miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19–miR-106a interaction

Imig, Jochen; Brunschweiger, Andreas; Brümmer, Anneke; Guennewig, Boris; Mittal, Nitish; Kishore, Shivendra; Tsikrika, Panagiota; Gerber, André P.; Zavolan, Mihaela; Hall, Jonathan

doi:10.1038/nchembio.1713

Cited by 175 publications

(149 citation statements)

References 60 publications

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“…CLIP strategies are nowadays popular for high-throughput analysis of physiological miRNA targets (Chi et al, 2009;Hafner et al, 2010;Leung et al, 2011;Chi et al, 2012;Clark et al, 2014;Grosswendt et al, 2014;Haecker and Renne, 2014;Liu et al, 2014a;Imig et al, 2015) and it is accompanied with a number of algorithms and databases facilitating identification of miRNA targets in high-throughput CLIP data (Hsieh and Wang, 2011;Yang et al, 2011;Balaga et www.efsa.europa.eu/publications 254 EFSA Supporting publication 2017:EN-1246…”

Section: Immunoprecipitation Of Small Rna:target Rna Complexesmentioning

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: Immunoprecipitation Of Small Rna:target Rna Complexesmentioning

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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“…Previous reports have demonstrated that lncRNAs exert regulatory control on gene function through their interaction with miRNAs, a family of small non-coding RNAs, which are important post-transcriptional regulators of gene expression (49)(50)(51). Based on these findings, the present study examine the potential roles of lncRNAs in binding to and regulating miRNAs.…”

Section: Discussionmentioning

confidence: 99%

Long non-coding RNA RP5-833A20.1 inhibits proliferation, metastasis and cell cycle progression by suppressing the expression of NFIA in U251 cells

Kang

Nie

et al. 2016

Molecular Medicine Reports

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Abstract. Early reports suggest that nuclear factor IA (NFIA) is important in the pathogenesis of glioma. Our previous study demonstrated that the long non-coding RNA (lncRNA), RP5-833A20.1, suppressed the expression of NFIA in THP-1 macrophage-derived foam cells. However, the effect and possible mechanism of RP5-833A20.1 on glioma remains to be fully elucidated, and whether the NFIA-dependent pathway is involved in its progression has not been investigated. In the present study, the mechanisms by which RP5-833A20.1 regulates the expression of NFIA in glioma were investigated. The expression levels of RP5-833A20.1 and NFIA were determined in U251 cells and clinical samples using reverse transcription-quantitative polymerase chain reaction (PCR) analysis. The effects of RP5-833A20.1 on cell proliferation, invasion, cell cycle and apoptosis were evaluated using in vitro assays. The potential changes in protein expression were investigated using western blot analysis. The methylation status of the CpG island in the NFIA promoter was determined using bisulfite PCR (BSP) sequencing. It was found that the expression of RP5-833A20.1 was downregulated, whereas the expression of NFIA was upregulated in glioma tissues, compared with corresponding adjacent nontumor tissues from 20 patients with glioma. The overexpression of RP5-833A20.1 inhibited proliferation and cell cycle progression, and induced apoptosis in the U251 cells. The mRNA and protein levels of NFIA were markedly inhibited by overexpression of RP5-833A20.1 in the U251 cells. The overexpression of RP5-833A20.1 increased the expression of microRNA-382-5p in the U251 cells. The BSP assay revealed that the overexpression of RP5-833A20.1 enhanced the methylation level of the NFIA promoter. These results demonstrated that RP5-833A20.1 inhibited tumor cell proliferation, induced apoptosis and inhibited cell-cycle progression by suppressing the expression of NFIA in U251 cells. Collectively, these results indicated RP5-833A20.1 as a novel therapeutic target for glioma.

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“…Therefore, certain cross-linking approaches such as AGO HITS-CLIP and PAR-CLIP have proven most reliable for target identification. Other methods, such as biotin-tagged miRNA approaches, work to various extents (Guo and Steitz 2014a;Tan et al 2014;Imig et al 2015).…”

Section: Viral Mirnas: Small Rnas Big Rolesmentioning

confidence: 99%

Viral noncoding RNAs: more surprises

et al. 2015

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Eukaryotic cells produce several classes of long and small noncoding RNA (ncRNA). Many DNA and RNA viruses synthesize their own ncRNAs. Like their host counterparts, viral ncRNAs associate with proteins that are essential for their stability, function, or both. Diverse biological roles—including the regulation of viral replication, viral persistence, host immune evasion, and cellular transformation—have been ascribed to viral ncRNAs. In this review, we focus on the multitude of functions played by ncRNAs produced by animal viruses. We also discuss their biogenesis and mechanisms of action.

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miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19–miR-106a interaction

Cited by 175 publications

References 60 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

Long non-coding RNA RP5-833A20.1 inhibits proliferation, metastasis and cell cycle progression by suppressing the expression of NFIA in U251 cells

Viral noncoding RNAs: more surprises

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