Special Issue "Control of Gene Expression by Transcription and Co-transcriptional Processes in Cell Homeostasis and Cell Fate Specification"

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: 31 December 2023 | Viewed by 1502

Special Issue 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

Special Issue Information

Dear Colleagues,

All cells properly change their transcriptome in response to various signals and to specify cell fate through the control of gene expression. The first and rate-limiting process in gene expression is transcription, in which RNA polymerase synthesizes RNA from a DNA template. In eukaryotes, RNA polymerase II (Pol II) transcribes all protein-coding and various non-coding RNA (ncRNA) genes. All Pol II-transcribed nascent RNAs need to be further processed and modified to become mature functional RNAs. Additionally, DNA is wrapped around the histone octamer to form nucleosomes, which is intrinsically an obstacle for transcription but is required for higher-order gene regulation.

In the past two decades, increasing evidence has revealed that transcription is intimately coupled with RNA processing and with nucleosomal histone modification 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 and cell-fate specification. This Special Issue focuses on gene expression control by transcription and co-transcriptional processes such as RNA processing (5’ capping, splicing, polyadenylation), RNA modification, RNA structural folding, R-loop formation, RNA degradation, RNP (ribonucleoprotein particle) formation, histone modification, chromatin remodeling, heterochromatin formation, and liquid–liquid phase separation (LLPS). We welcome submissions in the form of original research articles, brief reports, reviews, opinions, and methodology reports.

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

  • Transcriptional regulation in cell homeostasis;
  • Regulation of Pol II-CTD phosphorylation;
  • Transcription-coupled RNA processing (5’capping, splicing, polyadenylation, and transport);
  • Transcription-coupled RNA chemical modification;
  • Transcription-coupled histone modification;
  • Physical and functional crosstalk between transcription and RNA processing machineries;
  • Methods for detecting co-transcriptional processes;
  • Co-transcriptional nascent RNA targeting by ncRNAs (lncRNA, siRNA, miRNA, piRNA).

Dr. Yutaka Hirose
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 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. Cells is an international peer-reviewed open access semimonthly 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.


  • transcription regulation
  • RNA polymerase II
  • co-transcriptional RNA processing
  • chromatin regulation
  • epitranscriptome

Published Papers (1 paper)

Order results
Result details
Select all
Export citation of selected articles as:


20 pages, 2860 KiB  
The Role of S. cerevisiae Sub1/PC4 in Transcription Elongation Depends on the C-Terminal Region and Is Independent of the ssDNA Binding Domain
Cells 2022, 11(20), 3320; https://doi.org/10.3390/cells11203320 - 21 Oct 2022
Viewed by 1242
Saccharomyces cerevisiae Sub1 (ScSub1) has been defined as a transcriptional stimulatory protein due to its homology to the ssDNA binding domain (ssDBD) of human PC4 (hPC4). Recently, PC4/Sub1 orthologues have been elucidated in eukaryotes, prokaryotes, and bacteriophages with functions related to DNA metabolism. [...] Read more.
Saccharomyces cerevisiae Sub1 (ScSub1) has been defined as a transcriptional stimulatory protein due to its homology to the ssDNA binding domain (ssDBD) of human PC4 (hPC4). Recently, PC4/Sub1 orthologues have been elucidated in eukaryotes, prokaryotes, and bacteriophages with functions related to DNA metabolism. Additionally, ScSub1 contains a unique carboxyl–terminal region (CT) of unknown function up to date. Specifically, it has been shown that Sub1 is required for transcription activation, as well as other processes, throughout the transcription cycle. Despite the progress that has been made in understanding the mechanism underlying Sub1′s functions, some questions remain unanswered. As a case in point: whether Sub1’s roles in initiation and elongation are differentially predicated on distinct regions of the protein or how Sub1′s functions are regulated. Here, we uncover some residues that are key for DNA–ScSub1 interaction in vivo, localized in the ssDBD, and required for Sub1 recruitment to promoters. Furthermore, using an array of genetic and molecular techniques, we demonstrate that the CT region is required for transcription elongation by RNA polymerase II (RNAPII). Altogether, our data indicate that Sub1 plays a dual role during transcription—in initiation through the ssDBD and in elongation through the CT region. Full article
Show Figures

Figure 1

Back to TopTop