Topical Collection "Non-Coding RNA Methods"

Editors

Guest Editor
Dr. Piero Carninci

RIKEN Center for Life Science Technologies, Japan
E-Mail
Guest Editor
Dr. Florent Hubé

UMR7216 Epigenetics and Cell Fate, University of Paris Diderot - Paris 7, Lamarck Building, 35 rue Hélène Brion, 75013 Paris, France
Website | E-Mail
Interests: long non-coding RNAs; small non-coding RNAs; functional genomics; transcriptional regulation; RNA secondary structure; RNA–protein interactions

Topical Collection Information

Dear Colleagues,

Non-coding RNA is now accepting submissions for a Topical Collection on non-coding RNA methods. This Topical Collection is co guest-edited by Dr. Piero Carninci from the RIKEN Center for Life Science Technologies in Japan and Dr. Florent Hubé; from the National Center for Scientific Research (CNRS) in Paris. Accepted papers are published online immediately after copy editing. Non-Coding RNA is an Open Access journal. There are no Article Processing Charges (APCs) for papers submitted to the journal in 2018.

ncRNA is a rapidly growing field in which new research methods are continuously appearing. With this Topical Collection, we aim to collect a selection of articles on newly developed techniques of special interest for researchers in the ncRNA field.

We will consider manuscripts that report on new experimental and computational methods, as well as reviews of exceptional interest that focus on newly developed techniques for ncRNA research that include:

  • ncRNA analysis programs

  • ncRNA chromatography methods

  • ncRNA structure analysis

  • ncRNA function analysis

  • ncRNA by high-throughput screening

  • ncRNA database/annotation

  • ncRNA imaging

  • methods to detect the interactome of RNA (with proteins, with chromatin, etc.)

Dr. Piero Carninci
Dr. Florent Hubé
Guest Editors

Please use the online submission system and indicate in your cover letter that you would like to have your manuscript considered for the Topical Collection "Non Coding RNA methods". If you would like to enquire about the suitability of your article for this Topical Collection, please email your pre-submission enquiry to Dr. Piero Carninci  ([email protected]) or to Dr. Florent Hubé (flore[email protected]) with the ncRNA Editorial Office ([email protected]) in copy.

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the collection website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Non-Coding RNA is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) is waived for well-prepared manuscripts submitted to this issue. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (3 papers)

2018

Open AccessFeature PaperArticle Targeted Genomic Screen Reveals Focal Long Non-Coding RNA Copy Number Alterations in Cancer Cell Lines
Non-Coding RNA 2018, 4(3), 21; https://doi.org/10.3390/ncrna4030021
Received: 16 August 2018 / Revised: 10 September 2018 / Accepted: 10 September 2018 / Published: 13 September 2018
PDF Full-text (1776 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The landscape of somatic copy-number alterations (SCNAs) affecting long non-coding RNAs (lncRNAs) in human cancers remains largely unexplored. While the majority of lncRNAs remain to be functionally characterized, several have been implicated in cancer development and metastasis. Considering the plethora of lncRNAs genes
[...] Read more.
The landscape of somatic copy-number alterations (SCNAs) affecting long non-coding RNAs (lncRNAs) in human cancers remains largely unexplored. While the majority of lncRNAs remain to be functionally characterized, several have been implicated in cancer development and metastasis. Considering the plethora of lncRNAs genes that have been currently reported, it is conceivable that many more lncRNAs might function as oncogenes or tumor suppressor genes. We devised a strategy to detect focal lncRNA SCNAs using a custom DNA microarray platform probing 10,519 lncRNA genes. By screening a panel of 80 cancer cell lines, we detected numerous focal aberrations targeting one or multiple lncRNAs without affecting neighboring protein-coding genes. These focal aberrations are highly suggestive for a tumor suppressive or oncogenic role of the targeted lncRNA gene. Although functional validation remains an essential step in the further characterization of the involved candidate cancer lncRNAs, our results provide a direct way of prioritizing candidate lncRNAs that are involved in cancer pathogenesis. Full article
Figures

Figure 1

Open AccessArticle Z Probe, An Efficient Tool for Characterizing Long Non-Coding RNA in FFPE Tissues
Non-Coding RNA 2018, 4(3), 20; https://doi.org/10.3390/ncrna4030020
Received: 10 July 2018 / Revised: 22 August 2018 / Accepted: 27 August 2018 / Published: 5 September 2018
PDF Full-text (3149 KB) | HTML Full-text | XML Full-text
Abstract
Formalin-fixed paraffin embedded (FFPE) tissues are a valuable resource for biomarker discovery in order to understand the etiology of different cancers and many other diseases. Proteins are the biomarkers of interest with respect to FFPE tissues as RNA degradation is the major challenge
[...] Read more.
Formalin-fixed paraffin embedded (FFPE) tissues are a valuable resource for biomarker discovery in order to understand the etiology of different cancers and many other diseases. Proteins are the biomarkers of interest with respect to FFPE tissues as RNA degradation is the major challenge in these tissue samples. Recently, non-protein coding transcripts, long non-coding RNAs (lncRNAs), have gained significant attention due to their important biological actions and potential involvement in cancer. RNA sequencing (RNA-seq) or quantitative reverse transcription-polymerase chain reaction (qRT-PCR) are the only validated methods to evaluate and study lncRNA expression and neither of them provides visual representation as immunohistochemistry (IHC) provides for proteins. We have standardized and are reporting a sensitive Z probe based in situ hybridization method to visually identify and quantify lncRNA in FFPE tissues. This assay is highly sensitive and identifies transcripts visible within different cell types and tumors. We have detected a scarcely expressed tumor suppressor lncRNA NRON (non-coding repressor of nuclear factor of activated T-cells (NFAT)), a moderately expressed oncogenic lncRNA UCA1 (urothelial cancer associated 1), and a highly studied and expressed lncRNA MALAT1 (metastasis associated lung adenocarcinoma transcript 1) in different cancers. High MALAT1 staining was found in colorectal, breast and pancreatic cancer. Additionally, we have observed an increase in MALAT1 expression in different stages of colorectal cancer. Full article
Figures

Figure 1

Open AccessCommunication miRNAtools: Advanced Training Using the miRNA Web of Knowledge
Non-Coding RNA 2018, 4(1), 5; https://doi.org/10.3390/ncrna4010005
Received: 24 January 2018 / Revised: 13 February 2018 / Accepted: 14 February 2018 / Published: 16 February 2018
PDF Full-text (2804 KB) | HTML Full-text | XML Full-text
Abstract
Micro-RNAs (miRNAs) are small non-coding RNAs that act as negative regulators of the genomic output. Their intrinsic importance within cell biology and human disease is well known. Their mechanism of action based on the base pairing binding to their cognate targets have helped
[...] Read more.
Micro-RNAs (miRNAs) are small non-coding RNAs that act as negative regulators of the genomic output. Their intrinsic importance within cell biology and human disease is well known. Their mechanism of action based on the base pairing binding to their cognate targets have helped the development not only of many computer applications for the prediction of miRNA target recognition but also of specific applications for functional assessment and analysis. Learning about miRNA function requires practical training in the use of specific computer and web-based applications that are complementary to wet-lab studies. In order to guide the learning process about miRNAs, we have created miRNAtools (http://mirnatools.eu), a web repository of miRNA tools and tutorials. This article compiles tools with which miRNAs and their regulatory action can be analyzed and that function to collect and organize information dispersed on the web. The miRNAtools website contains a collection of tutorials that can be used by students and tutors engaged in advanced training courses. The tutorials engage in analyses of the functions of selected miRNAs, starting with their nomenclature and genomic localization and finishing with their involvement in specific cellular functions. Full article
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Graphical abstract

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

1) Mohammad Reza Naghdi, Katia Smail, Clarisse Mucha, Aurélie Devinck, Émilie Boutet, Jonathan Ouellet and Jonathan Perreault. Identification of new riboswitches and ribozymes: different approaches to uncover RNAs with interesting biochemical traits.
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