miR-EdiTar: a database of predicted A-to-I edited miRNA target sites

Laganà, Alessandro; Paone, Alessio; Veneziano, Dario; Cascione, Luciano; Gasparini, Pierluigi; Carasi, Stefania; Russo, Francesco; Nigita, Giovanni; Macca, Valentina; Giugno, Rosalba; Pulvirenti, Alfredo; Shasha, Dennis; Ferro, Alfredo; Croce, Carlo M.

doi:10.1093/bioinformatics/bts589

Cited by 31 publications

(20 citation statements)

References 23 publications

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“…There are other examples of RNA editing in cancer (see review by Skarda et al [125]), as well as databases compiling particular miRNA sequences subject to RNA editing[126]. Overall, it is clear that RNA editing is modified in tumors on a global scale; however, more work is required to understand the role of miRNA editing in the processes of tumorigenesis.…”

Section: Regulating the Regulators – How Many Ways?mentioning

confidence: 99%

Aberrant Regulation and Function of MicroRNAs in Cancer

2014

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Synopsis Malignant neoplasms are consistently among the top four leading causes of death in all age groups in the United States, despite a concerted effort toward developing novel therapeutic approaches[1]. Our understanding of and therapeutic strategy for treating each of these neoplastic diseases has been elevated through decades of research on the genetics, signaling pathways, and cellular biology that govern tumor cell initiation, progression and maintenance. Much of this work has concentrated on post-translational modifications and abnormalities at the DNA level, including point mutations, amplifications/deletions, and chromosomal translocations, and how these aberrant events affect the expression and function of protein-coding genes. Only recently has a novel class of conserved gene regulatory molecules been identified as major contributors to malignant neoplastic disease. This review focuses on how these small non-coding RNA molecules, termed microRNAs (miRNAs), can function as oncogenes or tumor suppressors, and how the misexpression of miRNAs and dysregulation of factors that regulate miRNAs contributes to the tumorigenic process. Specific focus is given to more recently discovered regulatory mechanisms that go awry in cancer, and how these changes alter miRNA expression, processing, and function.

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Section: Regulating the Regulators – How Many Ways?mentioning

confidence: 99%

Aberrant Regulation and Function of MicroRNAs in Cancer

2014

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“…A-to-I RNA editing has been discovered to occur in both intronic and exonic regions, 5 -and 3'-UTRs as well. RNA editing events can take place in several cellular contexts: in the gene expression pathway [Bazak et al, 2014], such as in the creation and/or destruction of splicing sites [Emeson et al, 1999] or in translation [Nishikura, 2010]; during gene regulation in miRNA/mRNA-binding regions [Nishikura, 2006;Borchert et al, 2009;Laganà et al, 2012]. Recently, it has been observed that RNA editing may occur in ncRNAs, particularly in pre-tRNAs [Su and Randau, 2011], pri-miRNAs [Kawahara et al, 2008;Kawahara, 2012], lncRNAs [Mitra et al, 2012], and lately piRNAs [Yang et al, 2015] and circRNAs [Ivanov et al, 2015].…”

Section: Detection and Evaluation Of Rna Modification Eventsmentioning

confidence: 99%

Noncoding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges

et al. 2016

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One of the most significant biological discoveries of the last decade is represented by the reality that the vast majority of the transcribed genomic output comprises diverse classes of noncoding RNAs (ncRNAs) that may play key roles and/or be affected by many biochemical cellular processes (i.e., RNA editing), with implications in human health and disease. With 90% of the human genome being transcribed and novel classes of ncRNA emerging (tRNA-derived small RNAs and circular RNAs among others), the great majority of the human transcriptome suggests that many important ncRNA functions/processes are yet to be discovered. An approach to filling such vast void of knowledge has been recently provided by the increasing application of next-generation sequencing (NGS), offering the unprecedented opportunity to obtain a more accurate profiling with higher resolution, increased throughput, sequencing depth, and low experimental complexity, concurrently posing an increasing challenge in terms of efficiency, accuracy, and usability of data analysis software. This review provides an overview of ncRNAs, NGS technology, and the most recent/popular computational approaches and the challenges they attempt to solve, which are essential to a more sensitive and comprehensive ncRNA annotation capable of furthering our understanding of this still vastly uncharted genomic territory.

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“…A-to-I editing is very widespread in the human genome [4] and spans both coding and non-coding regions, mainly within highly repetitive Alu elements, which can form the requisite double-stranded structure for ADAR-mediated editing. RNA editing has been shown to create different protein isoforms [5], modulate alternative splicing [6], and regulate transcript stability by modifying microRNAs and microRNA binding sites [7,8]. In the context of cancer, as this recent work shows, RNA editing may serve as an additional, and much more dynamic and flexible, counterpart to genomic-level mutations.…”

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confidence: 99%

RNA Editing Dynamically Rewrites the Cancer Code

2015

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Global analyses of cancer transcriptomes demonstrate that ADAR (adenosine deaminase, RNA-specific)-mediated RNA editing dynamically contributes to genetic alterations in cancer, and directly correlates with progression and prognosis. RNA editing is abundant and frequently elevated in cancer, and affects functionally and clinically relevant sites in both coding and non-coding regions of the transcriptome. Therefore, ADAR and differentially edited transcripts may be promising biomarkers or targets for therapy.

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miR-EdiTar: a database of predicted A-to-I edited miRNA target sites

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 31 publications

References 23 publications

Aberrant Regulation and Function of MicroRNAs in Cancer

Aberrant Regulation and Function of MicroRNAs in Cancer

Noncoding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges

RNA Editing Dynamically Rewrites the Cancer Code

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