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Feature Papers: Molecular Genetics and Genomics 2024
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Feature Papers: Molecular Genetics and Genomics 2024

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

Deadline for manuscript submissions: 20 December 2024 | Viewed by 5012

Special Issue Editor

Dr. Paolo Cinelli

E-Mail Website
Guest Editor
Center for Clinical Research, Clinic for Trauma Surgery, University Hospital Zurich, Sternwartstrasse 14, CH-8091 Zurich, Switzerland
Interests: transcriptomics; microarrays; gene expression analysis; genotyping; molecular genetics; mouse genetics; transgenic technologies; embryonic stem cells; pluripotency
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue, “Feature Papers: Molecular Genetics and Genomics 2024”, aims to collect high-quality research articles, review articles, and communications on advances in the research area of molecular genetics and genomics. Since this topical collection aims to illustrate, through selected works, frontier research in the field of molecular genetics and genomics, we encourage Editorial Board Members of the “Molecular Genetics and Genomics” Section to contribute feature papers reflecting the latest progress in their research field or to invite relevant senior experts and colleagues to make contributions to this Special Issue. We aim to represent our Section as an attractive open access publishing platform for molecular genetics research.

Topics include, but are not limited to:

  • Chromatin remodeling and dynamics;
  • Epigenetics, DNA methylation, histone modification, histone code;
  • DNA replication, repair, recombination, mobile DNA, mitochondrial DNA;
  • RNA biology;
  • Cell signaling, signal transduction, cell cycle, cell death, stem cells;
  • Post-transcriptional regulation of gene expression;
  • Developmental genetics;
  • Molecular basis of diseases.

Dr. Paolo Cinelli
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. 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

  • chromatin remodeling and dynamics
  • epigenetics, DNA methylation, histone modification, histone code
  • DNA replication, repair, recombination, mobile DNA, mitochondrial DNA
  • RNA biology
  • cell signaling, signal transduction, cell cycle, cell death, stem cells
  • post-transcriptional regulation of gene expression
  • developmental genetics
  • molecular basis of diseases

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (4 papers)

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Research

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13 pages, 3329 KiB  
Article
HybridQC: A SNP-Based Quality Control Application for Rapid Hybridity Verification in Diploid Plants
by Patrick Obia Ongom, Yakub Adebare Ajibade, Saba Baba Mohammed, Ibnou Dieng, Christian Fatokun and Ousmane Boukar
Genes 2024, 15(10), 1252; https://doi.org/10.3390/genes15101252 - 26 Sep 2024
Viewed by 918
Abstract
Background/Objectives: Hybridity authentication is an important component of quality assurance and control (QA/QC) in breeding programs. Here, we introduce HybridQC v1.0, a QA/QC software program specially designed for parental purity and hybridity determination. HybridQC rapidly detects molecular marker polymorphism between parents of [...] Read more.
Background/Objectives: Hybridity authentication is an important component of quality assurance and control (QA/QC) in breeding programs. Here, we introduce HybridQC v1.0, a QA/QC software program specially designed for parental purity and hybridity determination. HybridQC rapidly detects molecular marker polymorphism between parents of a cross and utilizes only the informative markers for hybridity authentication. Methods: HybridQC is written in Python and designed with a graphical user interface (GUI) compatible with Windows operating systems. We demonstrated the QA/QC analysis workflow and functionality of HybridQC using Kompetitive allele-specific PCR (KASP) SNP genotype data for cowpea (Vigna unguiculata). Its performance was validated in other crop data, including sorghum (Sorghum bicolor) and maize (Zea mays). Results: The application efficiently analyzed low-density SNP data from multiple cowpea bi-parental crosses embedded in a single Microsoft Excel file. HybridQC is optimized for the auto-generation of key summary statistics and visualization patterns for marker polymorphism, parental heterozygosity, non-parental alleles, missing data, and F1 hybridity. An added graphical interface correctly depicted marker efficiency and the proportions of true F1 versus self-fertilized progenies in the data sets used. The output of HybridQC was consistent with the results of manual hybridity discernment in sorghum and maize data sets. Conclusions: This application uses QA/QC SNP markers to rapidly verify true F1 progeny. It eliminates the extensive time often required to manually curate and process QA/QC data. This tool will enhance the optimization efforts in breeding programs, contributing to increased genetic gain. Full article
(This article belongs to the Special Issue Feature Papers: Molecular Genetics and Genomics 2024)
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19 pages, 2318 KiB  
Article
Impacts of Nucleosome Positioning Elements and Pre-Assembled Chromatin States on Expression and Retention of Transgenes
by Ronard Kwizera, Junkai Xie, Nathan Nurse, Chongli Yuan and Ann L. Kirchmaier
Genes 2024, 15(9), 1232; https://doi.org/10.3390/genes15091232 - 21 Sep 2024
Viewed by 1100
Abstract
Background/Objectives: Transgene applications, ranging from gene therapy to the development of stable cell lines and organisms, rely on maintaining the expression of transgenes. To date, the use of plasmid-based transgenes has been limited by the loss of their expression shortly after their delivery [...] Read more.
Background/Objectives: Transgene applications, ranging from gene therapy to the development of stable cell lines and organisms, rely on maintaining the expression of transgenes. To date, the use of plasmid-based transgenes has been limited by the loss of their expression shortly after their delivery into the target cells. The short-lived expression of plasmid-based transgenes has been largely attributed to host-cell-mediated degradation and/or silencing of transgenes. The development of chromatin-based strategies for gene delivery has the potential to facilitate defining the requirements for establishing epigenetic states and to enhance transgene expression for numerous applications. Methods: To assess the impact of “priming” plasmid-based transgenes to adopt accessible chromatin states to promote gene expression, nucleosome positioning elements were introduced at promoters of transgenes, and vectors were pre-assembled into nucleosomes containing unmodified histones or mutants mimicking constitutively acetylated states at residues 9 and 14 of histone H3 or residue 16 of histone H4 prior to their introduction into cells, then the transgene expression was monitored over time. Results: DNA sequences capable of positioning nucleosomes could positively impact the expression of adjacent transgenes in a distance-dependent manner in the absence of their pre-assembly into chromatin. Intriguingly, the pre-assembly of plasmids into chromatin facilitated the prolonged expression of transgenes relative to plasmids that were not pre-packaged into chromatin. Interactions between pre-assembled chromatin states and nucleosome positioning-derived effects on expression were also assessed and, generally, nucleosome positioning played the predominant role in influencing gene expression relative to priming with hyperacetylated chromatin states. Conclusions: Strategies incorporating nucleosome positioning elements and the pre-assembly of plasmids into chromatin prior to nuclear delivery can modulate the expression of plasmid-based transgenes. Full article
(This article belongs to the Special Issue Feature Papers: Molecular Genetics and Genomics 2024)
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17 pages, 858 KiB  
Article
Cyto-Histological Profile of MicroRNAs as Diagnostic Biomarkers in Differentiated Thyroid Carcinomas
by Maria de Lurdes Matos, Mafalda Pinto, Marta Alves, Sule Canberk, Ana Gonçalves, Maria João Bugalho, Ana Luísa Papoila and Paula Soares
Genes 2024, 15(3), 389; https://doi.org/10.3390/genes15030389 - 21 Mar 2024
Viewed by 1556
Abstract
Introduction: The repertoire of microRNAs (miRNAs) in thyroid carcinomas starts to be elucidated. Among differentiated thyroid carcinomas (DTCs), papillary thyroid carcinoma (PTC) is the most frequent. The assessment of miRNAs expression may contribute to refine the pre-surgical diagnosis in order to obtain a [...] Read more.
Introduction: The repertoire of microRNAs (miRNAs) in thyroid carcinomas starts to be elucidated. Among differentiated thyroid carcinomas (DTCs), papillary thyroid carcinoma (PTC) is the most frequent. The assessment of miRNAs expression may contribute to refine the pre-surgical diagnosis in order to obtain a personalized and more effective treatment for patients. Aims: This study aims to evaluate (1) the miRNAs in a series of DTCs, and their association with the presence of selected genetic mutations in order to improve diagnosis and predict the biologic behavior of DTC/PTC. (2) The reliability of molecular tests in Ultrasound-guided Fine Needle Aspiration Cytology (US-FNAC) for a more precise preoperative diagnosis. Material and Methods: This series includes 176 samples (98 cytology and 78 histology samples) obtained from 106 patients submitted to surgery, including 13 benign lesions (controls) and 93 DTCs (cases). The microRNA expression was assessed for miR-146b, miR-221, miR-222, and miR-15a through quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). The results were analyzed by the 2−ΔΔCT method, using miR16 as an endogenous control. Regarding PTC diagnosis, the discriminative ability of miRNAs expression was assessed by the area under the Receiver Operating Characteristic Curve (AUC). In PTCs, the association of miRNAs expression, clinicopathological features, and genetic mutations (BRAF, RAS, and TERTp) was evaluated. Results/Discussion: All the analyzed miRNAs presented a tendency to be overexpressed in DTCs/PTCs when compared with benign lesions, both in cytology and histology samples. In cytology, miRNAs expression levels were higher in malignant tumors than in benign tumors. In histology, the discriminative abilities regarding PTC diagnosis were as follows: miR-146b (AUC 0.94, 95% CI 0.87–1), miR-221 (AUC 0.79, 95% CI 0.68–0.9), miR-222 (AUC 0.76, 95% CI 0.63–0.89), and miR-15a (AUC 0.85, 95% CI 0.74–0.97). miR-146b showed 89% sensitivity (se) and 87% specificity (sp); miR-221 se = 68.4, sp = 90; miR-222 se = 73, sp = 70; and mi-R15a se = 72, sp = 80. MicroRNAs were associated with worst-prognosis clinicopathological characteristics in PTCs (p < 0.05), particularly for miR-222. Our data reveal a significant association between higher expression levels of miR-146b, miR-221, and miR-222 in the presence of the BRAF mutation (p < 0.001) and miR-146b (p = 0.016) and miR-221 (p = 0.010) with the RAS mutation, suggesting an interplay of these mutations with miRNAs expression. Despite this study having a relatively small sample size, overexpression of miRNAs in cytology may contribute to a more precise preoperative diagnosis. The miRNAs presented a good discriminative ability in PTC diagnosis. The association between the miRNAs expression profile and genetic alterations can be advantageous for an accurate diagnosis of DTCs/PTCs in FNAC. Full article
(This article belongs to the Special Issue Feature Papers: Molecular Genetics and Genomics 2024)
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Review

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18 pages, 917 KiB  
Review
Comprehensive Genetic Analysis of Associations between Obesity-Related Parameters and Physical Activity: A Scoping Review
by Agata Leońska-Duniec
Genes 2024, 15(9), 1137; https://doi.org/10.3390/genes15091137 - 28 Aug 2024
Viewed by 792
Abstract
Genetic epidemiological studies have shown that numerous genetic variants cumulatively increase obesity risk. Although genetically predisposed individuals are more prone to developing obesity, it has been shown that physical activity can modify the genetic predisposition to obesity. Therefore, genetic data obtained from earlier [...] Read more.
Genetic epidemiological studies have shown that numerous genetic variants cumulatively increase obesity risk. Although genetically predisposed individuals are more prone to developing obesity, it has been shown that physical activity can modify the genetic predisposition to obesity. Therefore, genetic data obtained from earlier studies, including 30 polymorphisms located in 18 genes, were analyzed using novel methods such as the total genetic score and Biofilter 2.4 software to combine genotypic and phenotypic information for nine obesity-related traits measured before and after the realization of the 12-week training program. The results revealed six genes whose genotypes were most important for post-training changes—LEP, LEPR, ADIPOQ, ADRA2A, ADRB3, and DRD2. Five noteworthy pairwise interactions, LEP × LEPR, ADRB2 × ADRB3, ADRA2A × ADRB3, ADRA2A × ADRB2, ADRA2A × DRD2, and three specific interactions demonstrating significant associations with key parameters crucial for health, total cholesterol (TC), high-density lipoprotein (HDL), and fat-free mass (FFM), were also identified. The molecular basis of training adaptation described in this study would have an enormous impact on the individualization of training programs, which, designed according to a given person’s genetic profile, will be effective and safe intervention strategies for preventing obesity and improving health. Full article
(This article belongs to the Special Issue Feature Papers: Molecular Genetics and Genomics 2024)
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