Common features of microRNA target prediction tools

Peterson, Sarah; Thompson, Jeffrey; Ufkin, Melanie; Sathyanarayana, Pradeep; Liaw, Lucy; Congdon, Clare Bates

doi:10.3389/fgene.2014.00023

Cited by 395 publications

(313 citation statements)

References 64 publications

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“…Unfortunately, in the study of this interaction, little-grounded assumptions were made that led to significant errors in the determination of miRNA binding sites in mRNA and interpretation of the obtained results. Existing programs for identification of miRNA binding sites in mRNA of target genes, unfortunately, predict many false-positive sites (Peterson et al, 2014). To increase the reliability of the predicted binding sites, we have studied orthologous genes of different animal species (Atambayeva et al, 2017).…”

Section: молекулярная и клеточная биологияmentioning

confidence: 99%

“…Unfortunately, in the publications related to the subject only a few substantiated assumptions were made that led to significant errors in determining the binding sites of miRNA in mRNA and interpreting of the obtained results. Existing programs for detecting miRNA binding sites in the mRNA of target genes, unfortunately, predict many false-positive sites (Peterson et al, 2014). To search for the binding sites, we used the MirTarget program, determining the characteristics of miRNA-mRNA interaction, including the detection of multiple miRNA binding sites (Ivashchenko et al, 2014).…”

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confidence: 99%

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The Characteristics of Mirna Binding Sites in Mrna of Zfhx3 Gene and Its Orthologs

Kondybaeva¹,

Акимниязова²,

Kamenova³

et al. 2018

Vestn. VOGiS

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Transcription factor gene ZFHX3 is one of the candidate genes involved in stroke development. The ZFHX3 protein contains oligopeptides encoded by trinucleotide repeats (TNRs). TNR variability is considered to be one of the causes of the disease, but their biological function has not yet been established. We assume that TNRs are the binding sites of miRNA to mRNA and are involved in regulation of ZFHX3 gene expression. The characteristics of miRNA–mRNA interaction were determined using MirTarget software. It has been shown that the first TNR in mRNA of the human ZFHX3 gene consists of the seven consecutive miR-12-32603-3p binding encoding polyGlu. The ZFHX3 protein of human polyGlu contains 30 Glu. In the orthologous proteins of 36 animal species the length of polyGlu varied from 27 Glu to 33 Glu. Negatively charged polyGlu of the ZFHX3 transcription factor probably interacted with positive DNA-binding proteins. The following mRNA region of the ZFHX3 gene contained the binding sites for miR-17-39416-3p, miR-5-15733-3p, miR-9-20317-3 encoding polyAla by 15 Ala lengths. In the 33 ZFHX3 orthologous proteins polyAla had the same length. The mRNA region of the human ZFHX3 gene with binding polysite of miR-1322-3p encoded polyGln consisting of 19 Gln. In the 41 orthologs of the ZFHX3 protein the length of polyGln varied from seven Gln to 23 Gln. The binding sites of miR-2-6184-3p, miR-5-14114-5p and miR-19-43437-5p were located with overlapping nucleotides sequences, and encode polyPro. In ZFHX3 human polyPro consisted of 12 Pro. In the orthologs, polyPro contained from 10 Pro to 14 Pro. The binding sites of miR-17-39416-3p, miR-9-20317-3p, miR-1-1819-3p, miR-5-15733-3p, miR-6-17815-3p, miR-18-39953-5p, miR-26862-5p, miR-1260b and miR-X-48174-3p in human ZFHX3 encoded polyGly by 22 Gly length. In the 28 orthologs of ZFHX3 the length of polyGly decreased to 11 Gly. The TNR regions could simultaneously bind several miRNAs, which increased the dependence of gene expression on miRNA. The oligopeptides encoded by the binding polysites of miRNA in mRNA in the orthologous ZFHX3 proteins were flanked by conserved oligopeptides.

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Section: молекулярная и клеточная биологияmentioning

confidence: 99%

mentioning

confidence: 99%

The Characteristics of Mirna Binding Sites in Mrna of Zfhx3 Gene and Its Orthologs

Kondybaeva¹,

Акимниязова²,

Kamenova³

et al. 2018

Vestn. VOGiS

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“…These include Targetscan, miRanda, DIANAmicroT, PicTAR, whose predictions were integrated into the miRBase, the central annotation database for miRNAs (Kozomara and Griffiths-Jones, 2014) and were also repeatedly evaluated in benchmark studies Ding et al, 2012a;Majoros et al, 2013;Peterson et al, 2014;Xu et al, 2014a). We add to these also MIRZA as it is one of the most recent algorithms, which in many aspects outperforms the other ones (Gumienny and Zavolan, 2015).…”

Section: Common Target Prediction Toolsmentioning

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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“…The target genes of miR-let-7e were predicted based on three public bioinformatics databases, including miRanda (www.microrna.org/) and TargetScan Human Release 6.2 (www.targetscan.org/) (15). The target genes were selected by miRanda if the mirSVR score ≤-0.1 and by TargetScan if the total context score was ≤-0.1 as previously descried (16).…”

Section: Interleukin-13 (Il-13) Stimulation Of Necsmentioning

confidence: 99%

MicroRNA‑let‑7e regulates the progression and development of allergic rhinitis by targeting suppressor of cytokine signaling 4 and activating Janus kinase 1/signal transducer and activator of transcription 3 pathway

Zhang

Jiang

et al. 2018

Exp Ther Med

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Abstract. The present study aimed to explore the microRNA-let-7e (miR-let-7e) expression in allergic rhinitis (AR), and to investigate the underlying molecular mechanisms. miR-let-7e expression in the nasal mucosa of mice and patients with AR were detected. The expression levels of three inflammatory factors, including histamine, immunoglobulin E and tumor necrosis factor-α (TNF-α), in the blood of AR mice and in interleukin (IL)-13-stimulated nasal epithelial cells (NECs) were also measured. Furthermore, the target gene of miR-let-7e was predicted and validated using a luciferase reporter assay. The expression levels of Janus kinase 1 (JAK1) and signal transducer and activator of transcription 3 (STAT3) were detected. The results demonstrated that miR-let-7e was downregulated in patients and mice with AR compared with the controls. In addition, the expression levels of inflammatory factors were higher in the blood of mice with AR compared with the control group, while miR-let-7e overexpression inhibited these levels in AR mice and IL-13-stimulated NECs. Furthermore, suppressor of cytokine signaling 4 (SOCS4) was revealed as a potential target gene of miR-let-7e and was negatively regulated by miR-let-7e. Overexpression of SOCS4 abrogated the anti-inflammatory activity of miR-let-7e overexpression. Finally, miR-let-7e overexpression activated the JAK1/STAT3 signaling pathway. In conclusion, miR-let-7e may serve an important role in the progression and development of AR, while overexpression of miR-let-7e had an anti-inflammatory effect by targeting SOCS4, which may be achieved by activation of the JAK1/STAT3 signaling pathway.

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Common features of microRNA target prediction tools

Cited by 395 publications

References 64 publications

The Characteristics of Mirna Binding Sites in Mrna of Zfhx3 Gene and Its Orthologs

The Characteristics of Mirna Binding Sites in Mrna of Zfhx3 Gene and Its Orthologs

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

MicroRNA‑let‑7e regulates the progression and development of allergic rhinitis by targeting suppressor of cytokine signaling 4 and activating Janus kinase 1/signal transducer and activator of transcription 3 pathway

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