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The 15th Anniversary of Genes: Feature Papers in the...
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The 15th Anniversary of Genes: Feature Papers in the "RNA" Section

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

Deadline for manuscript submissions: closed (31 December 2025) | Viewed by 1369

Special Issue Editor

Dr. Christiane Branlant

E-Mail Website
Guest Editor
DRE CNRS, IMoPA CNRS-UL Laboratory UMR7365, Biopôle, Campus Brabois-Santé, Avenue de la Forêt de Haye, 54500 Vandoeuvre les Nancy, France
Interests: RNA structure and function; ribosome biogenesis; RNA splicing; RNA and diseases; non-coding RNAs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue will celebrate the 15th anniversary of Genes and the 10th anniversary of the journal receiving its first impact factor.

RNA is a scientific field that is constantly evolving, with new RNA molecules carrying new functions being discovered regularly. Indeed, a large proportion of non-coding DNA is converted into RNA molecules, which exert a huge variety of functions.

The identification of their nucleotide sequences is rapid, but the determination of their secondary and tertiary structures, the characterization of their post-transcriptional modifications, and the identification of their precise functions remain difficult. Therefore,  crucial research is currently being undertaken in this field, with important applications in human heath, agriculture, agronomy and ecology.

This Special Issue, entitled “The 15th Anniversary of Genes: Feature Papers in the RNA Section”, will gather high-quality reviews and cutting-edge research articles on various aspects of the RNA field. It will comprise a selection of exclusive papers from the Editorial Board Members (EBMs) of the RNA Section, as well as invited papers from relevant experts.

Dr. Christiane Branlant
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

  • tRNAs
  • rRNAs
  • mRNAs
  • miRNAs
  • lncRNAs
  • sRNAs
  • siRNAs
  • RNA epigenetics
  • RNA modifications
  • RNA secondary and tertiary structure
  • viral RNAs
  • RNA binding proteins
  • RNA transcription
  • RNA translation

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Published Papers (1 paper)

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Research

14 pages, 2159 KB  
Article
Interdependent Regulation of Alternative Splicing by Serine/Arginine-Rich and Heterogeneous Nuclear Ribonucleoprotein Splicing Factors
by Megan E. Holmes and Klemens J. Hertel
Genes 2026, 17(1), 78; https://doi.org/10.3390/genes17010078 - 9 Jan 2026
Cited by 1 | Viewed by 979
Abstract
Background: Alternative pre-mRNA splicing is a combinatorial process involving serine/arginine-rich (SR) and heterogeneous nuclear ribonucleoprotein (hnRNP) splicing factors. These proteins can silence or enhance splicing based on their expression levels and binding positions. Objectives: To better understand the combinatorial and interdependent regulation between [...] Read more.
Background: Alternative pre-mRNA splicing is a combinatorial process involving serine/arginine-rich (SR) and heterogeneous nuclear ribonucleoprotein (hnRNP) splicing factors. These proteins can silence or enhance splicing based on their expression levels and binding positions. Objectives: To better understand the combinatorial and interdependent regulation between SR and hnRNP splicing factors during alternative splicing. Methods: Computational analyses were performed using cell knockdown and binding datasets from available databases. Results: Analyses of differential splicing data for 9 SR proteins and 21 hnRNP knockdowns revealed statistically significant interdependent regulation among several RNA-binding protein (RBP) combinations, albeit at different levels. Neither SR proteins nor hnRNPs showed strong preferences for collaborating with specific RBP classes in mediating exon inclusion. While SRSF3, hnRNPK, hnRNPC, and hnRNPL stand out as major influencers of alternative splicing, they do so predominantly independent of other RBPs. Minor influencers of alternative splicing, such as hnRNPDL and hnRNPR, predominantly regulate exon inclusion in concert with other RBPs, indicating that exon inclusion can be mediated by both single and multiple RBPs. Interestingly, the higher the number of RBPs that regulate the inclusion of an exon, the more variable exon inclusion preferences become. Interdependently regulated exons are more modular and can be characterized by weaker splice sites compared to their independently regulated counterparts. A comparison of RBP interdependence between HeLa and other cell lines provides a framework that explains cell-type-specific alternative splicing. Conclusions: Our study highlights the importance of the interdependent regulation of alternative exons and identifies characteristics of interdependently regulated exons that differ from independently regulated exons. Full article
(This article belongs to the Special Issue The 15th Anniversary of Genes: Feature Papers in the "RNA" Section)
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