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ncRNA
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Recent Advances in Chemical Biology to Study and Target ncRNAs
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Recent Advances in Chemical Biology to Study and Target ncRNAs

A special issue of Non-Coding RNA (ISSN 2311-553X).

Deadline for manuscript submissions: closed (31 October 2023) | Viewed by 8944

Special Issue Editors

Dr. Raphael Benhamou

E-Mail Website
Guest Editor
School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
Interests: chemical biology; organic chemistry; RNA biology; biochemistry
Dr. Eylon Yavin

E-Mail Website
Guest Editor
The Institute for Drug Research, The School of Pharmacy, The Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 9112102, Israel
Interests: PNA (peptide nucleic acid); FIT-PNA (forced-intercalation-PNA); CPP (cell penetrating peptides); RNA diagnostics, antisense
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent decades, ncRNAs have been shown to play a critical role in a myriad of cellular processes, impacting normal gene expression as well as disease progression, making them an attractive target for drug discovery. Moreover, their complex impacts on molecular biology still require revealing and studying. Recent developments in chemical biology have enabled us to interrogate and understand more about important ncRNAs at a molecular level.

In this context, this Special Issue aims to focus on novel advances in chemistry to study and target ncRNAs. We welcome reviews, novel methods and original research articles in the field of ncRNA chemical biology. The purpose of this Special Issue is to highlight the chemical tools developed for targeting disease-related ncRNAs or for questioning the nature and role of ncRNAs.

Notably, this Special Issue englobes various fields of research related to ncRNAs, such as chemical biology, medicinal chemistry, RNA biology, biochemistry and molecular biology. Furthermore, various specific topics are also included in the scope of the Special Issue, such as molecular dynamics simulations of ncRNAs, ncRNA targeting and cleavage strategies, ncRNA sequencing and structures, ncRNA chemical modifications, oligonucleotide and small molecule-based therapeutics targeting ncRNA, chemical probes to study ncRNA functions, regulations and structures. Work aiming to define the mechanism of ncRNA interactions as well as emerging strategies for the development of novel tools for the design and screening of ncRNA-targeted therapeutics is also welcome.

Dr. Raphael Benhamou
Dr. Eylon Yavin
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. Non-Coding RNA is an international peer-reviewed open access semimonthly 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 1800 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

  • ncRNA chemical biology
  • ncRNA medicinal chemistry
  • ncRNA biology
  • ncRNA probes
  • drugging ncRNAs
  • ncRNA biochemical tools
  • ncRNA as a target for drug discovery
  • ncRNA molecular regulation

Published Papers (5 papers)

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Research

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11 pages, 2147 KiB  
Communication
The Cystic Fibrosis Transmembrane Conductance Regulator Gene (CFTR) Is under Post-Transcriptional Control of microRNAs: Analysis of the Effects of agomiRNAs Mimicking miR-145-5p, miR-101-3p, and miR-335-5p
by Chiara Papi, Jessica Gasparello, Matteo Zurlo, Lucia Carmela Cosenza, Roberto Gambari and Alessia Finotti
Non-Coding RNA 2023, 9(2), 29; https://doi.org/10.3390/ncrna9020029 - 18 Apr 2023
Cited by 2 | Viewed by 1887
Abstract
(1) Background: MicroRNAs are involved in the expression of the gene encoding the chloride channel CFTR (Cystic Fibrosis Transmembrane Conductance Regulator); the objective of this short report is to study the effects of the treatment of bronchial epithelial Calu-3 cells with molecules mimicking [...] Read more.
(1) Background: MicroRNAs are involved in the expression of the gene encoding the chloride channel CFTR (Cystic Fibrosis Transmembrane Conductance Regulator); the objective of this short report is to study the effects of the treatment of bronchial epithelial Calu-3 cells with molecules mimicking the activity of pre-miR-145-5p, pre-miR-335-5p, and pre-miR-101-3p, and to discuss possible translational applications of these molecules in pre-clinical studies focusing on the development of protocols of possible interest in therapy; (2) Methods: CFTR mRNA was quantified by Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR). The production of the CFTR protein was assessed by Western blotting; (3) Results: The treatment of Calu-3 cells with agomiR-145-5p caused the highest inhibition of CFTR mRNA accumulation and CFTR production; (4) Conclusions: The treatment of target cells with the agomiR pre-miR-145-5p should be considered when CFTR gene expression should be inhibited in pathological conditions, such as polycystic kidney disease (PKD), some types of cancer, cholera, and SARS-CoV-2 infection. Full article
(This article belongs to the Special Issue Recent Advances in Chemical Biology to Study and Target ncRNAs)
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Review

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25 pages, 22344 KiB  
Review
Targeting MicroRNAs with Small Molecules
by Kisanet Tadesse and Raphael I. Benhamou
Non-Coding RNA 2024, 10(2), 17; https://doi.org/10.3390/ncrna10020017 - 14 Mar 2024
Viewed by 1878
Abstract
MicroRNAs (miRs) have been implicated in numerous diseases, presenting an attractive target for the development of novel therapeutics. The various regulatory roles of miRs in cellular processes underscore the need for precise strategies. Recent advances in RNA research offer hope by enabling the [...] Read more.
MicroRNAs (miRs) have been implicated in numerous diseases, presenting an attractive target for the development of novel therapeutics. The various regulatory roles of miRs in cellular processes underscore the need for precise strategies. Recent advances in RNA research offer hope by enabling the identification of small molecules capable of selectively targeting specific disease-associated miRs. This understanding paves the way for developing small molecules that can modulate the activity of disease-associated miRs. Herein, we discuss the progress made in the field of drug discovery processes, transforming the landscape of miR-targeted therapeutics by small molecules. By leveraging various approaches, researchers can systematically identify compounds to modulate miR function, providing a more potent intervention either by inhibiting or degrading miRs. The implementation of these multidisciplinary approaches bears the potential to revolutionize treatments for diverse diseases, signifying a significant stride towards the targeting of miRs by precision medicine. Full article
(This article belongs to the Special Issue Recent Advances in Chemical Biology to Study and Target ncRNAs)
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23 pages, 41554 KiB  
Review
Crosstalk between Long Non-Coding RNA and Spliceosomal microRNA as a Novel Biomarker for Cancer
by Maram Arafat and Ruth Sperling
Non-Coding RNA 2023, 9(4), 42; https://doi.org/10.3390/ncrna9040042 - 31 Jul 2023
Cited by 2 | Viewed by 1607
Abstract
Non-coding RNAs (ncRNAs) play diverse roles in regulating cellular processes and have been implicated in pathological conditions, including cancer, where interactions between ncRNAs play a role. Relevant here are (i) microRNAs (miRNAs), mainly known as negative regulators of gene expression in the cytoplasm. [...] Read more.
Non-coding RNAs (ncRNAs) play diverse roles in regulating cellular processes and have been implicated in pathological conditions, including cancer, where interactions between ncRNAs play a role. Relevant here are (i) microRNAs (miRNAs), mainly known as negative regulators of gene expression in the cytoplasm. However, identification of miRNAs in the nucleus suggested novel nuclear functions, and (ii) long non-coding RNA (lncRNA) regulates gene expression at multiple levels. The recent findings of miRNA in supraspliceosomes of human breast and cervical cancer cells revealed new candidates of lncRNA targets. Here, we highlight potential cases of crosstalk between lncRNA and supraspliceosomal miRNA expressed from the same genomic region, having complementary sequences. Through RNA:RNA base pairing, changes in the level of one partner (either miRNA or lncRNA), as occur in cancer, could affect the level of the other, which might be involved in breast and cervical cancer. An example is spliceosomal mir-7704 as a negative regulator of the oncogenic lncRNA HAGLR. Because the expression of spliceosomal miRNA is cell-type-specific, the list of cis-interacting lncRNA:spliceosomal miRNA presented here is likely just the tip of the iceberg, and such interactions are likely relevant to additional cancers. We thus highlight the potential of lncRNA:spliceosomal miRNA interactions as novel targets for cancer diagnosis and therapies. Full article
(This article belongs to the Special Issue Recent Advances in Chemical Biology to Study and Target ncRNAs)
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16 pages, 1223 KiB  
Review
LncRNA Functional Screening in Organismal Development
by Yang Li, Huicong Zhai, Lingxiu Tong, Cuicui Wang, Zhiming Xie and Ke Zheng
Non-Coding RNA 2023, 9(4), 36; https://doi.org/10.3390/ncrna9040036 - 28 Jun 2023
Viewed by 1400
Abstract
Controversy continues over the functional prevalence of long non-coding RNAs (lncRNAs) despite their being widely investigated in all kinds of cells and organisms. In animals, lncRNAs have aroused general interest from exponentially increasing transcriptomic repertoires reporting their highly tissue-specific and developmentally dynamic expression, [...] Read more.
Controversy continues over the functional prevalence of long non-coding RNAs (lncRNAs) despite their being widely investigated in all kinds of cells and organisms. In animals, lncRNAs have aroused general interest from exponentially increasing transcriptomic repertoires reporting their highly tissue-specific and developmentally dynamic expression, and more importantly, from growing experimental evidence supporting their functionality in facilitating organogenesis and individual fitness. In mammalian testes, while a great multitude of lncRNA species are identified, only a minority of them have been shown to be useful, and even fewer have been demonstrated as true requirements for male fertility using knockout models to date. This noticeable gap is attributed to the virtual existence of a large number of junk lncRNAs, the lack of an ideal germline culture system, difficulty in loss-of-function interrogation, and limited screening strategies. Facing these challenges, in this review, we discuss lncRNA functionality in organismal development and especially in mouse testis, with a focus on lncRNAs with functional screening. Full article
(This article belongs to the Special Issue Recent Advances in Chemical Biology to Study and Target ncRNAs)
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Other

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7 pages, 806 KiB  
Commentary
Small Nucleolar (Sno)RNA: Therapy Lays in Translation
by Ofri Rabany and Daphna Nachmani
Non-Coding RNA 2023, 9(3), 35; https://doi.org/10.3390/ncrna9030035 - 08 Jun 2023
Cited by 2 | Viewed by 1643
Abstract
The ribosome is one of the largest complexes in the cell. Adding to its complexity are more than 200 RNA modification sites present on ribosomal RNAs (rRNAs) in a single human ribosome. These modifications occur in functionally important regions of the rRNA molecule, [...] Read more.
The ribosome is one of the largest complexes in the cell. Adding to its complexity are more than 200 RNA modification sites present on ribosomal RNAs (rRNAs) in a single human ribosome. These modifications occur in functionally important regions of the rRNA molecule, and they are vital for ribosome function and proper gene expression. Until recent technological advancements, the study of rRNA modifications and their profiles has been extremely laborious, leaving many questions unanswered. Small nucleolar RNAs (snoRNAs) are non-coding RNAs that facilitate and dictate the specificity of rRNA modification deposition, making them an attractive target for ribosome modulation. Here, we propose that through the mapping of rRNA modification profiles, we can identify cell-specific modifications with high therapeutic potential. We also describe the challenges of achieving the targeting specificity needed to implement snoRNAs as therapeutic targets in cancers. Full article
(This article belongs to the Special Issue Recent Advances in Chemical Biology to Study and Target ncRNAs)
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