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Feature Papers in RNA
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Feature Papers in RNA

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "RNA".

Deadline for manuscript submissions: closed (10 December 2022) | Viewed by 10567

Special Issue Editors

Dr. Zihua Hu

E-Mail Website
Guest Editor
1. Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14203, USA
2. Department of Medicine, State University of New York at Buffalo, Buffalo, NY 14203, USA
3. New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
Interests: bioinformatics; genomics; gene regulation; miRNA; genetic variation
Special Issues, Collections and Topics in MDPI journals
Dr. Michel Ravelonandro

E-Mail Website
Guest Editor
INRAE, Universite de Bordeaux, Unite Mixte Rech 1332, Villenave D Ornon, CS, France
Interests: plants; pests; RNAi; gene regulation; bioinformatic challenging
Special Issues, Collections and Topics in MDPI journals
Dr. Lionel Benard

E-Mail Website
Guest Editor
CNRS, Institut de Biologie Physico_Chimique, UMR8226, Laboratoire de Biologie Cellulaire et Moléculaire des Eucaryotes, 75005 Paris, France
Interests: molecular biology; RNA biology; mRNA maturation and degradation; mRNA surveillance; translation; post-transcriptional regulation

Special Issue Information

Dear Colleagues, 

This Topical Collection, “Feature Papers in RNA”, aims to collect high-quality research articles, review articles, and communications on all aspects of RNA. It is dedicated to recent advances in the research area of RNA and comprises a selection of exclusive papers from the Editorial Board Members (EBMs) of the RNA Section, as well as invited papers from relevant experts. We also welcome senior experts in the field to make contributions to this Special Issue. We aim to represent our Section as an attractive open-access publishing platform for RNA research.

Dr. Zihua Hu
Dr. Michel Ravelonandro
Dr. Lionel Benard
Guest Editors

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. Genes is an international peer-reviewed open access monthly 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 2600 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.

Published Papers (3 papers)

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Research

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16 pages, 556 KiB  
Article
Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots
by Manato Akiyama, Yasubumi Sakakibara and Kengo Sato
Genes 2022, 13(11), 2155; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13112155 - 18 Nov 2022
Cited by 2 | Viewed by 1657
Abstract
Existing approaches to predicting RNA secondary structures depend on how the secondary structure is decomposed into substructures, that is, the architecture, to define their parameter space. However, architecture dependency has not been sufficiently investigated, especially for pseudoknotted secondary structures. In this study, [...] Read more.
Existing approaches to predicting RNA secondary structures depend on how the secondary structure is decomposed into substructures, that is, the architecture, to define their parameter space. However, architecture dependency has not been sufficiently investigated, especially for pseudoknotted secondary structures. In this study, we propose a novel algorithm for directly inferring base-pairing probabilities with neural networks that do not depend on the architecture of RNA secondary structures, and then implement this approach using two maximum expected accuracy (MEA)-based decoding algorithms: Nussinov-style decoding for pseudoknot-free structures and IPknot-style decoding for pseudoknotted structures. To train the neural networks connected to each base pair, we adopt a max-margin framework, called structured support vector machines (SSVM), as the output layer. Our benchmarks for predicting RNA secondary structures with and without pseudoknots show that our algorithm outperforms existing methods in prediction accuracy. Full article
(This article belongs to the Special Issue Feature Papers in RNA)
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16 pages, 5429 KiB  
Article
The Effect of Dicer Knockout on RNA Interference Using Various Dicer Substrate Small Interfering RNA (DsiRNA) Structures
by Min-Sun Song, Jessica Alluin and John J. Rossi
Genes 2022, 13(3), 436; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13030436 - 27 Feb 2022
Cited by 2 | Viewed by 4170
Abstract
Small interfering RNAs (siRNAs) are artificial molecules used to silence genes of interest through the RNA interference (RNAi) pathway, mediated by the endoribonuclease Dicer. Dicer-substrate small interfering RNAs (DsiRNAs) are an alternative to conventional 21-mer siRNAs, with an increased effectiveness of up to [...] Read more.
Small interfering RNAs (siRNAs) are artificial molecules used to silence genes of interest through the RNA interference (RNAi) pathway, mediated by the endoribonuclease Dicer. Dicer-substrate small interfering RNAs (DsiRNAs) are an alternative to conventional 21-mer siRNAs, with an increased effectiveness of up to 100-fold compared to traditional 21-mer designs. DsiRNAs have a novel asymmetric design that allows them to be processed by Dicer into the desired conventional siRNAs. DsiRNAs are a useful tool for sequence-specific gene silencing, but the molecular mechanism underlying their increased efficacy is not precisely understood. In this study, to gain a deeper understanding of Dicer function in DsiRNAs, we designed nicked DsiRNAs with and without tetra-loops to target a specific mRNA sequence, established a Dicer knockout in the HCT116 cell line, and analyzed the efficacy of various DsiRNAs on RNAi-mediated gene silencing activity. The gene silencing activity of all DsiRNAs was reduced in Dicer knockout cells. We demonstrated that tetra-looped DsiRNAs exhibited increased efficacy for gene silencing, which was mediated by Dicer protein. Thus, this study improves our understanding of Dicer function, a key component of RNAi silencing, which will inform RNAi research and applications. Full article
(This article belongs to the Special Issue Feature Papers in RNA)
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Review

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16 pages, 1715 KiB  
Review
C-to-U RNA Editing: A Site Directed RNA Editing Tool for Restoration of Genetic Code
by Sonali Bhakta and Toshifumi Tsukahara
Genes 2022, 13(9), 1636; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13091636 - 12 Sep 2022
Cited by 3 | Viewed by 4027
Abstract
The restoration of genetic code by editing mutated genes is a potential method for the treatment of genetic diseases/disorders. Genetic disorders are caused by the point mutations of thymine (T) to cytidine (C) or guanosine (G) to adenine (A), for which gene editing [...] Read more.
The restoration of genetic code by editing mutated genes is a potential method for the treatment of genetic diseases/disorders. Genetic disorders are caused by the point mutations of thymine (T) to cytidine (C) or guanosine (G) to adenine (A), for which gene editing (editing of mutated genes) is a promising therapeutic technique. In C-to-Uridine (U) RNA editing, it converts the base C-to-U in RNA molecules and leads to nonsynonymous changes when occurring in coding regions; however, for G-to-A mutations, A-to-I editing occurs. Editing of C-to-U is not as physiologically common as that of A-to-I editing. Although hundreds to thousands of coding sites have been found to be C-to-U edited or editable in humans, the biological significance of this phenomenon remains elusive. In this review, we have tried to provide detailed information on physiological and artificial approaches for C-to-U RNA editing. Full article
(This article belongs to the Special Issue Feature Papers in RNA)
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