-regulate target genes by forming imperfect base pairs with 39 untranslated regions (39 UTRs) of their mRNAs. Thousands of miRNAs have been discovered in several organisms. However, the target genes of almost all of these miRNAs remain to be identified. Here, we describe a method for isolating cDNA clones of target mRNAs that form base pairs in vivo with an endogenous miRNA of interest, in which the cDNAs are synthesized from the mRNAs using the miRNA as a reverse-transcription primer. The application of this method to Caenorhabditis elegans miRNA lin-4 under test conditions yielded many clones of the known target gene lin-14 that correspond to partial sequences 59 to lin-4 binding sites in the 39 UTR. The method was also applied to C. elegans miRNA let-7 and a new target gene responsible for the lethal phenotype in let-7 mutants was identified. These results demonstrate that the method is a useful way to identify targets on the basis of base pairing with individual miRNAs.

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A Novel Method to Detect Functional MicroRNA Targets

Cited by 53 publications

References 56 publications

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

MicroRNA-451 suppresses tumor cell growth by down-regulating IL6R gene expression

A novel biochemical method to identify target genes of individual microRNAs: Identification of a new Caenorhabditis elegans let-7 target

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