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BioChem
Special Issues
RNA and Protein Dynamics: Latest Advances and Prospects
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RNA and Protein Dynamics: Latest Advances and Prospects

A special issue of BioChem (ISSN 2673-6411).

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 10941

Special Issue Editors

Dr. Simona Panni

E-Mail Website
Guest Editor
Dipartimento di Biologia Ecologia Scienze della Terra (DiBEST), Università della Calabria, Via Pietro Bucci Cubo 6/C, 87036 Rende, Italy
Interests: molecular interactions; systems biology
Dr. Luana Licata

E-Mail Website
Guest Editor
Department of Biology, University of Rome Tor Vergata, Via Delle Ricerca Scientifica 1, 00133 Rome, Italy
Interests: protein–protein interactions; systems biology; bioinformatics
Dr. Raffaella Gallo

E-Mail Website
Guest Editor
Department of Experimental and Clinical Medicine, University “Magna Græcia”, Viale Europa, 88100 Catanzaro, Italy
Interests: cell biology and signalling; protein–protein interactions; phase separation; early secretory pathway; dual specificity kinases (DYRKs)

Special Issue Information

Dear Colleagues,

Recent advances in molecular biology have enabled the discovery and characterization of an unexpected multitude of RNA molecules involved in various physiological processes and have shed new light on the complex network of molecular interactions that occur in each cell to determine its fate. Many of these transcripts originate from apparently non-functional parts of the genome and are rapidly degraded. However, experimental studies have shown that some classes of ncRNAs, such as lncRNAs and microRNAs, are involved in virtually all cellular processes and direct widespread gene regulation at transcriptional and posttranscriptional levels, respectively. More controversial is the function of circRNAs, although the role of miRNA regulator has been convincingly demonstrated for some of them. Many ncRNAs have been proposed as new potential biomarkers and therapeutic targets. Overall, considerable progress has been achieved in deconstructing ncRNA-driven cellular homeostasis and its deregulation in pathologies, and the generation of massive, high-resolution datasets is rapidly transforming the classical vision of sole-protein cellular pathways in a more sophisticated protein–ncRNAs–genes interaction network. A key challenge at this point is to build the appropriate bioinformatics tools to integrate different datasets in order to model the connections and their functional role.

This Special Issue focuses on the latest advances in proteins and ncRNAs’ interactions and functions. The topics of interest include, but are not limited to:

  • Characterization of protein and RNA interactions.
  • Description of ncRNA regulatory networks.
  • Latest technical approaches to investigate protein and RNA function and localization.
  • Databases to annotate interaction data sets.
  • Bioinformatics tools to predict interactions or integrate data.

Dr. Simona Panni
Dr. Luana Licata
Dr. Raffaella Gallo
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. BioChem is an international peer-reviewed open access quarterly 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 1000 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

  • PPI
  • protein complexes
  • molecular interactions
  • protein localization
  • ncRNAs
  • lncRNAs
  • miRNAs
  • circRNAs
  • interaction networks
  • systems biology

Published Papers (4 papers)

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Research

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11 pages, 4408 KiB  
Article
New Method of Isothermal, Hairpin Assisted, Primer Independent Amplification of DNA
by Denis Sergeevich Naberezhnov, Alexander Andreevich Alferov, Yuriy Borisovich Kuzmin and Nikolay Evgenievich Kushlinskii
BioChem 2023, 3(3), 142-152; https://doi.org/10.3390/biochem3030010 - 19 Sep 2023
Viewed by 1051
Abstract
The isothermal amplification of nucleic acids refers to processes that quickly increase the amount of DNA at a constant temperature. These methods are mainly developed as alternatives to PCR for cases in which the application of a thermal cycler is not possible or [...] Read more.
The isothermal amplification of nucleic acids refers to processes that quickly increase the amount of DNA at a constant temperature. These methods are mainly developed as alternatives to PCR for cases in which the application of a thermal cycler is not possible or the assay method must be as rapid as possible. We have developed a new method of isothermal amplification based on the formation of hairpins at the ends of DNA fragments containing palindromic sequences and increased by the hydrolysis of one or both DNA strands by restriction endonuclease, known as hairpin-assisted isothermal reaction (HAIR). The key steps in HAIR are the formation of a self-complementary hairpin and the DNA breakage introduced by nickase. The end hairpins facilitate primer-free amplification, the amplicon strand cleavage by nickase produces additional 3′ ends that serve as new amplification points, and the amount of DNA can increase exponentially. The rate of amplification in HAIR is more than five times the rate of loop-mediated isothermal amplification (LAMP), and the total amount of DNA product of HAIR is more than double the amount of the LAMP product. Full article
(This article belongs to the Special Issue RNA and Protein Dynamics: Latest Advances and Prospects)
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Review

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16 pages, 684 KiB  
Review
Intracellular Organization of Proteins and Nucleic Acids via Biomolecular Condensates in Human Health and Diseases
by Raffaella Gallo
BioChem 2023, 3(1), 31-46; https://doi.org/10.3390/biochem3010003 - 01 Feb 2023
Viewed by 2534
Abstract
Eukaryotic cells are intracellularly divided into several compartments that provide spatiotemporal control over biochemical reactions. Phase separation of proteins and RNA is emerging as an important mechanism underlying the formation of intracellular compartments that are not delimited by membranes. These structures are also [...] Read more.
Eukaryotic cells are intracellularly divided into several compartments that provide spatiotemporal control over biochemical reactions. Phase separation of proteins and RNA is emerging as an important mechanism underlying the formation of intracellular compartments that are not delimited by membranes. These structures are also known as biomolecular condensates and have been shown to serve a myriad of cellular functions, such as organization of cytoplasm and nucleoplasm, stress response, signal transduction, gene regulation, and immune response. Here, the author will summarize our current understanding of intracellular phase separation, its biological functions, and how this phenomenon is regulated in eukaryotic cells. Additionally, the author will review recent evidence of the role of biomolecular condensates in the development of pathophysiological conditions, with special emphasis on cancer and immune signaling. Full article
(This article belongs to the Special Issue RNA and Protein Dynamics: Latest Advances and Prospects)
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14 pages, 1256 KiB  
Review
Current Technical Approaches to Study RNA–Protein Interactions in mRNAs and Long Non-Coding RNAs
by Johanna Mattay
BioChem 2023, 3(1), 1-14; https://doi.org/10.3390/biochem3010001 - 30 Dec 2022
Cited by 1 | Viewed by 3414
Abstract
It is commonly understood that RNA-binding proteins crucially determine the fate of their target RNAs. Vice versa, RNAs are becoming increasingly recognized for their functions in protein regulation and the dynamics of RNA-protein complexes. Long non-coding RNAs are emerging as potent regulators of [...] Read more.
It is commonly understood that RNA-binding proteins crucially determine the fate of their target RNAs. Vice versa, RNAs are becoming increasingly recognized for their functions in protein regulation and the dynamics of RNA-protein complexes. Long non-coding RNAs are emerging as potent regulators of proteins that exert unknown RNA-binding properties and moonlighting functions. A vast array of RNA- and protein-centric techniques have been developed for the identification of protein and RNA targets, respectively, including unbiased protein mass spectrometry and next-generation RNA sequencing as readout. Determining true physiological RNA and protein targets is challenging as RNA–protein interaction is highly dynamic, tissue- and cell-type-specific, and changes with the environment. Here I review current techniques for the analysis of RNA–protein interactions in living cells and in vitro. RNA-centric techniques are presented on the basis of cross-linking or the use of alternative approaches. Protein-centric approaches are discussed in combination with high-throughput sequencing. Finally, the impact of mutations in RNA–protein complexes on human disease is highlighted. Full article
(This article belongs to the Special Issue RNA and Protein Dynamics: Latest Advances and Prospects)
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19 pages, 2011 KiB  
Review
The Role of Epitranscriptomic Modifications in the Regulation of RNA–Protein Interactions
by Elzbieta Wanowska, Alexis McFeely and Joanna Sztuba-Solinska
BioChem 2022, 2(4), 241-259; https://doi.org/10.3390/biochem2040017 - 25 Nov 2022
Cited by 1 | Viewed by 2780
Abstract
Epitranscriptome refers to post-transcriptional modifications to RNA and their associated regulatory factors that can govern changes in an organism’s cells in response to various environmental stimuli. Recent studies have recognized over 170 distinct chemical signatures in RNA, and the list keeps expanding. These [...] Read more.
Epitranscriptome refers to post-transcriptional modifications to RNA and their associated regulatory factors that can govern changes in an organism’s cells in response to various environmental stimuli. Recent studies have recognized over 170 distinct chemical signatures in RNA, and the list keeps expanding. These modifications are hypothesized to have roles beyond simply fine-tuning the structure and function of RNA, as studies have linked them to various infectious and noninfectious diseases in humans. Dedicated cellular machinery comprising of RNA-binding proteins (RBPs) that can write, erase, and read these modifications drives the regulation of the epitranscriptomic code, and as such influences RNA metabolism and homeostasis. Equally, perturbations in the function of RBPs may disrupt RNA processing, further implicating them in pathogenesis. As such, the mechanisms underlying RNA modifications and their association with RBPs are emerging areas of interest within the field of biomedicine. This review focuses on understanding epitranscriptomic modifications, their effects on RNA–RBPs interactions, and their influence on cellular processes. Full article
(This article belongs to the Special Issue RNA and Protein Dynamics: Latest Advances and Prospects)
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