Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.9
2.8
Journals
Genes
Special Issues
Insights into RNA Coding and Transcriptional Regulation
share announcement

Insights into RNA Coding and Transcriptional Regulation

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

Deadline for manuscript submissions: 10 July 2026 | Viewed by 902

Special Issue Editor

Dr. Zihua Hu

E-Mail Website
Guest Editor
Department of Biostatistics, Department of Medicine, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
Interests: miRNA; genomics; RNA coding; gene regulation; transcriptomics; genetic variation

Special Issue Information

Dear Colleagues,

We are pleased to announce a forthcoming Special Issue of our journal dedicated to an exciting and rapidly evolving field of RNA biology, titled "Insights into RNA Coding and Transcriptional Regulation".

RNA serves both as a messenger that carries genetic instructions from DNA to the ribosome and plays a variety of regulatory roles that fine-tune gene expression. Recent advances in genomic technologies have revealed that RNA-based gene regulation, through different classes of non-coding RNAs, is involved in almost every aspect of biology. Those include piwi-associated RNAs, endogenous short-interfering RNAs, microRNAs, and long non-coding RNAs. They act as key regulators of gene expression in many different cellular pathways and systems.

This Special Issue will focus on research and review articles that explore the multifaceted roles of RNA in gene expression and regulation. We will consider manuscripts on topics including, but not limited to, studies on coding and non-coding RNAs, RNA modifications, splicing mechanisms, RNA–protein interactions, and RNA-based regulation of gene expression. Special attention will also be given to RNA sequencing and single-cell transcriptomics. We look forward to your contributions.

Dr. Zihua Hu
Guest Editor

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 250 words) can be sent to the Editorial Office for assessment.

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

  • RNA coding
  • transcriptomics
  • non-coding RNAs (ncRNA)
  • long non-coding RNA (lncRNA)
  • microRNA (miRNA)
  • RNA modifications
  • RNA splicing
  • RNA editing
  • RNA in transcriptional and post-transcriptional regulation
  • gene expression regulation
  • scRNA

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

25 pages, 14166 KB  
Article
Environmental Pollutant PCB 153 Is Associated with Candidate Alternative Splicing Alterations in Intellectual Disability-Associated Genes: An Exploratory RNA-Seq Splicing Analysis in a Neuronal Model
by Maria Lui, Aurelio Minuti, Simone D’Angiolini, Michele Scuruchi, Serena Silvestro and Osvaldo Artimagnella
Genes 2026, 17(6), 692; https://doi.org/10.3390/genes17060692 (registering DOI) - 13 Jun 2026
Abstract
Background/Objectives: Polychlorinated biphenyls (PCBs) are persistent environmental contaminants associated with chronic toxicity and neurological dysfunction. PCB 153 is among the most prevalent congeners detected in environmental and dietary matrices. Although transcriptional responses to PCB 153 have been described, its potential association with post-transcriptional [...] Read more.
Background/Objectives: Polychlorinated biphenyls (PCBs) are persistent environmental contaminants associated with chronic toxicity and neurological dysfunction. PCB 153 is among the most prevalent congeners detected in environmental and dietary matrices. Although transcriptional responses to PCB 153 have been described, its potential association with post-transcriptional regulation remains poorly defined. Here, we performed an exploratory computational RNA-seq splicing analysis of previously generated transcriptomic data from retinoic acid-differentiated SH-SY5Y cells exposed to a sub-cytotoxic concentration of PCB 153. Methods: RNA-seq data were analyzed to identify candidate differentially alternative splicing events (DASEs). Candidate events were further examined for retained intron (RI)-related premature termination codons (PTCs), and potential regulatory interactions, including DASE-RNA-binding protein (RBP) motif enrichment. Results: PCB 153 exposure was associated with differential expression of 32 RNA-binding protein (RBP) encoding genes and with 90 candidate DASEs. Disease enrichment analysis indicates that genes affected by candidate splicing alterations overlapped with gene sets annotated to intellectual disability and related neurodevelopmental phenotypes. Among retained intron events, several were predicted to introduce PTCs, suggesting potential effects on transcript stability or coding potential. Motif enrichment analysis identified positional enrichment of motifs corresponding to CELF2, NUMA1, PRPF8, and RBM22 within DASE-associated regions, nominating these RBPs as putative regulators associated with the observed splicing alterations. Conclusions: This computational study identifies candidate PCB 153-associated splicing alterations and RBP-related regulatory hypotheses in a neuron-like in vitro model, suggesting a potential mechanistic link between PCB 153 and neurodevelopmental dysfunction. Full article
(This article belongs to the Special Issue Insights into RNA Coding and Transcriptional Regulation)
►▼ Show Figures

Figure 1

14 pages, 1120 KB  
Article
Acute and Chronic High-Intensity Exercise Differentially Regulate the miRNA Biogenesis Pathway in Human Skeletal Muscle
by Zeyu Wu, Eveline S. Menezes, Natalia de M. Lyra e Silva, Benjamin B. Arhen, Lucas P. R. Beaupre, Craig A. Simpson, Chris McGlory, Fernanda G. De Felice and Brendon J. Gurd
Genes 2026, 17(6), 626; https://doi.org/10.3390/genes17060626 - 29 May 2026
Viewed by 231
Abstract
Background/Objectives: MicroRNAs (miRNAs) are key regulators of skeletal muscle adaptation; however, the extent to which exercise modulates the miRNA biogenesis pathway remains poorly understood. To investigate the impact of acute and chronic high-intensity exercise on components of miRNA biogenesis, and whether such [...] Read more.
Background/Objectives: MicroRNAs (miRNAs) are key regulators of skeletal muscle adaptation; however, the extent to which exercise modulates the miRNA biogenesis pathway remains poorly understood. To investigate the impact of acute and chronic high-intensity exercise on components of miRNA biogenesis, and whether such changes are reflected in miRNA expression across stages of their biogenesis, we performed secondary analyses of muscle biopsy samples from two previously published studies. Methods: Muscle biopsies were analyzed from the following protocols: nine men and eight women pre- and 3 h post- a bout of high-intensity interval cycling exercise (HIIE), and eleven men and eight women pre- and post- a 6-week period of high-intensity interval training (HIIT) or non-exercise control. mRNA expression of components of miRNA biogenesis including Drosha, Exportin-5, Dicer, and Ago2 were assessed following HIIE using RT-qPCR and their protein abundance was measured following HIIT using Western blotting. Primary (pri-miR-133a1, -133a2, -133b) and mature (miR-133a-3p, -133a-5p, -133b) miRNA expression were quantified following HIIT. Results: An acute bout of HIIE significantly decreased Drosha mRNA (p < 0.05) and resulted in a reduction in Dicer mRNA that approached significance (p < 0.10). Following 6 weeks of HIIT, no significant changes were detected in the protein abundance of Drosha, Exportin-5, Dicer, or Ago2. HIIT did not alter miR-133 expression at either the primary or mature transcript level across all isoforms. Conclusions: This study highlights the complexity of miRNA regulation in skeletal muscle and underscores the need for further research examining the temporal and mechanistic control of miRNA biogenesis in response to exercise. Full article
(This article belongs to the Special Issue Insights into RNA Coding and Transcriptional Regulation)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-2
Back to TopTop