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Exploring the Possibility of RNA in Diverse Biological Processes
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Exploring the Possibility of RNA in Diverse Biological Processes

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (15 January 2023) | Viewed by 21659

Special Issue Editors

Dr. Yajing Hao

E-Mail Website
Guest Editor
Department of Cellular & Molecular Medicine, University of California San Diego, San Diego, CA, USA
Interests: bioinformatics; RNA; ncRNA
Dr. Lantao Gou

E-Mail Website
Co-Guest Editor
Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
Interests: regulatory RNA; RNA and chromatin biology; reproduction and infertility
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Unlike DNA, RNA is single-stranded and behaves as a translator to convert genetic information from DNA to proteins in “Central Dogma”.  However, RNA is not only a massager molecule but also works as a regulator of gene expression in multiple contexts. With rapid research advancement, RNA molecules are extensively studied. Various RNAs with different features including structures, lengths, modifications, and cellular localizations have been recognized. In particular, identification of non-coding RNAs renovates the understanding of genome and enriches regulatory studies in molecular biology. More interestingly, different types of RNA interact with different RNA-binding proteins (RBPs) with unknown functions. RNA studies would better illustrate the functions of these RBPs. Current studies show that regulatory RNAs play important functions in various pathological and physiological processes. Exploring the possibility of RNA in diverse biological processes not only helps us to better understand the basic regulation principles but also has important implications in the development of therapies. According to the current understanding of RNA biology, the RNA field mainly includes the following five areas: RNA biogenesis pathways, RNA structures, functions for the various classes of RNAs, role of RNA in disease, and RNA-based and RNA-targeted therapies. For this Special Issue, we welcome original research articles and up-to-date review articles that provide novel insights into these RNA-centered topics.

Dr. Yajing Hao
Dr. Lantao Gou
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 regulation
  • co-transcriptional regulation
  • post-transcriptional regulation
  • RNA viruses
  • RNA therapy
  • non-coding RNA
  • RBPs
  • RNA structure
  • nonsense-mediated mRNA Decay
  • RNA modifications
  • RNA editing

Published Papers (7 papers)

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Editorial

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5 pages, 216 KiB  
Editorial
Exploring the Possibility of RNA in Diverse Biological Processes
by Yanchen Liu and Yajing Hao
Int. J. Mol. Sci. 2023, 24(13), 10674; https://doi.org/10.3390/ijms241310674 - 26 Jun 2023
Viewed by 997
Abstract
The total amount of RNA in a cell is 5 to 10 times greater than that of DNA [...] Full article
(This article belongs to the Special Issue Exploring the Possibility of RNA in Diverse Biological Processes)

Research

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20 pages, 3357 KiB  
Article
RNA Helicase DDX6 Regulates A-to-I Editing and Neuronal Differentiation in Human Cells
by Chia-Yu Shih, Yun-Chi Chen, Heng-Yi Lin and Chia-Ying Chu
Int. J. Mol. Sci. 2023, 24(4), 3197; https://doi.org/10.3390/ijms24043197 - 6 Feb 2023
Cited by 3 | Viewed by 2617
Abstract
The DEAD-box proteins, one family of RNA-binding proteins (RBPs), participate in post-transcriptional regulation of gene expression with multiple aspects. Among them, DDX6 is an essential component of the cytoplasmic RNA processing body (P-body) and is involved in translational repression, miRNA-meditated gene silencing, and [...] Read more.
The DEAD-box proteins, one family of RNA-binding proteins (RBPs), participate in post-transcriptional regulation of gene expression with multiple aspects. Among them, DDX6 is an essential component of the cytoplasmic RNA processing body (P-body) and is involved in translational repression, miRNA-meditated gene silencing, and RNA decay. In addition to the cytoplasmic function, DDX6 is also present in the nucleus, but the nuclear function remains unknown. To decipher the potential role of DDX6 in the nucleus, we performed mass spectrometry analysis of immunoprecipitated DDX6 from a HeLa nuclear extract. We found that adenosine deaminases that act on RNA 1 (ADAR1) interact with DDX6 in the nucleus. Utilizing our newly developed dual-fluorescence reporter assay, we elucidated the DDX6 function as negative regulators in cellular ADAR1p110 and ADAR2. In addition, depletion of DDX6 and ADARs results in the opposite effect on facilitation of RA-induced differentiation of neuronal lineage cells. Our data suggest the impact of DDX6 in regulation of the cellular RNA editing level, thus contributing to differentiation in the neuronal cell model. Full article
(This article belongs to the Special Issue Exploring the Possibility of RNA in Diverse Biological Processes)
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11 pages, 780 KiB  
Article
Evidence that Transcriptional Alterations in Sarcoptes scabiei Are under Tight Post-Transcriptional (microRNA) Control
by Pasi K. Korhonen, Tao Wang, Neil D. Young, Gangi R. Samarawickrama, Deepani D. Fernando, Guangxu Ma, Robin B. Gasser and Katja Fischer
Int. J. Mol. Sci. 2022, 23(17), 9719; https://doi.org/10.3390/ijms23179719 - 26 Aug 2022
Cited by 1 | Viewed by 1452
Abstract
Here, we explored transcriptomic differences among early egg (Ee), late egg (Le) and adult female (Af) stages of the scabies mite, Sarcoptes scabiei, using an integrative bioinformatic approach. We recorded a high, negative correlation between miRNAs and genes with decreased mRNA transcription [...] Read more.
Here, we explored transcriptomic differences among early egg (Ee), late egg (Le) and adult female (Af) stages of the scabies mite, Sarcoptes scabiei, using an integrative bioinformatic approach. We recorded a high, negative correlation between miRNAs and genes with decreased mRNA transcription between the developmental stages, indicating substantial post-transcriptional repression; we also showed a positive correlation between miRNAs and genes with increased mRNA transcription, suggesting indirect post-transcriptional regulation. The alterations in mRNA transcription between the egg and adult female stages of S. scabiei were inferred to be linked to metabolism (including carbohydrate and lipid degradation, amino acid and energy metabolism), environmental information processing (e.g., signal transduction and signalling molecules), genetic information processing (e.g., transcription and translation) and/or organismal systems. Taken together, these results provide insight into the transcription of this socioeconomically important parasitic mite, with a particular focus on the egg stage. This work encourages further, detailed laboratory studies of miRNA regulation across all developmental stages of S. scabiei and might assist in discovering new intervention targets in the egg stage of S. scabiei. Full article
(This article belongs to the Special Issue Exploring the Possibility of RNA in Diverse Biological Processes)
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16 pages, 6563 KiB  
Article
The DEAD-Box Protein Rok1 Coordinates Ribosomal RNA Processing in Association with Rrp5 in Drosophila
by Jie Chen, Yuantai Huang and Kang Zhang
Int. J. Mol. Sci. 2022, 23(10), 5685; https://doi.org/10.3390/ijms23105685 - 19 May 2022
Cited by 2 | Viewed by 1808
Abstract
Ribosome biogenesis and processing involve the coordinated action of many components. The DEAD-box RNA helicase (Rok1) is essential for cell viability, and the depletion of Rok1 inhibits pre-rRNA processing. Previous research on Rok1 and its cofactor Rrp5 has been performed primarily in yeast. [...] Read more.
Ribosome biogenesis and processing involve the coordinated action of many components. The DEAD-box RNA helicase (Rok1) is essential for cell viability, and the depletion of Rok1 inhibits pre-rRNA processing. Previous research on Rok1 and its cofactor Rrp5 has been performed primarily in yeast. Few functional studies have been performed in complex multicellular eukaryotes. Here, we used a combination of genetics and developmental experiments to show that Rok1 and Rrp5, which localize to the nucleolus, play key roles in the pre-rRNA processing and ribosome assembly in D. melanogaster. The accumulation of pre-rRNAs caused by Rok1 depletion can result in developmental defects. The loss of Rok1 enlarged the nucleolus and led to stalled ribosome assembly and pre-rRNA processing in the nucleolus, thereby blocking rRNA maturation and exacerbating the inhibition of mitosis in the brain. We also discovered that rrp54-2/4-2 displayed significantly increased ITS1 signaling by fluorescence in situ hybridization, and a reduction in ITS2. Rrp5 signal was highly enriched in the core of the nucleolus in the rok1167/167 mutant, suggesting that Rok1 is required for the accurate cellular localization of Rrp5 in the nucleolus. We have thus uncovered functions of Rok1 that reveal important implications for ribosome processing in eukaryotes. Full article
(This article belongs to the Special Issue Exploring the Possibility of RNA in Diverse Biological Processes)
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11 pages, 1285 KiB  
Communication
Gene Expression of Pregnancy Neutrophils Differs for Protease versus Lipopolysaccharide Stimulation
by Scott W. Walsh, Marwah Al Dulaimi and Jerome F. Strauss III
Int. J. Mol. Sci. 2022, 23(9), 4924; https://doi.org/10.3390/ijms23094924 - 28 Apr 2022
Cited by 3 | Viewed by 1564
Abstract
Neutrophils, which extensively infiltrate maternal systemic blood vessels in preeclampsia, express protease-activated receptor 1 (PAR-1) but only during pregnancy. Neutrophils are generally considered to be non-specific in their response, but the pregnancy-specific expression of PAR-1 could result in a gene expression profile unique [...] Read more.
Neutrophils, which extensively infiltrate maternal systemic blood vessels in preeclampsia, express protease-activated receptor 1 (PAR-1) but only during pregnancy. Neutrophils are generally considered to be non-specific in their response, but the pregnancy-specific expression of PAR-1 could result in a gene expression profile unique to pregnancy, which could help explain why the maternal inflammatory response in preeclampsia is systemic rather than localized. We sought to determine if gene expression of pregnancy neutrophils would differ if stimulated by a protease versus bacterial lipopolysaccharide (LPS). We isolated neutrophils from normal pregnant women at 30 weeks’ gestation and cultured them with elastase or LPS. We used elastase because it is a protease elevated in women with preeclampsia, and it activates pregnancy neutrophils via PAR-1. RNA was isolated from the neutrophils for sequencing of the transcriptomes. We discovered many differences in the gene expression profiles. For example, exposure to elastase resulted in three times more uniquely expressed genes than LPS, and the number of significantly differentially upregulated and downregulated genes was greater for elastase. Analysis of canonical pathways revealed similarities for innate immunity but also differences. LPS treatment enriched more pathways, but elastase activated more genes in each pathway. Elastase treatment enriched the MAPK signaling pathway, whereas LPS did not. This is significant because MAPK is a key mediator of transcriptional responses. These findings indicate that protease stimulation of pregnancy neutrophils results in a different profile than stimulation with LPS, which may help explain why the sterile inflammatory response of preeclampsia is systemic and unique to pregnancy. Full article
(This article belongs to the Special Issue Exploring the Possibility of RNA in Diverse Biological Processes)
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Review

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15 pages, 866 KiB  
Review
Alternative Polyadenylation Is a Novel Strategy for the Regulation of Gene Expression in Response to Stresses in Plants
by Jing Wu, Ligeng Ma and Ying Cao
Int. J. Mol. Sci. 2023, 24(5), 4727; https://doi.org/10.3390/ijms24054727 - 1 Mar 2023
Cited by 3 | Viewed by 2365
Abstract
Precursor message RNA requires processing to generate mature RNA. Cleavage and polyadenylation at the 3′-end in the maturation of mRNA is one of key processing steps in eukaryotes. The polyadenylation (poly(A)) tail of mRNA is an essential feature that is required to mediate [...] Read more.
Precursor message RNA requires processing to generate mature RNA. Cleavage and polyadenylation at the 3′-end in the maturation of mRNA is one of key processing steps in eukaryotes. The polyadenylation (poly(A)) tail of mRNA is an essential feature that is required to mediate its nuclear export, stability, translation efficiency, and subcellular localization. Most genes have at least two mRNA isoforms via alternative splicing (AS) or alternative polyadenylation (APA), which increases the diversity of transcriptome and proteome. However, most previous studies have focused on the role of alternative splicing on the regulation of gene expression. In this review, we summarize the recent advances concerning APA in the regulation of gene expression and in response to stresses in plants. We also discuss the mechanisms for the regulation of APA for plants in the adaptation to stress responses, and suggest that APA is a novel strategy for the adaptation to environmental changes and response to stresses in plants. Full article
(This article belongs to the Special Issue Exploring the Possibility of RNA in Diverse Biological Processes)
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Graphical abstract

28 pages, 5713 KiB  
Review
The Evolution of Single-Cell RNA Sequencing Technology and Application: Progress and Perspectives
by Shuo Wang, Si-Tong Sun, Xin-Yue Zhang, Hao-Ran Ding, Yu Yuan, Jun-Jie He, Man-Shu Wang, Bin Yang and Yu-Bo Li
Int. J. Mol. Sci. 2023, 24(3), 2943; https://doi.org/10.3390/ijms24032943 - 2 Feb 2023
Cited by 16 | Viewed by 9834
Abstract
As an emerging sequencing technology, single-cell RNA sequencing (scRNA-Seq) has become a powerful tool for describing cell subpopulation classification and cell heterogeneity by achieving high-throughput and multidimensional analysis of individual cells and circumventing the shortcomings of traditional sequencing for detecting the average transcript [...] Read more.
As an emerging sequencing technology, single-cell RNA sequencing (scRNA-Seq) has become a powerful tool for describing cell subpopulation classification and cell heterogeneity by achieving high-throughput and multidimensional analysis of individual cells and circumventing the shortcomings of traditional sequencing for detecting the average transcript level of cell populations. It has been applied to life science and medicine research fields such as tracking dynamic cell differentiation, revealing sensitive effector cells, and key molecular events of diseases. This review focuses on the recent technological innovations in scRNA-Seq, highlighting the latest research results with scRNA-Seq as the core technology in frontier research areas such as embryology, histology, oncology, and immunology. In addition, this review outlines the prospects for its innovative application in traditional Chinese medicine (TCM) research and discusses the key issues currently being addressed by scRNA-Seq and its great potential for exploring disease diagnostic targets and uncovering drug therapeutic targets in combination with multiomics technologies. Full article
(This article belongs to the Special Issue Exploring the Possibility of RNA in Diverse Biological Processes)
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