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Interplay between Pre-mRNA Splicing and Other Gene Expression Steps in Eukaryotes 3.0

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: closed (31 December 2022) | Viewed by 6673

Special Issue Editor

Dr. Naoyuki Kataoka

E-Mail Website
Guest Editor
Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, Tokyo, Japan
Interests: RNA processing; RNA transport; RNA diseases; hypoxia; epigenetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In eukaryotes, RNAs transcribed from genomic DNA are subjected to many regulatory processes, indicating their pivotal role in gene expression. Pre-mRNA splicing is a process to remove introns and ligate exons so that mRNA can be produced. This step is critical for higher eukaryotes and is vigorously regulated. After finding the Exon Junction Complex, several lines of evidence have noted that pre-mRNA splicing and other gene expression steps have influence over each other and there is an interplay between pre-mRNA splicing and other gene expression in higher eukaryotes.

As the Guest Editor of this Special Issue, “Interplay between Pre-mRNA Splicing and Other Gene Expression Steps in Eukaryotes 3.0”, in IJMS, I expect submissions from many researchers working on the wide spectrum of physiological processes in which RNAs are involved. The focus of this topic is the molecular link between pre-mRNA splicing and other steps in eukaryotes. Examples for this Special Issue include transcription-coupled splicing, coupling of splicing and mRNA export/localization, nonsense-mediated mRNA decay, enhancement of translation, and signal transduction pathway modulation by alternative splicing. Manuscripts regarding splicing changes during the development of organisms and aberrant splicing in human diseases are also very welcome. The formats for submissions include original research reports, reviews, perspectives/opinions and methodology articles.

Dr. Naoyuki Kataoka
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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Keywords

  • pre-mRNA splicing
  • Exon Junction Complex
  • alternative splicing
  • transcription
  • translation
  • RNA export
  • RNA localization
  • RNA decay

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Published Papers (3 papers)

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Research

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38 pages, 10478 KiB  
Article
Adaptation of the Porcine Pituitary Transcriptome, Spliceosome and Editome during Early Pregnancy
by Karol G. Makowczenko, Jan P. Jastrzebski, Marta Kiezun, Lukasz Paukszto, Kamil Dobrzyn, Nina Smolinska and Tadeusz Kaminski
Int. J. Mol. Sci. 2023, 24(6), 5946; https://doi.org/10.3390/ijms24065946 - 21 Mar 2023
Cited by 4 | Viewed by 2726
Abstract
The physiological mechanisms of the porcine reproduction are relatively well-known. However, transcriptomic changes and the mechanisms accompanying transcription and translation processes in various reproductive organs, as well as their dependence on hormonal status, are still poorly understood. The aim of this study was [...] Read more.
The physiological mechanisms of the porcine reproduction are relatively well-known. However, transcriptomic changes and the mechanisms accompanying transcription and translation processes in various reproductive organs, as well as their dependence on hormonal status, are still poorly understood. The aim of this study was to gain a principal understanding of alterations within the transcriptome, spliceosome and editome occurring in the pituitary of the domestic pig (Sus scrofa domestica L.), which controls basic physiological processes in the reproductive system. In this investigation, we performed extensive analyses of data obtained by high-throughput sequencing of RNA from the gilts’ pituitary anterior lobes during embryo implantation and the mid-luteal phase of the estrous cycle. During analyses, we obtained detailed information on expression changes of 147 genes and 43 long noncoding RNAs, observed 784 alternative splicing events and also found the occurrence of 8729 allele-specific expression sites and 122 RNA editing events. The expression profiles of the selected 16 phenomena were confirmed by PCR or qPCR techniques. As a final result of functional meta-analysis, we acquired knowledge regarding intracellular pathways that induce changes in the processes accompanying transcription and translation regulation, which may induce modifications in the secretory activity of the porcine adenohypophyseal cells. Full article
(This article belongs to the Special Issue Interplay between Pre-mRNA Splicing and Other Gene Expression Steps in Eukaryotes 3.0)
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Review

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18 pages, 2669 KiB  
Review
Defenders of the Transcriptome: Guard Protein-Mediated mRNA Quality Control in Saccharomyces cerevisiae
by Luisa Querl and Heike Krebber
Int. J. Mol. Sci. 2024, 25(19), 10241; https://doi.org/10.3390/ijms251910241 - 24 Sep 2024
Viewed by 369
Abstract
Cell survival depends on precise gene expression, which is controlled sequentially. The guard proteins surveil mRNAs from their synthesis in the nucleus to their translation in the cytoplasm. Although the proteins within this group share many similarities, they play distinct roles in controlling [...] Read more.
Cell survival depends on precise gene expression, which is controlled sequentially. The guard proteins surveil mRNAs from their synthesis in the nucleus to their translation in the cytoplasm. Although the proteins within this group share many similarities, they play distinct roles in controlling nuclear mRNA maturation and cytoplasmic translation by supporting the degradation of faulty transcripts. Notably, this group is continuously expanding, currently including the RNA-binding proteins Npl3, Gbp2, Hrb1, Hrp1, and Nab2 in Saccharomyces cerevisiae. Some of the human serine–arginine (SR) splicing factors (SRSFs) show remarkable similarities to the yeast guard proteins and may be considered as functional homologues. Here, we provide a comprehensive summary of their crucial mRNA surveillance functions and their implications for cellular health. Full article
(This article belongs to the Special Issue Interplay between Pre-mRNA Splicing and Other Gene Expression Steps in Eukaryotes 3.0)
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13 pages, 1262 KiB  
Review
Contribution of Retrotransposons to the Pathogenesis of Type 1 Diabetes and Challenges in Analysis Methods
by Anja Štangar, Jernej Kovač, Robert Šket, Tine Tesovnik, Ana Zajec, Barbara Čugalj Kern, Barbara Jenko Bizjan, Tadej Battelino and Klemen Dovč
Int. J. Mol. Sci. 2023, 24(4), 3104; https://doi.org/10.3390/ijms24043104 - 4 Feb 2023
Cited by 3 | Viewed by 2900
Abstract
Type 1 diabetes (T1D) is one of the most common chronic diseases of the endocrine system, associated with several life-threatening comorbidities. While the etiopathogenesis of T1D remains elusive, a combination of genetic susceptibility and environmental factors, such as microbial infections, are thought to [...] Read more.
Type 1 diabetes (T1D) is one of the most common chronic diseases of the endocrine system, associated with several life-threatening comorbidities. While the etiopathogenesis of T1D remains elusive, a combination of genetic susceptibility and environmental factors, such as microbial infections, are thought to be involved in the development of the disease. The prime model for studying the genetic component of T1D predisposition encompasses polymorphisms within the HLA (human leukocyte antigen) region responsible for the specificity of antigen presentation to lymphocytes. Apart from polymorphisms, genomic reorganization caused by repeat elements and endogenous viral elements (EVEs) might be involved in T1D predisposition. Such elements are human endogenous retroviruses (HERVs) and non-long terminal repeat (non-LTR) retrotransposons, including long and short interspersed nuclear elements (LINEs and SINEs). In line with their parasitic origin and selfish behaviour, retrotransposon-imposed gene regulation is a major source of genetic variation and instability in the human genome, and may represent the missing link between genetic susceptibility and environmental factors long thought to contribute to T1D onset. Autoreactive immune cell subtypes with differentially expressed retrotransposons can be identified with single-cell transcriptomics, and personalized assembled genomes can be constructed, which can then serve as a reference for predicting retrotransposon integration/restriction sites. Here we review what is known to date about retrotransposons, we discuss the involvement of viruses and retrotransposons in T1D predisposition, and finally we consider challenges in retrotransposons analysis methods. Full article
(This article belongs to the Special Issue Interplay between Pre-mRNA Splicing and Other Gene Expression Steps in Eukaryotes 3.0)
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