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Regulation by Non-Coding RNAs 2025
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Regulation by Non-Coding RNAs 2025

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

Deadline for manuscript submissions: 30 May 2025 | Viewed by 4715

Special Issue Editor

Prof. Dr. Won-Ha Lee

E-Mail Website
Guest Editor
School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
Interests: atherosclerosis; rheumatoid arthritis; epitranscriptomics; inflammation; lncRNAs; endoplasmic reticulum (ER) stress

Special Issue Information

Dear Colleagues,

Non-Coding RNAs (ncRNAs) are currently a hot research topic in many fields of biology, medicine, and chemistry. They illuminate the intricate mechanisms underlying cellular function and dysfunction. From the realms of metabolism to the intricacies of cancer and inflammation, ncRNAs emerge as pivotal players orchestrating a symphony of biological processes.

Embark on a journey through the regulatory landscape, where ncRNAs wield their influence over gene expression, shaping the very fabric of development, growth, and disease progression. Explore the multifaceted roles of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) as they navigate through pathways of stem cell regeneration, apoptosis, and autophagy.

This curated compilation seeks to unravel the mysteries surrounding ncRNA-mediated regulation, shedding light on the intricate interplay between these molecules and their target counterparts. From elucidating underlying mechanisms to unveiling novel interactor pairs, this special issue serves as a beacon for researchers delving into the captivating world of ncRNA biology.

For this Special Issue, we invite both original research articles and reviews providing readers of IJMS with novel data regarding the most relevant ncRNA biology.

Dr. Won-Ha Lee
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. 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

  • lncRNAs
  • circRNAs
  • miRNAs

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Published Papers (4 papers)

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Research

12 pages, 2588 KiB  
Article
Long Non-Coding RNA LOC113219358 Regulates Immune Responses in Apis mellifera Through Protein Interactions
by Minjie Huang, Xiaodong Tan, Shuyuan Yang, Zhenzhen Zhou, Deqian Wang and Jie Dong
Int. J. Mol. Sci. 2025, 26(2), 676; https://doi.org/10.3390/ijms26020676 - 15 Jan 2025
Viewed by 504
Abstract
Long non-coding RNAs (lncRNAs) are emerging as critical regulators in honeybee physiology, influencing development, behavior, and stress responses. This study investigates the role of lncRNA LOC113219358 in the immune response and neurophysiological regulation of Apis mellifera brains. Using RNA interference (RNAi) and RNA [...] Read more.
Long non-coding RNAs (lncRNAs) are emerging as critical regulators in honeybee physiology, influencing development, behavior, and stress responses. This study investigates the role of lncRNA LOC113219358 in the immune response and neurophysiological regulation of Apis mellifera brains. Using RNA interference (RNAi) and RNA sequencing (RNA-seq), we demonstrate that silencing lncLOC113219358 significantly alters the expression of 162 mRNA transcripts, including genes associated with detoxification, energy metabolism, and neuronal signaling. Functional enrichment analysis revealed involvement in neuropeptide signaling, ATP synthesis, and oxidative phosphorylation pathways. Acetylcholinesterase (AChE), Glutathione-S-transferase (GST) and cytochrome P450 (CYP450) activities were significantly downregulated with 48 h of RNAi treatment. Additionally, RNA pull-down assays identified 113 proteins interacting with lncLOC113219358, including ATP synthase subunits, heat shock proteins, and major royal jelly proteins, suggesting its role in cellular stress responses and neural activity modulation. These findings provide mechanistic insights into how lncLOC113219358 mediates honeybee responses to environmental stressors, contributing to our understanding of lncRNA-regulated neural and immune functions in pollinators. Full article
(This article belongs to the Special Issue Regulation by Non-Coding RNAs 2025)
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15 pages, 6384 KiB  
Article
CircCSPP1 Competitively Binds miR-10a to Regulate BMP7 Expression and Affects the Proliferation of Dermal Papilla Cells
by Xiaoyang Lv, Jie Wang, Yeling Xu, Hui Zhou, Yutao Li and Wei Sun
Int. J. Mol. Sci. 2024, 25(21), 11547; https://doi.org/10.3390/ijms252111547 - 27 Oct 2024
Viewed by 1024
Abstract
A series of differentially expressed circular RNAs (circRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) were identified through sequencing in the hair follicle tissues of Hu sheep with small-waved and straight wool patterns. Based on these findings, the circCSPP1-miR-10a-BMP7 (Bone Morphogenetic Protein 7) [...] Read more.
A series of differentially expressed circular RNAs (circRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) were identified through sequencing in the hair follicle tissues of Hu sheep with small-waved and straight wool patterns. Based on these findings, the circCSPP1-miR-10a-BMP7 (Bone Morphogenetic Protein 7) regulatory network was constructed. The preliminary study highlighted that miR-10a and the BMP7 gene exhibited not only significant differential expression across hair follicle tissues with different patterns in Hu sheep but also had an impact on the proliferation of hair papilla cells. The proliferation of hair papilla cells is intricately linked to hair follicle development and growth. Consequently, we selected the circCSPP1-miR-10a-BMP7 regulatory network to validate its role in promoting hair papilla cell proliferation in Hu sheep. Firstly, the authenticity of circCSPP1 was successfully confirmed through RNase R digestion and reverse primer amplification. Additionally, nucleoplasmic localization analysis determined that circCSPP1 was predominantly distributed in the cytoplasm. Using the dual-luciferase gene reporter system, we verified the targeting relationship between circCSPP1 and miR-10a, building upon our previous validation of the miR-10a-BMP7 interaction. This clarified the competing endogenous RNA (ceRNA) mechanism within the circCSPP1-miR-10a-BMP7. Furthermore, rescue experiments confirmed that circCSPP1 competitively binds to miR-10a, thereby regulating BMP7 expression and influencing the proliferation of hair papilla cells in Hu sheep. This discovery provides a solid foundation for future investigations into the mechanisms underlying wool curvature and the formation of lambskin patterns, offering insights into the complex regulatory networks that govern these phenotypic traits in Hu sheep. Full article
(This article belongs to the Special Issue Regulation by Non-Coding RNAs 2025)
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15 pages, 2523 KiB  
Article
Chromosome-Scale Genome Assembly of the Sheep-Biting Louse Bovicola ovis Using Nanopore Sequencing Data and Pore-C Analysis
by Chian Teng Ong, Karishma T. Mody, Antonino S. Cavallaro, Yakun Yan, Loan T. Nguyen, Renfu Shao, Neena Mitter, Timothy J. Mahony and Elizabeth M. Ross
Int. J. Mol. Sci. 2024, 25(14), 7824; https://doi.org/10.3390/ijms25147824 - 17 Jul 2024
Cited by 1 | Viewed by 1288
Abstract
Bovicola ovis, commonly known as the sheep-biting louse, is an ectoparasite that adversely affects the sheep industry. Sheep louse infestation lowers the quality of products, including wool and leather, causing a loss of approximately AUD 123M per annum in Australia alone. The [...] Read more.
Bovicola ovis, commonly known as the sheep-biting louse, is an ectoparasite that adversely affects the sheep industry. Sheep louse infestation lowers the quality of products, including wool and leather, causing a loss of approximately AUD 123M per annum in Australia alone. The lack of a high-quality genome assembly for the sheep-biting louse, as well as any closely related livestock lice, has hindered the development of louse research and management control tools. In this study, we present the assembly of B. ovis with a genome size of ~123 Mbp based on a nanopore long-read sequencing library and Illumina RNA sequencing, complemented with a chromosome-level scaffolding using the Pore-C multiway chromatin contact dataset. Combining multiple alignment and gene prediction tools, a comprehensive annotation on the assembled B. ovis genome was conducted and recalled 11,810 genes as well as other genomic features including orf, ssr, rRNA and tRNA. A manual curation using alignment with the available closely related louse species, Pediculus humanus, increased the number of annotated genes to 16,024. Overall, this study reported critical genetic resources and biological insights for the advancement of sheep louse research and the development of sustainable control strategies in the sheep industry. Full article
(This article belongs to the Special Issue Regulation by Non-Coding RNAs 2025)
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14 pages, 3343 KiB  
Article
Identification and Functional Analysis of circRNAs during Goat Follicular Development
by Jie Liu, Conghui Guo, Junjie Fu, Dewu Liu, Guangbin Liu, Baoli Sun, Ming Deng, Yongqing Guo and Yaokun Li
Int. J. Mol. Sci. 2024, 25(14), 7548; https://doi.org/10.3390/ijms25147548 - 9 Jul 2024
Cited by 2 | Viewed by 1190
Abstract
Litter size is a crucial quantitative trait in animals, closely linked to follicular development. Circular RNA (circRNA), a type of single-stranded closed-loop endogenous RNA with stable expression, plays pivotal roles in various biological processes, yet its function in goat follicular development remains unclear. [...] Read more.
Litter size is a crucial quantitative trait in animals, closely linked to follicular development. Circular RNA (circRNA), a type of single-stranded closed-loop endogenous RNA with stable expression, plays pivotal roles in various biological processes, yet its function in goat follicular development remains unclear. In this study, we collected large (follicle diameter > 3 mm) and small (1 mm < follicle diameter < 3 mm) follicles from black goats in the Chuanzhong region for circRNA sequencing, with the aim of elucidating the functional circRNAs that influence follicle development in goats. Differential analysis revealed that 17 circRNAs were upregulated in large follicles, and 28 circRNAs were upregulated in small follicles. Functional enrichment analysis revealed significant enrichment of pathways related to reproduction, including cellular response to follicle-stimulating hormone stimulus, the PI3K-Akt signaling pathway, the MAPK signaling pathway, and the Notch signaling pathway. Based on the ceRNA mechanism, 45 differentially expressed circRNAs were found to target and bind a total of 418 miRNAs, and an intercalation network including miR-324-3p (circRNA2497, circRNA5650), miR-202-5p (circRNA3333, circRNA5501), and miR-493-3p (circRNA4995, circRNA5508) was constructed. In addition, conservation analysis revealed that 2,239 circRNAs were conserved between goats and humans. Prediction of translation potential revealed that 154 circRNAs may potentially utilize both N6-methyladenosine (m6A) and internal ribosome entry site (IRES) translation mechanisms. Furthermore, the differential expression and circularization cleavage sites of five circRNAs were validated through RT-qPCR and DNA sequencing. Our study constructed a circRNA map in goat follicle development, offering a theoretical foundation for enhancing goat reproductive performance. Full article
(This article belongs to the Special Issue Regulation by Non-Coding RNAs 2025)
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