Control of Gene Expression by Co-Transcriptional Processes in Cell Homeostasis and Cell Fate Specification: Second Edition

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Nuclei: Function, Transport and Receptors".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 1934

Special Issue Editor


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Guest Editor
Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
Interests: molecular biology; transcription; cell biology; gene expression; gene regulation
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Special Issue Information

Dear Colleagues,

Cells properly change the transcriptome through the regulation of gene expression in response to cell proliferation, differentiation, and various extracellular signals. In eukaryotes, the expression of all protein-coding genes and many non-coding RNA (ncRNA) genes is transcribed by RNA polymerase II (Pol II). The Pol II-transcribed nascent RNAs undergo various processing and modifications to become mature and functional RNAs.

In the past two decades, increasing evidence has revealed that transcription is intimately coupled with RNA processing and chromatin regulation through extensive interaction networks. Therefore, understanding the molecular detail and the biological significance of these co-transcriptional processes is essential for deciphering gene control mechanisms in cell homeostasis, cell fate specification, and associated diseases. This Special Issue focuses on the regulation of gene expression by co-transcriptional processes such as transcription, RNA processing (5’capping, splicing, polyadenylation), RNA modification, RNA transport, RNA degradation, histone modification, and biomolecular condensates formation.

 The formats for submissions include original research articles, brief reports, reviews, opinions, and methodology reports.

Topics of this Special Issue include, but are not limited to:

  • Coupling between transcription and RNA processing
  • Transcription elongation
  • RNA processing (5’capping, splicing, polyadenylation)
  • RNA modification
  • RNA transport
  • Histone modification
  • Diseases associated with dysregulation of co-transcriptional processes
  • ncRNAs (lncRNA, siRNA, piRNA) interacting with nascent RNAs
  • methods for detecting co-transcriptional processes

Dr. Yutaka Hirose
Guest Editor

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Keywords

  • gene transcription
  • transcription elongation
  • RNA processing
  • RNA modification
  • RNA transport
  • lncRNA
  • histone modification
  • biomolecular condensates
  • diseases associated with dysregulation of gene regulation

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Published Papers (1 paper)

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Research

17 pages, 2735 KiB  
Article
Cap-Specific m6Am Methyltransferase PCIF1/CAPAM Regulates mRNA Stability of RAB23 and CNOT6 through the m6A Methyltransferase Activity
by Ai Sugita, Ryoya Kano, Hiroyasu Ishiguro, Natsuki Yanagisawa, Soichiro Kuruma, Shotaro Wani, Aki Tanaka, Yoshiaki Tabuchi, Yoshiaki Ohkuma and Yutaka Hirose
Cells 2024, 13(20), 1689; https://doi.org/10.3390/cells13201689 - 12 Oct 2024
Viewed by 1556
Abstract
Chemical modifications of cellular RNAs play key roles in gene expression and host defense. The cap-adjacent N6,2′-O-dimethyladenosine (m6Am) is a prevalent modification of vertebrate and viral mRNAs and is catalyzed by the newly discovered N6 methyltransferase [...] Read more.
Chemical modifications of cellular RNAs play key roles in gene expression and host defense. The cap-adjacent N6,2′-O-dimethyladenosine (m6Am) is a prevalent modification of vertebrate and viral mRNAs and is catalyzed by the newly discovered N6 methyltransferase PCIF1. However, its role in gene expression remains unclear due to conflicting reports on its effects on mRNA stability and translation. In this study, we investigated the impact of siRNA-mediated transient suppression of PCIF1 on global mRNA expression in HeLa cells. We identified a subset of differentially expressed genes (DEGs) that exhibited minimal overlap with previously reported DEGs. Subsequent validation revealed that PCIF1 positively and negatively regulates RAB23 and CNOT6 expression, respectively, at both the mRNA and protein levels. Mechanistic analyses demonstrated that PCIF1 regulates the stability of these target mRNAs rather than their transcription, and rescue experiments confirmed the requirement of PCIF1’s methyltransferase activity for these regulations. Furthermore, MeRIP-qPCR analysis showed that PCIF1 suppression significantly reduced the m6A levels of RAB23 and CNOT6 mRNAs. These findings suggest that PCIF1 regulates the stability of specific mRNAs in opposite ways through m6A modification, providing new insights into the role of m6Am in the regulation of gene expression. Full article
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