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Recent Development of Bioinformatics Tools of RNA

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Bioinformatics and Systems Biology".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 9673

Special Issue Editor


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Guest Editor
John W. Deming Department of Medicine, Tulane University, New Orleans, LA, USA
Interests: statistics; sequencing; gene expression; DNA sequence analysis; statistical modeling

Special Issue Information

Dear Colleagues,

Recent studies have shown that there are many noncoding RNAs (ncRNAs) that are not translated into proteins but play important roles in various cellular functions. For example, several studies have suggested more long noncoding RNAs (lncRNAs) exist than messenger RNAs in higher eukaryotes including human, and elucidating the functions of these lncRNAs is an urgent task in current molecular biology. On the other hand, various types of RNA-related omics data such as transcriptome (e.g., RNA-seq), epi-transcriptome (e.g., m6A-seq, m1A-seq), structurome (e.g., DMS-seq, SHAPE-seq), and interactome (e.g., CLIP-seq) are accumulating. Integrating these omics data with bioinformatic approaches has also become important in RNA biology. In addition to natural RNAs, artificial RNAs such as RNA aptamers are also attracting attention from researchers as a new generation of target molecules for drug discovery; the computational design of RNA sequences (e.g., RNA aptamer design, RNA inverse folding) is an important problem in this field. This Special Issue covers all aspects of RNA informatics. We welcome papers on both fundamental computational methods for analyzing RNAs and omics data analysis of RNAs.

Dr. Md Mehedi Hasan
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. Current Issues in Molecular Biology 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 2200 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

  • RNA aptamer
  • RNA alignment
  • gene expression
  • bioinformatics

Published Papers (4 papers)

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Research

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16 pages, 3159 KiB  
Article
MicroRNA-10 Family Promotes the Epithelial-to-Mesenchymal Transition in Renal Fibrosis by the PTEN/Akt Pathway
by Chaokun Wang, Yichen Shuai, Chuan Zhao, Fengrui Yang, Weilian Su, Zhifen Ning and Guoxia Li
Curr. Issues Mol. Biol. 2022, 44(12), 6059-6074; https://doi.org/10.3390/cimb44120413 - 2 Dec 2022
Cited by 2 | Viewed by 1501
Abstract
Renal fibrosis (RF) is a common reason for renal failure, and epithelial-mesenchymal transition (EMT) is a vital mechanism that promotes the development of RF. It is known that microRNA-10 (miR-10) plays an important role in cancer EMT; however, whether it takes part in [...] Read more.
Renal fibrosis (RF) is a common reason for renal failure, and epithelial-mesenchymal transition (EMT) is a vital mechanism that promotes the development of RF. It is known that microRNA-10 (miR-10) plays an important role in cancer EMT; however, whether it takes part in the EMT process of RF remains unclear. Therefore, we established an in vivo model of unilateral ureteral obstruction (UUO), and an in vitro model using TGF-β1, to investigate whether and how miR-10a and miR-10b take part in the EMT of RF. In addition, the combinatorial effects of miR-10a and miR-10b were assessed. We discovered that miR-10a and miR-10b are overexpressed in UUO mice, and miR-10a, miR-10b, and miRs-10a/10b knockout attenuated RF and EMT in UUO-treated mouse kidneys. Moreover, miR-10a and miR-10b overexpression combinatorially promoted RF and EMT in TGF-β1-treated HK-2 cells. Inhibiting miR-10a and miR-10b attenuated RF and EMT induced by TGF-β1. Mechanistically, miR-10a and miR-10b suppressed PTEN expression by binding to its mRNA3′-UTR and promoting the Akt pathway. Moreover, PTEN overexpression reduced miR-10a and miR-10b effects on Akt phosphorylation (p-Akt), RF, and EMT in HK-2 cells treated with TGF-β1. Taken together, miR-10a and miR-10b act combinatorially to negatively regulate PTEN, thereby activating the Akt pathway and promoting the EMT process, which exacerbates RF progression. Full article
(This article belongs to the Special Issue Recent Development of Bioinformatics Tools of RNA)
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9 pages, 1239 KiB  
Article
GCEN: An Easy-to-Use Toolkit for Gene Co-Expression Network Analysis and lncRNAs Annotation
by Wen Chen, Jing Li, Shulan Huang, Xiaodeng Li, Xuan Zhang, Xiang Hu, Shuanglin Xiang and Changning Liu
Curr. Issues Mol. Biol. 2022, 44(4), 1479-1487; https://doi.org/10.3390/cimb44040100 - 25 Mar 2022
Cited by 6 | Viewed by 3599
Abstract
Gene co-expression network analysis has been widely used in gene function annotation, especially for long noncoding RNAs (lncRNAs). However, there is a lack of effective cross-platform analysis tools. For biologists to easily build a gene co-expression network and to predict gene function, we [...] Read more.
Gene co-expression network analysis has been widely used in gene function annotation, especially for long noncoding RNAs (lncRNAs). However, there is a lack of effective cross-platform analysis tools. For biologists to easily build a gene co-expression network and to predict gene function, we developed GCEN, a cross-platform command-line toolkit developed with C++. It is an efficient and easy-to-use solution that will allow everyone to perform gene co-expression network analysis without the requirement of sophisticated programming skills, especially in cases of RNA-Seq research and lncRNAs function annotation. Because of its modular design, GCEN can be easily integrated into other pipelines. Full article
(This article belongs to the Special Issue Recent Development of Bioinformatics Tools of RNA)
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10 pages, 1395 KiB  
Article
Identification and Characterization of Polymorphisms in piRNA Regions
by José Roberto Sobrinho Lima, Jhully Azevedo-Pinheiro, Roberta Borges Andrade, André Salim Khayat, Paulo Pimentel de Assumpção, Ândrea Ribeiro-dos-Santos, Sidney Emanuel Batista dos Santos and Fabiano Cordeiro Moreira
Curr. Issues Mol. Biol. 2022, 44(2), 942-951; https://doi.org/10.3390/cimb44020062 - 15 Feb 2022
Cited by 1 | Viewed by 2010
Abstract
piRNAs are a class of noncoding RNAs that perform functions in epigenetic regulation and silencing of transposable elements, a mechanism conserved among most mammals. At present, there are more than 30,000 known piRNAs in humans, of which more than 80% are derived from [...] Read more.
piRNAs are a class of noncoding RNAs that perform functions in epigenetic regulation and silencing of transposable elements, a mechanism conserved among most mammals. At present, there are more than 30,000 known piRNAs in humans, of which more than 80% are derived from intergenic regions, and approximately 20% are derived from the introns and exons of pre-mRNAs. It was observed that the expression of the piRNA profile is specific in several organs, suggesting that they play functional roles in different tissues. In addition, some studies suggest that changes in regions that encode piRNAs may have an impact on their function. To evaluate the conservation of these regions and explore the existence of a seed region, SNP and INDEL variant rates were investigated in several genomic regions and compared to piRNA region variant rates. Thus, data analysis, data collection, cleaning, treatment, and exploration were implemented using the R programming language with the help of the RStudio platform. We found that piRNA regions are highly conserved after considering INDELs and do not seem to present an identifiable seed region after considering SNPs and INDEL variants. These findings may contribute to future studies attempting to determine how polymorphisms in piRNA regions can impact diseases. Full article
(This article belongs to the Special Issue Recent Development of Bioinformatics Tools of RNA)
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Review

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14 pages, 550 KiB  
Review
tRFs and tRNA Halves: Novel Cellular Defenders in Multiple Biological Processes
by Jiani Hou, Qianqing Li, Jun Wang and Wenfa Lu
Curr. Issues Mol. Biol. 2022, 44(12), 5949-5962; https://doi.org/10.3390/cimb44120405 - 28 Nov 2022
Cited by 1 | Viewed by 1913
Abstract
tRNA fragments derived from angiogenin or Dicer cleavage are referred to as tRNA-derived fragments (tRFs) and tRNA halves. tRFs and tRNA halves have been identified in both eukaryotes and prokaryotes and are precisely cleaved at specific sites on either precursor or mature tRNA [...] Read more.
tRNA fragments derived from angiogenin or Dicer cleavage are referred to as tRNA-derived fragments (tRFs) and tRNA halves. tRFs and tRNA halves have been identified in both eukaryotes and prokaryotes and are precisely cleaved at specific sites on either precursor or mature tRNA transcripts rather than via random degradation. tRFs and tRNA halves are highly involved in regulating transcription and translation in a canonical or non-canonical manner in response to cellular stress. In this review, we summarize the biogenesis and types of tRFs and tRNA halves, clarify the biological functions and molecular mechanisms of tRNA fragments in both physiological and pathological processes with a particular focus on their cytoprotective roles in defending against oxidation and apoptosis, and highlight their potential application as biomarkers in determining cell fate. Full article
(This article belongs to the Special Issue Recent Development of Bioinformatics Tools of RNA)
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