miRGen 2.0: a database of microRNA genomic information and regulation

Alexiou, Panagiotis; Vergoulis, Thanasis; Gleditzsch, Martin; Prekas, George; Dalamagas, Theodore; Megraw, Molly; Große, Ivo; Sellis, Timos; Hatzigeorgiou, Artemis G.

doi:10.1093/nar/gkp888

Cited by 131 publications

(91 citation statements)

References 21 publications

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“…DIANA-MicroT tools are being developed in Artemis Hatzigeorgiou's laboratory for over a decade (Kiriakidou et al, 2004;Sethupathy et al, 2006;Megraw et al, 2007;Maragkakis et al, 2009;Alexiou et al, 2010;Maragkakis et al, 2011;Reczko et al, 2011;Vergoulis et al, 2012;Vlachos et al, 2012;Paraskevopoulou et al, 2013a;Paraskevopoulou et al, 2013b;Paraskevopoulou et al, 2016). MicroT is specifically trained on a positive and a negative set of miRNA binding sites located in 3'-UTR and CDS regions.…”

Section: Targetscan (Http://wwwtargetscanorg/vert_71/)mentioning

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: Targetscan (Http://wwwtargetscanorg/vert_71/)mentioning

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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“…To identify putative candidate genes regulated by these abnormally expressed microRNAs, we used the miRGen17 algorithm for in silico prediction of human mRNA targets. We identified 10 potential mRNA targets that could be negatively regulated by the 3 microRNAs (see Supplementary Table 2), which were then evaluated by qPCR.…”

Section: Resultsmentioning

confidence: 99%

“…We identified candidate mRNAs whose expression was likely to be modulated by the differentially expressed microRNAs found in the microarray experiments using the miRGen algorithm (version 2.0) 17. We selected candidate mRNAs by searching for the keywords neurogenesis, cell differentiation, cell migration, and cell proliferation.…”

Section: Methodsmentioning

confidence: 99%

Dysregulation of NEUROG2 plays a key role in focal cortical dysplasia

Avansini

Torres

Vieira

et al. 2018

Annals of Neurology

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ObjectiveFocal cortical dysplasias (FCDs) are an important cause of drug‐resistant epilepsy. In this work, we aimed to investigate whether abnormal gene regulation, mediated by microRNA, could be involved in FCD type II.MethodsWe used total RNA from the brain tissue of 16 patients with FCD type II and 28 controls. MicroRNA expression was initially assessed by microarray. Quantitative polymerase chain reaction, in situ hybridization, luciferase reporter assays, and deep sequencing for genes in the mTOR pathway were performed to validate and further explore our initial study.Resultshsa‐let‐7f (p = 0.039), hsa‐miR‐31 (p = 0.0078), and hsa‐miR34a (p = 0.021) were downregulated in FCD type II, whereas a transcription factor involved in neuronal and glial fate specification, NEUROG2 (p < 0.05), was upregulated. We also found that the RND2 gene, a NEUROG2‐target, is upregulated (p < 0.001). In vitro experiments showed that hsa‐miR‐34a downregulates NEUROG2 by binding to its 5′‐untranslated region. Moreover, we observed strong nuclear expression of NEUROG2 in balloon cells and dysmorphic neurons and found that 28.5% of our patients presented brain somatic mutations in genes of the mTOR pathway.InterpretationOur findings suggest a new molecular mechanism, in which NEUROG2 has a pivotal and central role in the pathogenesis of FCD type II. In this way, we found that the downregulation of hsa‐miR‐34a leads to upregulation of NEUROG2, and consequently to overexpression of the RND2 gene. These findings indicate that a faulty coupling in neuronal differentiation and migration mechanisms may explain the presence of aberrant cells and complete dyslamination in FCD type II. Ann Neurol 2018;83:623–635

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“…The growing body of transcriptomic data on miRNA expression has fueled the growth of resources that analyze miRNA expression patterns in normal tissues. Certain databases have been created using computational predictions and experimental results, for example miRBase (18), miRNAMap2.0 (19), miRGen (20), miRGator v2.0 (21) and miRecords (22). Other databases, such as TargetScan (2), PicTar (23) and TargetMiner (24), are based on algorithms designed to predict microRNA targets according to the complementary pairing with the target.…”

Section: Web-based Tools For Micrornas Involved In Human Cancer (Review)mentioning

confidence: 99%

Web-based tools for microRNAs involved in human cancer

2016

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Abstract. MicroRNAs (miRNAs/miRs) are a family of small, endogenous and evolutionarily-conserved non-coding RNAs that are involved in the regulation of several cellular and functional processes. miRNAs can act as oncogenes or tumor suppressors in all types of cancer, and could be used as prognostic and diagnostic biomarkers. Databases and computational algorithms are behind the majority of the research performed on miRNAs. These tools assemble and curate the relevant information on miRNAs and present it in a user-friendly manner. The current review presents 14 online databases that address every aspect of miRNA cancer research. Certain databases focus on miRNAs and a particular type of cancer, while others analyze the behavior of miRNAs in different malignancies at the same time. Additional databases allow researchers to search for mutations in miRNAs or their targets, and to review the naming history of a particular miRNA. All these databases are open-access, and are a valuable tool for those researchers working with these molecules, particularly those who lack access to an advanced computational infrastructure.

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miRGen 2.0: a database of microRNA genomic information and regulation

Cited by 131 publications

References 21 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

Dysregulation of NEUROG2 plays a key role in focal cortical dysplasia

Web-based tools for microRNAs involved in human cancer

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