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Research on Non-coding RNA Structure and Function
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Research on Non-coding RNA Structure and Function

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "RNA".

Deadline for manuscript submissions: closed (15 May 2022) | Viewed by 13691

Special Issue Editors

Dr. Lina Ma

E-Mail Website
Guest Editor
China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
Interests: ncRNA curation and annotation; multi-omics integrative analysis; software and database
Dr. Tao Huang

E-Mail Website
Guest Editor
Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
Interests: bioinformatics; genetics; genomics; machine learning; ceRNA network; predictive modeling
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Xianyang Fang

E-Mail Website
Guest Editor
1. School of Life Sciences, Tsinghua University, Beijing 100084, China
2. Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
Interests: RNA integrative structural biology; position-selective labeling strategies for large RNAs; structure determination of large RNAs and RNA-protein complexes

Special Issue Information

Dear Colleagues, 

Non-coding RNAs (ncRNAs), a large group of RNAs that possess little or no protein-coding potentials, play important and diverse roles. The many different ncRNA categories include rRNAs, tRNAs, snoRNAs, microRNAs, lncRNAs, circRNAs, piRNAs, etc., which show specific sequence features and biological functions. Moreover, the secondary and tertiary structures of ncRNAs are crucial for their maturation and molecular functions. While covariation analysis of the primary sequences helps to identify conserved RNA structures, the combination of next-generation sequencing and RNA structure probing techniques enables analyzing RNA secondary structures at the transcriptome-wide level. Many tools have been developed to predict both the secondary and tertiary structures of ncRNAs. Despite this, we still know very little about the structure–function association of ncRNAs.

Compared with the numerous studies on protein structures and functions, ncRNAs are extremely understudied. How do sequence differences determine the ncRNA structural differences and functional diversities? Is the RNA structure correlated with the coding potential? Will there be an AlphaFold2-like software for RNA structure prediction? There are very limited databases deciphering ncRNA structure. It is not clear how ncRNAs mediate various associated interactions, and the landscape of ncRNA-mediated interactome has not been fully characterized.

To address these questions, we would like to organize a Special Issue focusing on the potential topics, including but not limited to:

  1. Sequence analysis of ncRNA
  2. RNA coding potential prediction
  3. Prediction of ncRNA structure
  4. RNA structure probing techniques
  5. RNA tertiary structure analysis
  6. ncRNA-mediated interactome
  7. Functional analysis of ncRNA
  8. Structure–function association of ncRNA

Dr. Lina Ma
Dr. Tao Huang
Dr. Xianyang Fang
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. Genes 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 2600 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

  • lncRNA
  • circRNA
  • microRNA
  • piRNA
  • snoRNA
  • sequence
  • structure
  • function
  • maturation
  • covariation

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Published Papers (4 papers)

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Research

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14 pages, 2555 KiB  
Article
Structural Organization of S516 Group I Introns in Myxomycetes
by Betty M. N. Furulund, Bård O. Karlsen, Igor Babiak, Peik Haugen and Steinar D. Johansen
Genes 2022, 13(6), 944; https://doi.org/10.3390/genes13060944 - 25 May 2022
Cited by 1 | Viewed by 2631
Abstract
Group I introns are mobile genetic elements encoding self-splicing ribozymes. Group I introns in nuclear genes are restricted to ribosomal DNA of eukaryotic microorganisms. For example, the myxomycetes, which represent a distinct protist phylum with a unique life strategy, are rich in nucleolar [...] Read more.
Group I introns are mobile genetic elements encoding self-splicing ribozymes. Group I introns in nuclear genes are restricted to ribosomal DNA of eukaryotic microorganisms. For example, the myxomycetes, which represent a distinct protist phylum with a unique life strategy, are rich in nucleolar group I introns. We analyzed and compared 75 group I introns at position 516 in the small subunit ribosomal DNA from diverse and distantly related myxomycete taxa. A consensus secondary structure revealed a conserved group IC1 ribozyme core, but with a surprising RNA sequence complexity in the peripheral regions. Five S516 group I introns possess a twintron organization, where a His-Cys homing endonuclease gene insertion was interrupted by a small spliceosomal intron. Eleven S516 introns contained direct repeat arrays with varying lengths of the repeated motif, a varying copy number, and different structural organizations. Phylogenetic analyses of S516 introns and the corresponding host genes revealed a complex inheritance pattern, with both vertical and horizontal transfers. Finally, we reconstructed the evolutionary history of S516 nucleolar group I introns from insertion of mobile-type introns at unoccupied cognate sites, through homing endonuclease gene degradation and loss, and finally to the complete loss of introns. We conclude that myxomycete S516 introns represent a family of genetic elements with surprisingly dynamic structures despite a common function in RNA self-splicing. Full article
(This article belongs to the Special Issue Research on Non-coding RNA Structure and Function)
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18 pages, 3737 KiB  
Article
Hsa_circ_0006692 Promotes Lung Cancer Progression via miR-205-5p/CDK19 Axis
by Jinrong Liao, Zeng Chen, Xingguan Luo, Ying Su, Tao Huang, Haipeng Xu, Keyu Lin, Qianlan Zheng, Lurong Zhang, Gen Lin and Xiandong Lin
Genes 2022, 13(5), 846; https://doi.org/10.3390/genes13050846 - 10 May 2022
Cited by 11 | Viewed by 3164
Abstract
Circular RNA (CircRNA) is related to tumor development. Nevertheless, the regulation and function of hsa_circ_0006692 and its interactions with miR-205-5p and CDK19 in the development of non-small-cell lung cancer (NSCLC) were un-explored. The correlations of expression levels of hsa_circ_0006692 in NSCLC specimens and [...] Read more.
Circular RNA (CircRNA) is related to tumor development. Nevertheless, the regulation and function of hsa_circ_0006692 and its interactions with miR-205-5p and CDK19 in the development of non-small-cell lung cancer (NSCLC) were un-explored. The correlations of expression levels of hsa_circ_0006692 in NSCLC specimens and cells with pathological characteristics were studied. The interactions of hsa_circ_0006692 with miR-205-5p and CDK19 were assessed with real-time PCR, RNA-binding protein immunoprecipitation (RIP), luciferase reporter, RNA pull-down, and fluorescence in situ hybridization (FISH). The roles of hsa_circ_0006692 on cell growth, invasion, and migration in vitro and metastasis in vivo were evaluated. Hsa_circ_0006692 was over-expressed in 60 cases of NSCLC specimens and cells, which was positively correlated with TNM stage, tumor size, and invasion of the lung basal layer. The results of the in vitro and in vivo studies revealed that the over-expression of hsa_circ_0006692 facilitated NSCLC cell growth, migration, and invasion, cell cycle arrest at the S phase, and the activation of BCL-2, CCND1, and PCNA. The results of the dual-luciferase reporter assay, RNA immunoprecipitation, and pull-down assays indicated that hsa_circ_0006692 sponged miR-205-5p, which targeted CDK19 and facilitated the malignant behaviors of lung cancer cells. Hsa_circ_0006692 modulated EMT of lung cancer cells via the stimulation of CDH1, CDH2, VIMENTIN, and MMP7. This study revealed that hsa_circ_0006692 promoted NSCLC progression via enhancing cell growth, invasion, and metastasis through sponging mir-205-5p, up-regulating the downstream oncogene CDK19 and modulating EMT of lung cancer cells. The circ-0006692/mir-205-5p/CDK19 axis might serve as a prognosis biomarker and target for drugs aimed against NSCLC. Full article
(This article belongs to the Special Issue Research on Non-coding RNA Structure and Function)
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17 pages, 2938 KiB  
Article
Long Intergenic Non-Protein Coding RNA 02381 Promotes the Proliferation and Invasion of Ovarian Endometrial Stromal Cells through the miR-27b-3p/CTNNB1 Axis
by Xiaoqing Wang, Peili Wu, Cheng Zeng, Jingwen Zhu, Yingfang Zhou, Ye Lu and Qing Xue
Genes 2022, 13(3), 433; https://doi.org/10.3390/genes13030433 - 26 Feb 2022
Cited by 6 | Viewed by 2784
Abstract
Purpose: Catenin Beta 1 (CTNNB1) is a key regulator of cell proliferation and invasion in endometriosis; however, its upstream factor is not clear. Long noncoding RNAs may participate in endometriosis. The aim of this study was to investigate the mechanism of interaction between [...] Read more.
Purpose: Catenin Beta 1 (CTNNB1) is a key regulator of cell proliferation and invasion in endometriosis; however, its upstream factor is not clear. Long noncoding RNAs may participate in endometriosis. The aim of this study was to investigate the mechanism of interaction between LINC02381 and CTNNB1 in endometriosis. Method: Screening and validation of RNAs were completed by whole transcriptional sequencing and qRT-PCR. The subcellular localization of LINC02381 was determined by RNA in situ hybridization and nucleo-cytoplasmic separation. Plasmids were transfected for functional experiments. Luciferase assay was used to verify the binding relationship. Results: The expression of LINC02381 and CTNNB1 was significantly increased in ovarian ectopic endometrial tissues (OSAs) and ectopic endometrial stromal cells (ESCs). When LINC02381 was downregulated in ESCs, the expression of CTNNB1, metallopeptidase 9 (MMP9) and cyclinD1, as well as ESCs invasion and proliferation, decreased. LINC02381 was mainly present in the cytoplasm of ESCs, indicating that it may act as a competitive endogenous RNA. Bioinformatic analysis revealed that microRNA-27b-3p (miR-27b-3p) is a downstream target of LINC02381. miR-27b-3p decreased in OSAs and ESCs. Moreover, when miR-27b-3p was upregulated in ESCs, the expression of CTNNB1, MMP9 and cyclinD1, as well as the invasion and proliferation ability of ESCs, were reduced. Additionally, rescue experiments demonstrated that the expression of CTNNB1, MMP9 and cyclinD1, as well as the invasion and proliferation ability, were significantly increased in the group transfected with both sh-LINC02381 and a miR-27b-3p inhibitor. Conclusion: LINC02381 upregulated CTNNB1 by adsorbing miR-27b-3p, causing increased proliferation and invasion of ESCs. Full article
(This article belongs to the Special Issue Research on Non-coding RNA Structure and Function)
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Review

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13 pages, 581 KiB  
Review
Transfer RNA-Derived Small RNAs in the Pathogenesis of Parasitic Protozoa
by Ruofan Peng, Herbert J. Santos and Tomoyoshi Nozaki
Genes 2022, 13(2), 286; https://doi.org/10.3390/genes13020286 - 31 Jan 2022
Cited by 9 | Viewed by 3861
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are newly identified non-coding small RNAs that have recently attracted attention due to their functional significance in both prokaryotes and eukaryotes. tsRNAs originated from the cleavage of precursor or mature tRNAs by specific nucleases. According to the [...] Read more.
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are newly identified non-coding small RNAs that have recently attracted attention due to their functional significance in both prokaryotes and eukaryotes. tsRNAs originated from the cleavage of precursor or mature tRNAs by specific nucleases. According to the start and end sites, tsRNAs can be broadly divided into tRNA halves (31–40 nucleotides) and tRNA-derived fragments (tRFs, 14–30 nucleotides). tsRNAs have been reported in multiple organisms to be involved in gene expression regulation, protein synthesis, and signal transduction. As a novel regulator, tsRNAs have also been identified in various protozoan parasites. The conserved biogenesis of tsRNAs in early-branching eukaryotes strongly suggests the universality of this machinery, which requires future research on their shared and potentially disparate biological functions. Here, we reviewed the recent studies of tsRNAs in several representative protozoan parasites including their biogenesis and the roles in parasite biology and intercellular communication. Furthermore, we discussed the remaining questions and potential future works for tsRNAs in this group of organisms. Full article
(This article belongs to the Special Issue Research on Non-coding RNA Structure and Function)
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