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Non-coding RNA Modification, Structure, Function and Application

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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 4924

Special Issue Editors


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Guest Editor
1. Cancer Center, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
2. College of Medicine, Tzu Chi University, Hualien, Taiwan
Interests: non-coding RNA; RNA Methylation; immunotherapeutic; cellular and molecular biology; molecular biology; cancer biology; exosome; endocrine-related cancer

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Guest Editor
1. Division of Urology, Department of Surgery, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
2. Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
Interests: prostate cancer; surgical urology; androgen deprivation therapy; health data mining; precision medicine
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, with the development of new technologies, non-coding RNA (ncRNA) such as microRNA (miRNA), long-chain non-coding RNA (lncRNA), and circular RNA (circRNA) have been discovered. The discovery of these ncRNAs has caused major changes in the field of biomedicine. From the initial ubiquitous transcripts devoid of any regulatory function, it has been proven that they can control gene performance by combining with "targets" (for example, functions such as epigenetics, transcription, or translation). ncRNA is a powerful regulator of almost all biological processes.

Now people have realized that ncRNA plays a key role in physiology and pathology via a subtle and complex network regulation method. For example, the identification and exploration of the underlying mechanism of ncRNA provides new insights for elucidating the pathophysiology of cancer and provides possible new accurate diagnostic biomarkers or potential therapeutic targets for cancer diagnosis and treatment. This Special Issue will also introduce the interaction effects of RNA modification on ncRNA.

All aspects of research involving non-coding RNA are welcome, such as their biogenesis, regulation, and role in disease progression. The focus of the journal will be on publishing translational research and well-designed basic research with translational and clinical significance. Original research and review articles are welcome. Topics of interest include but are not limited to:

  • Regulation of non-coding RNA;
  • Targets and regulatory functions of non-coding RNA;
  • Epigenetics and non-coding RNA;
  • The biological function of non-coding RNA;
  • Non-coding RNA as a biomarker;
  • Non-coding RNA-based therapies;
  • Prognostic value of non-coding RNA;
  • Non-coding RNA and RNA methylation.

Dr. Ren-Jun Hsu
Dr. Juiming Liu
Guest Editors

Manuscript Submission Information

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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.

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Keywords

  • non-coding RNA
  • transcriptional control
  • regulatory network
  • RNA methylation

Published Papers (2 papers)

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19 pages, 4857 KiB  
Article
Overexpression of Pericentromeric HSAT2 DNA Increases Expression of EMT Markers in Human Epithelial Cancer Cell Lines
by Nikita Ponomartsev, Danil Zilov, Ekaterina Gushcha, Alexandra Travina, Alexander Sergeev and Natella Enukashvily
Int. J. Mol. Sci. 2023, 24(8), 6918; https://doi.org/10.3390/ijms24086918 - 7 Apr 2023
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Abstract
Pericentromeric tandemly repeated DNA of human satellites 1, 2, and 3 (HS1, HS2, and HS3) is actively transcribed in some cells. However, the functionality of the transcription remains obscure. Studies in this area have been hampered by the absence of a gapless genome [...] Read more.
Pericentromeric tandemly repeated DNA of human satellites 1, 2, and 3 (HS1, HS2, and HS3) is actively transcribed in some cells. However, the functionality of the transcription remains obscure. Studies in this area have been hampered by the absence of a gapless genome assembly. The aim of our study was to map a transcript that we have previously described as HS2/HS3 on chromosomes using a newly published gapless genome assembly T2T-CHM13, and create a plasmid overexpressing the transcript to assess the influence of HS2/HS3 transcription on cancer cells. We report here that the sequence of the transcript is tandemly repeated on nine chromosomes (1, 2, 7, 9, 10, 16, 17, 22, and Y). A detailed analysis of its genomic localization and annotation in the T2T-CHM13 assembly revealed that the sequence belonged to HSAT2 (HS2) but not to the HS3 family of tandemly repeated DNA. The transcript was found on both strands of HSAT2 arrays. The overexpression of the HSAT2 transcript increased the transcription of the genes encoding the proteins involved in the epithelial-to-mesenchymal transition, EMT (SNAI1, ZEB1, and SNAI2), and the genes that mark cancer-associated fibroblasts (VIM, COL1A1, COL11A1, and ACTA2) in cancer cell lines A549 and HeLa. Co-transfection of the overexpression plasmid and antisense nucleotides eliminated the transcription of EMT genes observed after HSAT2 overexpression. Antisense oligonucleotides also decreased transcription of the EMT genes induced by tumor growth factor beta 1 (TGFβ1). Thus, our study suggests HSAT2 lncRNA transcribed from the pericentromeric tandemly repeated DNA is involved in EMT regulation in cancer cells. Full article
(This article belongs to the Special Issue Non-coding RNA Modification, Structure, Function and Application)
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18 pages, 4354 KiB  
Article
Circ003429 Regulates Unsaturated Fatty Acid Synthesis in the Dairy Goat Mammary Gland by Interacting with miR-199a-3p, Targeting the YAP1 Gene
by Peixin Jiao, Meimei Zhang, Ziwei Wang, Gege Liang, Xiaolai Xie, Yonggen Zhang, Zhi Chen, Qianming Jiang and Juan J. Loor
Int. J. Mol. Sci. 2022, 23(7), 4068; https://doi.org/10.3390/ijms23074068 - 6 Apr 2022
Cited by 7 | Viewed by 2109
Abstract
Fatty acid composition is a key factor affecting the flavor and quality of goat milk. CircRNAs are now recognized as important regulators of transcription, and they play an important role in the control of fatty acid synthesis. Thus, understanding the regulatory mechanisms controlling [...] Read more.
Fatty acid composition is a key factor affecting the flavor and quality of goat milk. CircRNAs are now recognized as important regulators of transcription, and they play an important role in the control of fatty acid synthesis. Thus, understanding the regulatory mechanisms controlling this process in ruminant mammary glands is of great significance. In the present study, mammary tissue from dairy goats during early lactation and the dry period (nonlactating) were collected and used for high-throughput sequencing. Compared to levels during the dry period, the expression level of circ003429 during early lactation was lower (12.68-fold downregulated). In isolated goat mammary epithelial cells, circ003429 inhibited the synthesis of triglycerides (TAG) and decreased the content of unsaturated fatty acids (C16:1, C18:1, and C18:2), indicating that this circRNA plays an important role in regulating lipid synthesis. A binding site for miR-199a-3p in the circ003429 sequence was detected, and a dual-luciferase reporter system revealed that circ003429 targets miR-199a-3p. Overexpression of circ003429 (pcDNA-circ003429) downregulated the abundance of miR-199a-3p. In contrast, overexpression of miR-199a-3p increased TAG content and decreased mRNA abundance of Yes-associated protein 1 (YAP1) (a target gene of miR-199a-3p), and TAG content was decreased and mRNA abundance was increased in response to overexpression of circ003429. These results indicate that circ003429 alleviates the inhibitory effect of miR-199a-3p on the mRNA abundance of YAP1 by binding miR-199a-3p, resulting in subsequent regulation of the synthesis of TAG and unsaturated fatty acids. Full article
(This article belongs to the Special Issue Non-coding RNA Modification, Structure, Function and Application)
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