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ncRNA
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Advances in Non-coding RNA Databases and Resources
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Advances in Non-coding RNA Databases and Resources

A special issue of Non-Coding RNA (ISSN 2311-553X). This special issue belongs to the section "Computational Biology".

Deadline for manuscript submissions: closed (20 January 2022) | Viewed by 16377

Special Issue Editor

Dr. Pieter-Jan Volders

E-Mail Website
Guest Editor
Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
Interests: long non-coding RNA; circRNA; micropeptides; cancer transcriptomics

Special Issue Information

Dear Colleagues,

Advancements in RNA sequencing technologies and bioinformatic approaches led to the discovery of a plethora of non-coding RNA species. However, the functional annotation of these non-coding RNAs is often lacking. This annotation is required to further research these non-coding RNAs and identify non-coding RNA drug targets or biomarkers. As such, the field needs the development of public non-coding RNA resources and databases with high-quality annotation.

The purpose of this Special Issue is to present the community with a unique collection of non-coding RNA databases and resources to aid in unraveling the individual functions of non-coding RNAs. This collection can include curated databases, databases based on original research, integrative databases, large-scale RNA sequencing efforts, and other large-scale functional annotation efforts. In addition, the application or use-cases of existing databases and resources is welcome.

Dr. Pieter-Jan Volders
Guest Editor

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 submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue 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 semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). 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.

Keywords

  • non-coding RNA
  • database
  • long non-coding RNA
  • circular RNA

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Published Papers (3 papers)

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Research

16 pages, 3471 KiB  
Article
ITAS: Integrated Transcript Annotation for Small RNA
by Alexey Stupnikov, Vitaly Bezuglov, Ivan Skakov, Victoria Shtratnikova, J. Richard Pilsner, Alexander Suvorov and Oleg Sergeyev
Non-Coding RNA 2022, 8(3), 30; https://doi.org/10.3390/ncrna8030030 - 2 May 2022
Cited by 5 | Viewed by 3813
Abstract
Transcriptomics analysis of various small RNA (sRNA) biotypes is a new and rapidly developing field. Annotations for microRNAs, tRNAs, piRNAs and rRNAs contain information on transcript sequences and loci that is vital for downstream analyses. Several databases have been established to provide this [...] Read more.
Transcriptomics analysis of various small RNA (sRNA) biotypes is a new and rapidly developing field. Annotations for microRNAs, tRNAs, piRNAs and rRNAs contain information on transcript sequences and loci that is vital for downstream analyses. Several databases have been established to provide this type of data for specific RNA biotypes. However, these sources often contain data in different formats, which makes the bulk analysis of several sRNA biotypes in a single pipeline challenging. Information on some transcripts may be incomplete or conflicting with other entries. To overcome these challenges, we introduce ITAS, or Integrated Transcript Annotation for Small RNA, a filtered, corrected and integrated transcript annotation containing information on several types of small RNAs, including tRNA-derived small RNA, for several species (Homo sapiens, Rattus norvegicus, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans). ITAS is presented in a format applicable for the vast majority of bioinformatic transcriptomics analysis, and it was tested in several case studies for human-derived data against existing alternative databases. Full article
(This article belongs to the Special Issue Advances in Non-coding RNA Databases and Resources)
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19 pages, 7880 KiB  
Article
FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis
by Mirolyuba Ilieva, Henry E. Miller, Arav Agarwal, Gabriela K. Paulus, Jens Hedelund Madsen, Alexander J. R. Bishop, Sakari Kauppinen and Shizuka Uchida
Non-Coding RNA 2022, 8(1), 13; https://doi.org/10.3390/ncrna8010013 - 28 Jan 2022
Cited by 14 | Viewed by 7413
Abstract
Most long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes and their expression is often restricted to specific cell types, certain time points during development, and various stress and disease conditions, respectively. To revisit this long-held concept, we focused on [...] Read more.
Most long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes and their expression is often restricted to specific cell types, certain time points during development, and various stress and disease conditions, respectively. To revisit this long-held concept, we focused on fibroblasts, a common cell type in various organs and tissues. Using fibroblasts and changes in their expression profiles during fibrosis as a model system, we show that the overall expression level of lncRNA genes is significantly lower than that of protein-coding genes. Furthermore, we identified lncRNA genes whose expression is upregulated during fibrosis. Using dermal fibroblasts as a model, we performed loss-of-function experiments and show that the knockdown of the lncRNAs LINC00622 and LINC01711 result in gene expression changes associated with cellular and inflammatory responses, respectively. Since there are no lncRNA databases focused on fibroblasts and fibrosis, we built a web application, FibroDB, to further promote functional and mechanistic studies of fibrotic lncRNAs. Full article
(This article belongs to the Special Issue Advances in Non-coding RNA Databases and Resources)
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10 pages, 1170 KiB  
Article
CLASH Analyst: A Web Server to Identify In Vivo RNA–RNA Interactions from CLASH Data
by Wei-Sheng Wu, Jordan S. Brown, Pin-Hao Chen, Sheng-Cian Shiue, Dong-En Lee and Heng-Chi Lee
Non-Coding RNA 2022, 8(1), 6; https://doi.org/10.3390/ncrna8010006 - 12 Jan 2022
Cited by 5 | Viewed by 4050
Abstract
Non-coding RNAs, such as miRNAs and piRNAs, play critical roles in gene regulation through base-pairing interactions with their target molecules. The recent development of the crosslinking, ligation, and sequencing of hybrids (CLASH) method has allowed scientists to map transcriptome-wide RNA–RNA interactions by identifying [...] Read more.
Non-coding RNAs, such as miRNAs and piRNAs, play critical roles in gene regulation through base-pairing interactions with their target molecules. The recent development of the crosslinking, ligation, and sequencing of hybrids (CLASH) method has allowed scientists to map transcriptome-wide RNA–RNA interactions by identifying chimeric reads consisting of fragments from regulatory RNAs and their targets. However, analyzing CLASH data requires scientists to use advanced bioinformatics, and currently available tools are limited for users with little bioinformatic experience. In addition, many published CLASH studies do not show the full scope of RNA–RNA interactions that were captured, highlighting the importance of reanalyzing published data. Here, we present CLASH Analyst, a web server that can analyze raw CLASH data within a fully customizable and easy-to-use interface. CLASH Analyst accepts raw CLASH data as input and identifies the RNA chimeras containing the regulatory and target RNAs according to the user’s interest. Detailed annotation of the captured RNA–RNA interactions is then presented for the user to visualize within the server or download for further analysis. We demonstrate that CLASH Analyst can identify miRNA- and piRNA-targeting sites reported from published CLASH data and should be applicable to analyze other RNA–RNA interactions. CLASH Analyst is freely available for academic use. Full article
(This article belongs to the Special Issue Advances in Non-coding RNA Databases and Resources)
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