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New Horizon for Non-coding RNAs
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New Horizon for Non-coding RNAs

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

Deadline for manuscript submissions: 20 May 2025 | Viewed by 6758

Special Issue Editor

Dr. Hiroki Sato

E-Mail Website
Guest Editor
Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka-Higashi, Asahikawa 078-8510, Hokkaido, Japan
Interests: cancer genomics; carcinogenesis of pancreatic cancer; carcinogenesis of biliary tract cancer; cancer cahexia of hepatobiliary tract and pancreas cancer; cancer-related sarcopenia; hepatobliliary tract cancer related microRNA/non-coding RNA; pancreas cancer related microRNA/non-coding RNA; biomaker of the early detection of cancer; neuroendocrine tumor/carcinoma
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Noncoding RNAs (ncRNAs) constitute an abundant and heterogeneous class of transcripts including microRNAs, long noncoding RNAs, and circular RNAs. They have emerged in the past decade as key players in the regulation of transcriptional programs. Their activity complements transcription factors, either by providing a further level of control of downstream targets or by establishing feedback loops impacting the transcription factor itself. While many examples of the role of ncRNAs have been reported in the literature, we still lack a detailed understanding of the mechanisms underlying their interactions. Classification strategies are thus plagued by frequent mis‑annotations. Contributions to this Special Issue will provide new insights into the identification of ncRNAs, suggest both experimental and computational approaches to clarify their mechanism of action, and describe their activity in the larger context of regulatory networks.

Dr. Hiroki Sato
Guest Editor

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Keywords

  • microRNAs
  • long noncoding RNAs
  • circular RNAs
  • transcriptional control
  • regulatory networks
  • function prediction

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Published Papers (4 papers)

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Research

15 pages, 5294 KiB  
Article
tsRNA-00764 Regulates Estrogen and Progesterone Synthesis and Lipid Deposition by Targeting PPAR-γ in Duck Granulosa Cells
by Yaru Chen, Yan Wu, Jinsong Pi, Ming Fu, Jie Shen, Hao Zhang and Jinping Du
Int. J. Mol. Sci. 2024, 25(20), 11251; https://doi.org/10.3390/ijms252011251 - 19 Oct 2024
Viewed by 493
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are novel regulatory small non-coding RNAs that have been found to modulate many life activities in recent years. However, the exact functions of tsRNAs in follicle development remain unclear. Follicle development is a remarkably complex process that follows [...] Read more.
Transfer RNA-derived small RNAs (tsRNAs) are novel regulatory small non-coding RNAs that have been found to modulate many life activities in recent years. However, the exact functions of tsRNAs in follicle development remain unclear. Follicle development is a remarkably complex process that follows a strict hierarchy and is strongly associated with reproductive performance in ducks. The process of converting small yellow follicles into hierarchal follicles is known as follicle selection, which directly determines the number of mature follicles. We performed small RNA sequencing during follicle selection in ducks and identified tsRNA-00764 as the target of interest based on tsRNA expression profiles in this study. Bioinformatics analyses and luciferase reporter assays further revealed that peroxisome proliferator-activated receptor-γ (PPAR-γ) was the target gene of tsRNA-00764. Moreover, tsRNA-00764 knockdown promoted estrogen and progesterone synthesis and lipid deposition in duck granulosa cells, while a PPAR-γ inhibitor reversed the above phenomenon. Taken together, these results demonstrate that tsRNA-00764, differentially expressed in pre-hierarchal and hierarchy follicles, modulates estrogen and progesterone synthesis and lipid deposition by targeting PPAR-γ in duck granulosa cells, serving as a potential novel mechanism of follicle selection. Overall, our findings provide a theoretical foundation for further exploration of the molecular mechanisms underlying follicle development and production performance in ducks. Full article
(This article belongs to the Special Issue New Horizon for Non-coding RNAs)
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19 pages, 4876 KiB  
Article
LncRNA and Protein Expression Profiles Reveal Heart Adaptation to High-Altitude Hypoxia in Tibetan Sheep
by Zhaohua He, Shaobin Li, Fangfang Zhao, Hongxian Sun, Jiang Hu, Jiqing Wang, Xiu Liu, Mingna Li, Zhidong Zhao and Yuzhu Luo
Int. J. Mol. Sci. 2024, 25(1), 385; https://doi.org/10.3390/ijms25010385 - 27 Dec 2023
Viewed by 1449
Abstract
The Tibetan sheep has an intricate mechanism of adaptation to low oxygen levels, which is influenced by both genetic and environmental factors. The heart plays a crucial role in the adaptation of Tibetan sheep to hypoxia. In the present study, we utilized transcriptomic [...] Read more.
The Tibetan sheep has an intricate mechanism of adaptation to low oxygen levels, which is influenced by both genetic and environmental factors. The heart plays a crucial role in the adaptation of Tibetan sheep to hypoxia. In the present study, we utilized transcriptomic and proteomic technologies to comprehensively analyze and identify the long non-coding RNAs (lncRNAs), genes, proteins, pathways, and gene ontology (GO) terms associated with hypoxic adaptation in Tibetan sheep at three different altitudes (2500 m, 3500 m, and 4500 m). By integrating the differentially expressed (DE) lncRNA target genes, differentially expressed proteins (DEPs), and differentially expressed genes (DEGs), we were able to identify and characterize the mechanisms underlying hypoxic adaptation in Tibetan sheep. Through this integration, we identified 41 shared genes/proteins, and functional enrichment analyses revealed their close association with lipid metabolism, glycolysis/gluconeogenesis, and angiogenesis. Additionally, significant enrichment was observed in important pathways such as the PPAR signaling pathway, glycolysis/gluconeogenesis, the oxoacid metabolic process, and angiogenesis. Furthermore, the co-expression network of lncRNAs and mRNAs demonstrated that lncRNAs (MSTRG.4748.1, ENSOART00020025894, and ENSOART00020036371) may play a pivotal role in the adaptation of Tibetan sheep to the hypoxic conditions of the plateau. In conclusion, this study expands the existing database of lncRNAs and proteins in Tibetan sheep, and these findings may serve as a reference for the prevention of altitude sickness in humans. Full article
(This article belongs to the Special Issue New Horizon for Non-coding RNAs)
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18 pages, 11655 KiB  
Article
Transcriptome Analysis of mRNA and lncRNA Related to Muscle Growth and Development in Gannan Yak and Jeryak
by Yali Wei, Dashan Guo, Yanbin Bai, Zhanxin Liu, Jingsheng Li, Zongchang Chen, Bingang Shi, Zhidong Zhao, Jiang Hu, Xiangmin Han, Jiqing Wang, Xiu Liu, Shaobin Li and Fangfang Zhao
Int. J. Mol. Sci. 2023, 24(23), 16991; https://doi.org/10.3390/ijms242316991 - 30 Nov 2023
Cited by 3 | Viewed by 1330
Abstract
The production performance of Jeryak, resulting from the F1 generation of the cross between Gannan yak and Jersey cattle, exhibits a significantly superior outcome compared with that of Gannan yak. Therefore, we used an RNA-seq approach to identify differentially expressed mRNAs (DEMs) and [...] Read more.
The production performance of Jeryak, resulting from the F1 generation of the cross between Gannan yak and Jersey cattle, exhibits a significantly superior outcome compared with that of Gannan yak. Therefore, we used an RNA-seq approach to identify differentially expressed mRNAs (DEMs) and differentially expressed lncRNAs (DELs) influencing muscle growth and development in Gannan yaks and Jeryaks. A total of 304 differentially expressed lncRNAs and 1819 differentially expressed mRNAs were identified based on the screening criteria of |log 2 FC| > 1 and FDR < 0.05. Among these, 132 lncRNAs and 1081 mRNAs were found to be down-regulated, while 172 lncRNAs and 738 mRNAs were up-regulated. GO and KEGG analyses showed that the identified DELs and DEMs were enriched in the entries of pathways associated with muscle growth and development. On this basis, we constructed an lncRNA–mRNA interaction network. Interestingly, two candidate DELs (MSTRG.16260.9 and MSTRG.22127.1) had targeting relationships with 16 (MYC, IGFBP5, IGFBP2, MYH4, FGF6, etc.) genes related to muscle growth and development. These results could provide a basis for further studies on the roles of lncRNAs and mRNAs in muscle growth in Gannan yaks and Jeryak breeds. Full article
(This article belongs to the Special Issue New Horizon for Non-coding RNAs)
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28 pages, 15447 KiB  
Article
Novel Transcriptomic Interactomes of Noncoding RNAs in the Heart under Altered Thyroid Hormonal States
by Viswanathan Rajagopalan, Sankalpa Chakraborty and Richard Lin
Int. J. Mol. Sci. 2023, 24(7), 6560; https://doi.org/10.3390/ijms24076560 - 31 Mar 2023
Cited by 2 | Viewed by 2287
Abstract
Noncoding RNAs are emerging as vital players in cardiovascular diseases. Thyroid hormones (THs) are crucial for cardiovascular survival; however, correction of systemic hypothyroidism (low serum THs) may not improve cardiac tissue-level hypothyroidism or cardiac function. Mechanistically, the understanding of noncoding transcriptomic interactions influencing [...] Read more.
Noncoding RNAs are emerging as vital players in cardiovascular diseases. Thyroid hormones (THs) are crucial for cardiovascular survival; however, correction of systemic hypothyroidism (low serum THs) may not improve cardiac tissue-level hypothyroidism or cardiac function. Mechanistically, the understanding of noncoding transcriptomic interactions influencing TH-mediated cardiac effects is unclear. Adult C57BL/6J mixed-sex mice were randomized into Control, Hypothyroid (HypoTH), Hyperthyroid (HyperTH), and HypoTH-Triiodothyronine restoration groups. Physiological, morphological, biochemical, molecular, and whole transcriptomic studies and appropriate statistical analyses were performed. HypoTH showed significant atrophy, depressed cardiac function, and decreased serum THs versus controls, and Triiodothyronine supplementation restored them. HyperTH significantly increased serum THs with hypertrophy. Real-time PCR showed significantly altered inflammatory and immune lncRNAs. The transcriptomic sequencing revealed significant differential expressions of lncRNAs, miRNAs, and mRNAs. Eleven novel circRNAs significantly decreased with increased THs. Multiple pathways were GO-/KEGG-enriched, including cardiac, thyroid, cancer, mitochondrial, inflammatory, adrenergic, metabolic, immune-mediated, vesicular, etc. We also uncovered significant novel co-expression and interactions of lncRNA-miRNA, lncRNA-miRNA-mRNA, lncRNA-mRNA, circRNA-miRNA, and miRNA-mRNA, and splicing events. This includes a novel pathway by which the predominant cardiac TH receptor alpha may interact with specific lncRNAs and miRNAs. This is the first study reporting a comprehensive transcriptome-wide interactome in the cardiac–thyroid axis. Full article
(This article belongs to the Special Issue New Horizon for Non-coding RNAs)
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