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Molecular Mechanisms on Transcription Regulation by RNA Polymerase II (Pol II)

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Macromolecules".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 7906

Special Issue Editor

Prof. Dr. Hidehisa Takahashi

E-Mail Website
Guest Editor
Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
Interests: RNA polymerase II; mediator; transcription elongation; transcription termination; phase separation

Special Issue Information

Dear Colleagues,

Recent studies highlight the involvement of non-membrane intracellular structures or liquid droplets, such as RNA granules, heterochromatin, and other nuclear speckles in various cellular functions. The formation of liquid droplets is driven by liquid–liquid phase separation (LLPS) through the aggregation of proteins that contain intrinsically disordered regions (IDRs). Increasing evidence has shown that LLPS plays a critical role in transcription regulation by RNA polymerase II, including the regulation of super-enhancer, transcription elongation, splicing, and other co-transcriptional processes; however, detailed mechanisms and the biological significance have not yet been elucidated. In this Special Issue, we focus on the findings of novel mechanisms of transcription regulation by RNA Polymerase II and provide an overview of the future of this field, which will add novel insights into many cellular functions. We also welcome molecular research on RNA Polymerase II (Pol II)-related fields.

Prof. Dr. Hidehisa Takahashi
Guest Editor

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Keywords

  • transcription regulation
  • phase separation
  • RNA polymerase II

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Published Papers (3 papers)

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Research

16 pages, 2357 KiB  
Article
The Catalytic Subunit of Schizosaccharomyces pombe CK2 (Cka1) Negatively Regulates RNA Polymerase II Transcription through Phosphorylation of Positive Cofactor 4 (PC4)
by Diego A. Rojas, Fabiola Urbina, Aldo Solari and Edio Maldonado
Int. J. Mol. Sci. 2022, 23(16), 9499; https://doi.org/10.3390/ijms23169499 - 22 Aug 2022
Cited by 2 | Viewed by 2164
Abstract
Positive cofactor 4 (PC4) is a transcriptional coactivator that plays important roles in transcription and DNA replication. In mammals, PC4 is phosphorylated by CK2, and this event downregulates its RNA polymerase II (RNAPII) coactivator function. This work describes the effect of fission yeast [...] Read more.
Positive cofactor 4 (PC4) is a transcriptional coactivator that plays important roles in transcription and DNA replication. In mammals, PC4 is phosphorylated by CK2, and this event downregulates its RNA polymerase II (RNAPII) coactivator function. This work describes the effect of fission yeast PC4 phosphorylation on RNAPII transcription in a cell extract, which closely resembles the cellular context. We found that fission yeast PC4 is strongly phosphorylated by the catalytic subunit of CK2 (Cka1), while the regulatory subunit (Ckb1) downregulates the PC4 phosphorylation. The addition of Cka1 to an in vitro transcription assay can diminish the basal transcription from the Ad-MLP promoter; however, the addition of recombinant fission yeast PC4 or Ckb1 can stimulate the basal transcription in a cell extract. Fission yeast PC4 is phosphorylated in a domain which has consensus phosphorylation sites for CK2, and two serine residues were identified as critical for CK2 phosphorylation. Mutation of one of the serine residues in PC4 does not completely abolish the phosphorylation; however, when the two serine residues are mutated, CK2 is no longer able to phosphorylate PC4. The mutant which is not phosphorylated is able to stimulate transcription even though it is previously phosphorylated by Cka1, while the wild type and the point mutant are inactivated by Cka1 phosphorylation, and they cannot stimulate transcription by RNAPII in cell extracts. Those results demonstrate that CK2 can regulate the coactivator function of fission yeast PC4 and suggests that this event could be important in vivo as well. Full article
(This article belongs to the Special Issue Molecular Mechanisms on Transcription Regulation by RNA Polymerase II (Pol II))
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15 pages, 3291 KiB  
Article
RNA Polymerase II Transcription in Pneumocystis: TFIIB from Pneumocystis carinii Can Replace the Transcriptional Functions of Fission Yeast Schizosaccharomyces pombe TFIIB In Vivo and In Vitro
by Diego A. Rojas, Fabiola Urbina, Aldo Solari and Edio Maldonado
Int. J. Mol. Sci. 2022, 23(12), 6865; https://doi.org/10.3390/ijms23126865 - 20 Jun 2022
Viewed by 1980
Abstract
The Pneumocystis genus is an opportunistic fungal pathogen that infects patients with AIDS and immunocompromised individuals. The study of this fungus has been hampered due to the inability to grow it in a (defined media/pure) culture. However, the use of modern molecular techniques [...] Read more.
The Pneumocystis genus is an opportunistic fungal pathogen that infects patients with AIDS and immunocompromised individuals. The study of this fungus has been hampered due to the inability to grow it in a (defined media/pure) culture. However, the use of modern molecular techniques and genomic analysis has helped researchers to understand its complex cell biology. The transcriptional process in the Pneumocystis genus has not been studied yet, although it is assumed that it has conventional transcriptional machinery. In this work, we have characterized the function of the RNA polymerase II (RNAPII) general transcription factor TFIIB from Pneumocystis carinii using the phylogenetically related biological model Schizosaccharomyces pombe. The results of this work show that Pneumocystis carinii TFIIB is able to replace the essential function of S. pombe TFIIB both in in vivo and in vitro assays. The S. pombe strain harboring the P carinii TFIIB grew slower than the parental wild-type S. pombe strain in complete media and in minimal media. The S. pombe cells carrying out the P. carinii TFIIB are larger than the wild-type cells, indicating that the TFIIB gene replacement confers a phenotype, most likely due to defects in transcription. P. carinii TFIIB forms very weak complexes with S. pombe TATA-binding protein on a TATA box promoter but it is able to form stable complexes in vitro when S. pombe TFIIF/RNAPII are added. P. carinii TFIIB can also replace the transcriptional function of S. pombe TFIIB in an in vitro assay. The transcription start sites (TSS) of the endogenous adh gene do not change when P. carinii TFIIB replaces S. pombe TFIIB, and neither does the TSS of the nmt1 gene, although this last gene is poorly transcribed in vivo in the presence of P. carinii TFIIB. Since transcription by RNA polymerase II in Pneumocystis is poorly understood, the results described in this study are promising and indicate that TFIIB from P. carinii can replace the transcriptional functions of S. pombe TFIIB, although the cells expressing the P. carini TFIIB show an altered phenotype. However, performing studies using a heterologous approach, like this one, could be relevant to understanding the basic molecular processes of Pneumocystis such as transcription and replication. Full article
(This article belongs to the Special Issue Molecular Mechanisms on Transcription Regulation by RNA Polymerase II (Pol II))
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24 pages, 3405 KiB  
Article
The Association of Rpb4 with RNA Polymerase II Depends on CTD Ser5P Phosphatase Rtr1 and Influences mRNA Decay in Saccharomyces cerevisiae
by Ana I. Garrido-Godino, Abel Cuevas-Bermúdez, Francisco Gutiérrez-Santiago, Maria del Carmen Mota-Trujillo and Francisco Navarro
Int. J. Mol. Sci. 2022, 23(4), 2002; https://doi.org/10.3390/ijms23042002 - 11 Feb 2022
Cited by 4 | Viewed by 2561
Abstract
Rtr1 is an RNA polymerase II (RNA pol II) CTD-phosphatase that influences gene expression during the transition from transcription initiation to elongation and during transcription termination. Rtr1 interacts with the RNA pol II and this interaction depends on the phosphorylation state of the [...] Read more.
Rtr1 is an RNA polymerase II (RNA pol II) CTD-phosphatase that influences gene expression during the transition from transcription initiation to elongation and during transcription termination. Rtr1 interacts with the RNA pol II and this interaction depends on the phosphorylation state of the CTD of Rpb1, which may influence dissociation of the heterodimer Rpb4/7 during transcription. In addition, Rtr1 was proposed as an RNA pol II import factor in RNA pol II biogenesis and participates in mRNA decay by autoregulating the turnover of its own mRNA. Our work shows that Rtr1 acts in RNA pol II assembly by mediating the Rpb4/7 association with the rest of the enzyme. RTR1 deletion alters RNA pol II assembly and increases the amount of RNA pol II associated with the chromatin that lacks Rpb4, decreasing Rpb4-mRNA imprinting and, consequently, increasing mRNA stability. Thus, Rtr1 interplays RNA pol II biogenesis and mRNA decay regulation. Our data also indicate that Rtr1 mediates mRNA decay regulation more broadly than previously proposed by cooperating with Rpb4. Interestingly, our data include new layers in the mechanisms of gene regulation and in the crosstalk between mRNA synthesis and decay by demonstrating how the association of Rpb4/7 to the RNA pol II influences mRNA decay. Full article
(This article belongs to the Special Issue Molecular Mechanisms on Transcription Regulation by RNA Polymerase II (Pol II))
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