An estimate of the total number of true human miRNAs.
Julia Alles,Tobias Fehlmann,Ulrike Fischer,Christina Backes,Galata,Marie Minet,Martin Hart,Masood Abu-Halima,Friedrich A. Grässer,Hans-Peter Lenhof,Andreas Keller,Eckart Meese +11 more
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TLDR
The experimentally validated miRNAs will contribute to revising targetomes hypothesized by utilizing falsely annotated miRNA candidates, 1115 of which are currently annotated in miRBase V22.Abstract:
While the number of human miRNA candidates continuously increases, only a few of them are completely characterized and experimentally validated. Toward determining the total number of true miRNAs, we employed a combined in silico high- and experimental low-throughput validation strategy. We collected 28 866 human small RNA sequencing data sets containing 363.7 billion sequencing reads and excluded falsely annotated and low quality data. Our high-throughput analysis identified 65% of 24 127 mature miRNA candidates as likely false-positives. Using northern blotting, we experimentally validated miRBase entries and novel miRNA candidates. By exogenous overexpression of 108 precursors that encode 205 mature miRNAs, we confirmed 68.5% of the miRBase entries with the confirmation rate going up to 94.4% for the high-confidence entries and 18.3% of the novel miRNA candidates. Analyzing endogenous miRNAs, we verified the expression of 8 miRNAs in 12 different human cell lines. In total, we extrapolated 2300 true human mature miRNAs, 1115 of which are currently annotated in miRBase V22. The experimentally validated miRNAs will contribute to revising targetomes hypothesized by utilizing falsely annotated miRNAs.read more
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Release of redox enzymes and micro-RNAs in extracellular vesicles, during infection and inflammation.
Stefano Caserta,Pietro Ghezzi +1 more
TL;DR: In this article, a review of the possible redox states of protein cysteines and the role of redox enzymes in their regulation is presented, including the extracellular forms of some of these enzymes, their association with exosomes/extracellular vesicles and their involvement with micro-RNAs/mRNAs involved in oxidative processes, relevant in infection and inflammation.
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Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells.
TL;DR: In this paper, the authors applied modified cross-linking ligation and sequencing of hybrids (qCLASH) to BRAF-mutant melanoma cells and found that up to 60% interactions occur via non-canonical seed pairing with a strong contribution of the 3′ miRNA sequence.
Journal ArticleDOI
Fetal Membrane Epigenetics.
Tamas Zakar,Jonathan W. Paul +1 more
TL;DR: Data generated using clinical samples and cell culture models strongly suggests that epigenetic events are associated with the phenotypic transitions of fetal membrane cells during the establishment, maintenance and termination of pregnancy potentially driving and consolidating the changes as pregnancy progresses.
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The Role of miRNAs, miRNA Clusters, and isomiRs in Development of Cancer Stem Cell Populations in Colorectal Cancer.
Victoria A. Stark,Caroline O. B. Facey,Vignesh Viswanathan,Vignesh Viswanathan,Bruce M. Boman,Bruce M. Boman +5 more
TL;DR: In this article, the specific miRNA cluster classifications and isomiRs that are predicted to target the ALDH1, CD166, BMI1, LRIG1, and LGR5 genes were discussed.
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MicroRNAs in Papillary Thyroid Cancer: What Is New in Diagnosis and Treatment
Maria Papaioannou,Angeliki G. Chorti,Anthoula Chatzikyriakidou,Kleanthis Giannoulis,Sohail Bakkar,Theodossis S. Papavramidis +5 more
TL;DR: MiRNAs are proposed as new diagnostic and therapeutic tools regarding PTC and could be essential biomarkers for PTC diagnosis applied in serum and FNA samples, while their contribution to prognosis is of great importance.
References
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MicroRNAs: Genomics, Biogenesis, Mechanism, and Function
TL;DR: Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.
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MicroRNAs: Target Recognition and Regulatory Functions
TL;DR: The current understanding of miRNA target recognition in animals is outlined and the widespread impact of miRNAs on both the expression and evolution of protein-coding genes is discussed.
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The functions of animal microRNAs
TL;DR: Evidence is mounting that animal miRNAs are more numerous, and their regulatory impact more pervasive, than was previously suspected.
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Characteristics of a Human Cell Line Transformed by DNA from Human Adenovirus Type 5
TL;DR: Human embryonic kidney cells have been transformed by exposing cells to sheared fragments of adenovirus type 5 DNA, and the transformed cells exhibited many of the characteristics of transformation including the elaboration of a virus-specific tumour antigen.
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miRBase: annotating high confidence microRNAs using deep sequencing data.
Ana Kozomara,Sam Griffiths-Jones +1 more
TL;DR: An update of the miRBase database is described, including the collation and use of deep sequencing data sets to assign levels of confidence to miR base entries, and a high confidence subset of miR Base entries are provided, based on the pattern of mapped reads.