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Post-transcriptional Regulation in Mammals
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Post-transcriptional Regulation in Mammals

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 6876

Special Issue Editors

Dr. Carlo Maria Di Liegro

E-Mail Website
Guest Editor
Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90100 Palermo, Italy
Interests: mammalian nervous system development and function; post-transcriptional regulation of gene expression; RNA-binding proteins (RBPs) interacting with mRNAs encoding H1.0 and H3.3 histone variants in developing rat brain; extracellular vesicles (EVs) released by normal and tumor brain cells
Dr. Gabriella Schiera

E-Mail Website
Guest Editor
Department of Biomedicine, Neurosciences and Advanced Diagnostics (Bi.N.D.), University of Palermo, 90100 Palermo, Italy
Interests: differentiation of neural cells; extracellular vesicles (EVs) released by normal and tumor brain cells; formation and maintenance of the blood–brain barrier (BBB); in vitro model of BBB, co-culturing astrocytes, neurons and endothelial cells; preparation of three-dimensional cultures of brain cells on poly-lactate scaffolds; study of RBPs interacting with mRNAs encoding H1.0 and H3.3 histone variants in developing rat brain

Special Issue Information

Dear Colleagues,

The realization that transcriptional regulation of gene expression cannot explain most of the phenomena faced when studying both embryonal and adult cells has revealed the existence of a cohort of RNA-binding proteins (RBPS), miRNAs, long non-coding RNAs, and circular RNAs, now giving us an understanding of how finely tuned cell activity really is.

Spaces filled by messengers anchored and transported by unknown cytoskeleton elements, once apparently confused, now offer a more ordered organization in which discrete structures, collectively called granules, are systematically reshaped to adapt to the ever-changing conditions of cells and tissues, and could represent specific regions of regulation in which selected proteins and mRNAs can interact in a protected environment.

Moreover, the discovery that certain regions of the involved RBPs have intrinsically disordered regions (IDRs), and that these amino acid sequences could be responsible for the creation of membrane-less cell structures via the mechanism of a liquid–liquid phase separation, has led to envisioning alternative ways in which cells may regulate gene expression based on localization of the translation of the messenger RNAs. On the other hand, many observations have confirmed that these peculiar structures, under altered conditions, can also form disordered aggregates, contributing, for example, to neurodegeneration.

It is quite clear, in summary, that great progress has been made in the observation and comprehension of the mechanisms regulating cell activity and cross-talk between cells, and specifically in the post-transcriptional phase of the regulation; however, many questions still remain in the understanding of cell organization.

This Special Issue is intended as a chance for scientists to publish original research on post-transcriptional mechanisms regulating cell metabolism or to organize a review on specific aspects of this topic; welcome are investigations that attempt to comprehend the pathologic aspects of the regulation in question.

Dr. Carlo Maria Di Liegro
Dr. Gabriella Schiera
Guest Editors

Manuscript Submission Information

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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. Genes is an international peer-reviewed open access monthly 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 2600 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.

Keywords

  • post-transcriptional regulation
  • mRNA localization
  • mRNA granules
  • RNA-binding proteins (RBPs)
  • miRNAs
  • ncRNA
  • intrinsically disordered regions (IDRs)

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Published Papers (3 papers)

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Research

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16 pages, 1517 KiB  
Article
A Comparative Overview of the Role of Human Ribonucleases in Nonsense-Mediated mRNA Decay
by Paulo J. da Costa, Juliane Menezes, Raquel Guedes, Filipa P. Reis, Alexandre Teixeira, Margarida Saramago, Sandra C. Viegas, Cecília M. Arraiano and Luísa Romão
Genes 2024, 15(10), 1308; https://doi.org/10.3390/genes15101308 - 10 Oct 2024
Cited by 1 | Viewed by 1439
Abstract
Eukaryotic cells possess surveillance mechanisms that detect and degrade defective transcripts. Aberrant transcripts include mRNAs with a premature termination codon (PTC), targeted by the nonsense-mediated decay (NMD) pathway, and mRNAs lacking a termination codon, targeted by the nonstop decay (NSD) pathway. The eukaryotic [...] Read more.
Eukaryotic cells possess surveillance mechanisms that detect and degrade defective transcripts. Aberrant transcripts include mRNAs with a premature termination codon (PTC), targeted by the nonsense-mediated decay (NMD) pathway, and mRNAs lacking a termination codon, targeted by the nonstop decay (NSD) pathway. The eukaryotic exosome, a ribonucleolytic complex, plays a crucial role in mRNA processing and turnover through its catalytic subunits PM/Scl100 (Rrp6 in yeast), DIS3 (Rrp44 in yeast), and DIS3L1. Additionally, eukaryotic cells have other ribonucleases, such as SMG6 and XRN1, that participate in RNA surveillance. However, the specific pathways through which ribonucleases recognize and degrade mRNAs remain elusive. In this study, we characterized the involvement of human ribonucleases, both nuclear and cytoplasmic, in the mRNA surveillance mechanisms of NMD and NSD. We performed knockdowns of SMG6, PM/Scl100, XRN1, DIS3, and DIS3L1, analyzing the resulting changes in mRNA levels of selected natural NMD targets by RT-qPCR. Additionally, we examined the levels of different human β-globin variants under the same conditions: wild-type, NMD-resistant, NMD-sensitive, and NSD-sensitive. Our results demonstrate that all the studied ribonucleases are involved in the decay of certain endogenous NMD targets. Furthermore, we observed that the ribonucleases SMG6 and DIS3 contribute to the degradation of all β-globin variants, with an exception for βNS in the former case. This is also the case for PM/Scl100, which affects all β-globin variants except the NMD-sensitive variants. In contrast, DIS3L1 and XRN1 show specificity for β-globin WT and NMD-resistant variants. These findings suggest that eukaryotic ribonucleases are target-specific rather than pathway-specific. In addition, our data suggest that ribonucleases play broader roles in mRNA surveillance and degradation mechanisms beyond just NMD and NSD. Full article
(This article belongs to the Special Issue Post-transcriptional Regulation in Mammals)
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10 pages, 2185 KiB  
Article
FexSplice: A LightGBM-Based Model for Predicting the Splicing Effect of a Single Nucleotide Variant Affecting the First Nucleotide G of an Exon
by Atefeh Joudaki, Jun-ichi Takeda, Akio Masuda, Rikumo Ode, Koichi Fujiwara and Kinji Ohno
Genes 2023, 14(9), 1765; https://doi.org/10.3390/genes14091765 - 6 Sep 2023
Cited by 3 | Viewed by 1890
Abstract
Single nucleotide variants (SNVs) affecting the first nucleotide G of an exon (Fex-SNVs) identified in various diseases are mostly recognized as missense or nonsense variants. Their effect on pre-mRNA splicing has been seldom analyzed, and no curated database is available. We previously reported [...] Read more.
Single nucleotide variants (SNVs) affecting the first nucleotide G of an exon (Fex-SNVs) identified in various diseases are mostly recognized as missense or nonsense variants. Their effect on pre-mRNA splicing has been seldom analyzed, and no curated database is available. We previously reported that Fex-SNVs affect splicing when the length of the polypyrimidine tract is short or degenerate. However, we cannot readily predict the splicing effects of Fex-SNVs. We here scrutinized the available literature and identified 106 splicing-affecting Fex-SNVs based on experimental evidence. We similarly identified 106 neutral Fex-SNVs in the dbSNP database with a global minor allele frequency (MAF) of more than 0.01 and less than 0.50. We extracted 115 features representing the strength of splicing cis-elements and developed machine-learning models with support vector machine, random forest, and gradient boosting to discriminate splicing-affecting and neutral Fex-SNVs. Gradient boosting-based LightGBM outperformed the other two models, and the length and nucleotide compositions of the polypyrimidine tract played critical roles in the discrimination. Recursive feature elimination showed that the LightGBM model using 15 features achieved the best performance with an accuracy of 0.80 ± 0.12 (mean and SD), a Matthews Correlation Coefficient (MCC) of 0.57 ± 0.15, an area under the curve of the receiver operating characteristics curve (AUROC) of 0.86 ± 0.08, and an area under the curve of the precision–recall curve (AUPRC) of 0.87 ± 0.09 using a 10-fold cross-validation. We developed a web service program, named FexSplice that accepts a genomic coordinate either on GRCh37/hg19 or GRCh38/hg38 and returns a predicted probability of aberrant splicing of A, C, and T variants. Full article
(This article belongs to the Special Issue Post-transcriptional Regulation in Mammals)
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Review

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25 pages, 1834 KiB  
Review
Role of Post-Transcriptional Regulation in Learning and Memory in Mammals
by Carlo Maria Di Liegro, Gabriella Schiera, Giuseppe Schirò and Italia Di Liegro
Genes 2024, 15(3), 337; https://doi.org/10.3390/genes15030337 - 5 Mar 2024
Cited by 2 | Viewed by 2736
Abstract
After many decades, during which most molecular studies on the regulation of gene expression focused on transcriptional events, it was realized that post-transcriptional control was equally important in order to determine where and when specific proteins were to be synthesized. Translational regulation is [...] Read more.
After many decades, during which most molecular studies on the regulation of gene expression focused on transcriptional events, it was realized that post-transcriptional control was equally important in order to determine where and when specific proteins were to be synthesized. Translational regulation is of the most importance in the brain, where all the steps of mRNA maturation, transport to different regions of the cells and actual expression, in response to specific signals, constitute the molecular basis for neuronal plasticity and, as a consequence, for structural stabilization/modification of synapses; notably, these latter events are fundamental for the highest brain functions, such as learning and memory, and are characterized by long-term potentiation (LTP) of specific synapses. Here, we will discuss the molecular bases of these fundamental events by considering both the role of RNA-binding proteins (RBPs) and the effects of non-coding RNAs involved in controlling splicing, editing, stability and translation of mRNAs. Importantly, it has also been found that dysregulation of mRNA metabolism/localization is involved in many pathological conditions, arising either during brain development or in the adult nervous system. Full article
(This article belongs to the Special Issue Post-transcriptional Regulation in Mammals)
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