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Biology
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Editorial Board Members’ Collection Series: The Dynamics of RNA–Protein Interactions
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Editorial Board Members’ Collection Series: The Dynamics of RNA–Protein Interactions

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Biochemistry and Molecular Biology".

Deadline for manuscript submissions: closed (31 March 2025) | Viewed by 9274

Special Issue Editors

Dr. Je-Hyun Yoon

E-Mail Website
Guest Editor
Department of Oncology Science, College of Medicine, University of Oklahoma, Oklahoma City, OK 73104, USA
Interests: microRNAs; lncRNAs; ribonucleoproteins; RNAomics; extracellular RNA; senescence; RNA localization
Special Issues, Collections and Topics in MDPI journals
Dr. Brett Keiper

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
Interests: regulated translation initiation of mRNA in differentiating and transformed cells

Special Issue Information

Dear Colleagues,

Dynamic interactions of RNA and protein allow eukaryotic cells to regulate various cellular processes, including mRNA splicing, decay, localization, translation, and many others, under normal or stress conditions. The maintenance of RNA and protein interactions preserve cellular integrity, and the loss of these regulatory processes frequently drive numerous human diseases.

In this Special Issue, entitled “Editorial Board Members’ Collection Series: The Dynamics of RNA–Protein Interactions”, we welcome original relevant research articles and reviews which highlight the dynamic regulatory mechanisms underlying RNA and protein interactions, ultimately aiming to improve current knowledge of RNA biology and contributing to human health. Potential research areas include (but are not limited to): basic research and methodology into RNA and protein interactions performed by RNA-binding proteins, mRNAs, and noncoding RNAs. We have an additional interest in the accumulation of these biomolecules in subcellular organelles and specialized compartments like RNA granules and membraneless organelles.

We look forward to receiving your contributions.

Dr. Je-Hyun Yoon
Dr. Brett Keiper
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. Biology 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 2700 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

  • RNA-binding proteins
  • mRNA splicing
  • mRNA decay
  • mRNA translation
  • RNA localization
  • microRNAs
  • siRNAs
  • long noncoding RNAs
  • phase separation
  • RNA granules
  • membraneless organelles

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Published Papers (3 papers)

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Research

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16 pages, 2671 KiB  
Article
Low-Dose Ionizing Radiation-Crosslinking Immunoprecipitation (LDIR-CLIP) Identified Irradiation-Sensitive RNAs for RNA-Binding Protein HuR-Mediated Decay
by Ji Won Lee, Hyejin Mun, Jeong-Hyun Kim, Seungbeom Ko, Young-Kook Kim, Min Ji Shim, Kyungmin Kim, Chul Woong Ho, Hyun Bong Park, Meesun Kim, Chaeyoung Lee, Si Ho Choi, Jung-Woong Kim, Ji-Hoon Jeong, Je-Hyun Yoon, Kyung-Won Min and Tae Gen Son
Biology 2023, 12(12), 1533; https://doi.org/10.3390/biology12121533 - 15 Dec 2023
Viewed by 2562
Abstract
Although ionizing radiation (IR) is widely used for therapeutic and research purposes, studies on low-dose ionizing radiation (LDIR) are limited compared with those on other IR approaches, such as high-dose gamma irradiation and ultraviolet irradiation. High-dose IR affects DNA damage response and nucleotide–protein [...] Read more.
Although ionizing radiation (IR) is widely used for therapeutic and research purposes, studies on low-dose ionizing radiation (LDIR) are limited compared with those on other IR approaches, such as high-dose gamma irradiation and ultraviolet irradiation. High-dose IR affects DNA damage response and nucleotide–protein crosslinking, among other processes; however, the molecular consequences of LDIR have been poorly investigated. Here, we developed a method to profile RNA species crosslinked to an RNA-binding protein, namely, human antigen R (HuR), using LDIR and high-throughput RNA sequencing. The RNA fragments isolated via LDIR-crosslinking and immunoprecipitation sequencing were crosslinked to HuR and protected from RNase-mediated digestion. Upon crosslinking HuR to target mRNAs such as PAX6, ZFP91, NR2F6, and CAND2, the transcripts degraded rapidly in human cell lines. Additionally, PAX6 and NR2F6 downregulation mediated the beneficial effects of LDIR on cell viability. Thus, our approach provides a method for investigating post-transcriptional gene regulation using LDIR. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: The Dynamics of RNA–Protein Interactions)
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Review

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14 pages, 3969 KiB  
Review
C. elegans Germline as Three Distinct Tumor Models
by Mariah Jones, Mina Norman, Alex Minh Tiet, Jiwoo Lee and Myon Hee Lee
Biology 2024, 13(6), 425; https://doi.org/10.3390/biology13060425 - 8 Jun 2024
Viewed by 3172
Abstract
Tumor cells display abnormal growth and division, avoiding the natural process of cell death. These cells can be benign (non-cancerous growth) or malignant (cancerous growth). Over the past few decades, numerous in vitro or in vivo tumor models have been employed to understand [...] Read more.
Tumor cells display abnormal growth and division, avoiding the natural process of cell death. These cells can be benign (non-cancerous growth) or malignant (cancerous growth). Over the past few decades, numerous in vitro or in vivo tumor models have been employed to understand the molecular mechanisms associated with tumorigenesis in diverse regards. However, our comprehension of how non-tumor cells transform into tumor cells at molecular and cellular levels remains incomplete. The nematode C. elegans has emerged as an excellent model organism for exploring various phenomena, including tumorigenesis. Although C. elegans does not naturally develop cancer, it serves as a valuable platform for identifying oncogenes and the underlying mechanisms within a live organism. In this review, we describe three distinct germline tumor models in C. elegans, highlighting their associated mechanisms and related regulators: (1) ectopic proliferation due to aberrant activation of GLP-1/Notch signaling, (2) meiotic entry failure resulting from the loss of GLD-1/STAR RNA-binding protein, (3) spermatogenic dedifferentiation caused by the loss of PUF-8/PUF RNA-binding protein. Each model requires the mutations of specific genes (glp-1, gld-1, and puf-8) and operates through distinct molecular mechanisms. Despite these differences in the origins of tumorigenesis, the internal regulatory networks within each tumor model display shared features. Given the conservation of many of the regulators implicated in C. elegans tumorigenesis, it is proposed that these unique models hold significant potential for enhancing our comprehension of the broader control mechanisms governing tumorigenesis. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: The Dynamics of RNA–Protein Interactions)
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13 pages, 838 KiB  
Review
RNA Binding by the m6A Methyltransferases METTL16 and METTL3
by Kyle D. Mansfield
Biology 2024, 13(6), 391; https://doi.org/10.3390/biology13060391 - 29 May 2024
Cited by 6 | Viewed by 2451
Abstract
Methyltransferases are a wide-ranging, yet well-conserved, class of molecules that have been found to modify a wide variety of substrates. Interest in RNA methylation has surged in recent years with the identification of the major eukaryotic mRNA m6A methyltransferase METTL3. METTL16 has also [...] Read more.
Methyltransferases are a wide-ranging, yet well-conserved, class of molecules that have been found to modify a wide variety of substrates. Interest in RNA methylation has surged in recent years with the identification of the major eukaryotic mRNA m6A methyltransferase METTL3. METTL16 has also been identified as an RNA m6A methyltransferase; however, much less is known about its targets and actions. Interestingly, in addition to their catalytic activities, both METTL3 and METTL16 also have “methylation-independent” functions, including translational regulation, which have been discovered. However, evidence suggests that METTL16’s role as an RNA-binding protein may be more significant than is currently recognized. In this review, we will introduce RNA methylation, specifically m6A, and the enzymes responsible for its deposition. We will discuss the varying roles that these enzymes perform and delve deeper into their RNA targets and possible roles as methylation-independent RNA binding proteins. Finally, we will touch upon the many open questions still remaining. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: The Dynamics of RNA–Protein Interactions)
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