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Modulation of Transcription: Imag(in)ing a Fundamental Mechanism
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Modulation of Transcription: Imag(in)ing a Fundamental Mechanism

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

Deadline for manuscript submissions: 20 May 2025 | Viewed by 3725

Special Issue Editor

Dr. Marco Biggiogera

E-Mail Website
Guest Editor
Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
Interests: cell nucleus; chromatin and transcription; transmission electron microscopy; cytochemistry; super resolution microscopy

Special Issue Information

Dear Colleagues,

Transcription of DNA into RNA is a key step in the complex process of gene expression, and it is crucial to all living organisms. Conversion of the nucleotide information into a final functional product is therefore strictly regulated through a variety of sophisticated mechanisms that underlie such phenomena as cell differentiation, development, response to external conditions and much more. Any step in the gene expression pathway may be controlled, from its initiation to protein stability. Transcription factors, gene regulatory elements and epigenetic mechanisms constitute only the tip of the iceberg of the molecular mediators involved in this network.

Enormous progress has been achieved in understanding the fundamentals of transcription modulation. However, the majority of the current information is mainly derived from biochemical and biomolecular approaches. In recent years, the potential of imaging techniques has expanded to include high-resolution technologies and the possibility to localize and follow various processes in real time, among which include numerous steps of gene expression regulation.

Hence, the aim of this Special Issue is to improve our current understanding in the field of transcription modulation, with particular attention to imaging approaches. Original articles, up-to-date reviews and perspectives addressing this topic are welcomed.

Also, we would like to acknowledge Dr. Claudio Casali (https://orcid.org/0000-0001-8002-8262)'s input on the development of this Special Issue.

Dr. Marco Biggiogera
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Published Papers (2 papers)

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15 pages, 7762 KiB  
Article
Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Dorsi Muscle of Gannan Yak and Jeryak
by Zhidong Zhao, Dashan Guo, Yali Wei, Jingsheng Li, Xue Jia, Yanmei Niu, Zhanxin Liu, Yanbin Bai, Zongchang Chen, Bingang Shi, Xiaolan Zhang, Jiang Hu, Jiqing Wang, Xiu Liu and Shaobin Li
Int. J. Mol. Sci. 2024, 25(11), 6029; https://doi.org/10.3390/ijms25116029 - 30 May 2024
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Abstract
Jeryak is the F1 generation of the cross between Gannan yak and Jersey cattle, which has the advantages of fast growth and high adaptability. The growth and development of skeletal muscle is closely linked to meat production and the quality of meat. However, [...] Read more.
Jeryak is the F1 generation of the cross between Gannan yak and Jersey cattle, which has the advantages of fast growth and high adaptability. The growth and development of skeletal muscle is closely linked to meat production and the quality of meat. However, the molecular regulatory mechanisms of muscle growth differences between Gannan yak and Jeryak analyzed from the perspective of chromatin opening have not been reported. In this study, ATAC-seq was used to analyze the difference of chromatin openness in longissimus muscle of Gannan yak and Jeryak. It was found that chromatin accessibility was more enriched in Jeryak compared to Gannan yak, especially in the range of the transcription start site (TSS) ± 2 kb. GO and KEGG enrichment analysis indicate that differential peak-associated genes are involved in the negative regulation of muscle adaptation and the Hippo signaling pathway. Integration analysis of ATAC-seq and RNA-seq revealed overlapping genes were significantly enriched during skeletal muscle cell differentiation and muscle organ morphogenesis. At the same time, we screened FOXO1, ZBED6, CRY2 and CFL2 for possible involvement in skeletal muscle development, constructed a genes and transcription factors network map, and found that some transcription factors (TFs), including YY1, KLF4, KLF5 and Bach1, were involved in skeletal muscle development. Overall, we have gained a comprehensive understanding of the key factors that impact skeletal muscle development in various breeds of cattle, providing new insights for future analysis of the molecular regulatory mechanisms involved in muscle growth and development. Full article
(This article belongs to the Special Issue Modulation of Transcription: Imag(in)ing a Fundamental Mechanism)
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Review

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26 pages, 5320 KiB  
Review
Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals
by Daria M. Motorina, Yuliya A. Galimova, Nadezhda V. Battulina and Evgeniya S. Omelina
Int. J. Mol. Sci. 2024, 25(10), 5231; https://doi.org/10.3390/ijms25105231 - 11 May 2024
Viewed by 1861
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe [...] Read more.
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes—plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object. Full article
(This article belongs to the Special Issue Modulation of Transcription: Imag(in)ing a Fundamental Mechanism)
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