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Genes, Volume 10, Issue 3 (March 2019) – 73 articles

Cover Story (view full-size image): The unexpected lysis of a 1 m3 culture of Halobacterium salinarum strain S9 was found to be caused by a novel caudovirus, pictured in the right panel of the diagram. We named it ChaoS9, partly because of the damage it had caused, and sequenced its 55,145 bp dsDNA genome. The closest relatives were found to be the myohaloviruses phiH1 and phiCh1, both of which infect extremely halophilic archaea (Class Halobacteria). Strong conservation of the tail genes contrasts with major differences of the head genes. Even more surprising is the similarity of the major capsid protein with that of tailed halovirus HHTV-1. Presumably, the evolutionary history of ChaoS9 exemplifies widespread recombination between tailed haloviruses. Another curious feature are many, closely matching CRISPR spacers to ChaoS9 in metagenomic data from hypersaline Antarctic lakes. View this paper.
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18 pages, 2081 KiB  
Review
The Role of 3′ to 5′ Reverse RNA Polymerization in tRNA Fidelity and Repair
by Allan W. Chen, Malithi I. Jayasinghe, Christina Z. Chung, Bhalchandra S. Rao, Rosan Kenana, Ilka U. Heinemann and Jane E. Jackman
Genes 2019, 10(3), 250; https://doi.org/10.3390/genes10030250 - 26 Mar 2019
Cited by 10 | Viewed by 5088
Abstract
The tRNAHis guanylyltransferase (Thg1) superfamily includes enzymes that are found in all three domains of life that all share the common ability to catalyze the 3′ to 5′ synthesis of nucleic acids. This catalytic activity, which is the reverse of all other [...] Read more.
The tRNAHis guanylyltransferase (Thg1) superfamily includes enzymes that are found in all three domains of life that all share the common ability to catalyze the 3′ to 5′ synthesis of nucleic acids. This catalytic activity, which is the reverse of all other known DNA and RNA polymerases, makes this enzyme family a subject of biological and mechanistic interest. Previous biochemical, structural, and genetic investigations of multiple members of this family have revealed that Thg1 enzymes use the 3′ to 5′ chemistry for multiple reactions in biology. Here, we describe the current state of knowledge regarding the catalytic features and biological functions that have been so far associated with Thg1 and its homologs. Progress toward the exciting possibility of utilizing this unusual protein activity for applications in biotechnology is also discussed. Full article
(This article belongs to the Special Issue Synthetic DNA and RNA Programming)
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19 pages, 1801 KiB  
Article
Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?
by Romain Lannes, Carène Rizzon and Emmanuelle Lerat
Genes 2019, 10(3), 249; https://doi.org/10.3390/genes10030249 - 26 Mar 2019
Cited by 8 | Viewed by 3244
Abstract
Epigenetic modifications have an important role to explain part of the intra- and inter-species variation in gene expression. They also have a role in the control of transposable elements (TEs) whose activity may have a significant impact on genome evolution by promoting various [...] Read more.
Epigenetic modifications have an important role to explain part of the intra- and inter-species variation in gene expression. They also have a role in the control of transposable elements (TEs) whose activity may have a significant impact on genome evolution by promoting various mutations, which are expected to be mostly deleterious. A change in the local epigenetic landscape associated with the presence of TEs is expected to affect the expression of neighboring genes since these modifications occurring at TE sequences can spread to neighboring sequences. In this work, we have studied how the epigenetic modifications of genes are conserved and what the role of TEs is in this conservation. For that, we have compared the conservation of the epigenome associated with human duplicated genes and the differential presence of TEs near these genes. Our results show higher epigenome conservation of duplicated genes from the same family when they share similar TE environment, suggesting a role for the differential presence of TEs in the evolutionary divergence of duplicates through variation in the epigenetic landscape. Full article
(This article belongs to the Special Issue Repetitive DNA Sequences)
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13 pages, 1147 KiB  
Article
Food Tracking Perspective: DNA Metabarcoding to Identify Plant Composition in Complex and Processed Food Products
by Antonia Bruno, Anna Sandionigi, Giulia Agostinetto, Lorenzo Bernabovi, Jessica Frigerio, Maurizio Casiraghi and Massimo Labra
Genes 2019, 10(3), 248; https://doi.org/10.3390/genes10030248 - 25 Mar 2019
Cited by 37 | Viewed by 6072
Abstract
One of the main goals of the quality control evaluation is to identify contaminants in raw material, or contamination after a food is processed and before it is placed on the market. During the treatment processes, contamination, both accidental and economically motivated, can [...] Read more.
One of the main goals of the quality control evaluation is to identify contaminants in raw material, or contamination after a food is processed and before it is placed on the market. During the treatment processes, contamination, both accidental and economically motivated, can generate incongruence between declared and real composition. In our study, we evaluated if DNA metabarcoding is a suitable tool for unveiling the composition of processed food, when it contains small trace amounts. We tested this method on different types of commercial plant products by using tnrL marker and we applied amplicon-based high-throughput sequencing techniques to identify plant components in different food products. Our results showed that DNA metabarcoding can be an effective approach for food traceability in different type of processed food. Indeed, the vast majority of our samples, we identified the species composition as the labels reported. Although some critical issues still exist, mostly deriving from the starting composition (i.e., variable complexity in taxa composition) of the sample itself and the different processing level (i.e., high or low DNA degradation), our data confirmed the potential of the DNA metabarcoding approach also in quantitative analyses for food composition quality control. Full article
(This article belongs to the Special Issue DNA Barcoding and Metabarcoding of Complex Matrices)
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15 pages, 1984 KiB  
Article
Golgi Oncoprotein GOLPH3 Gene Expression Is Regulated by Functional E2F and CREB/ATF Promoter Elements
by Beatriz Peñalver-González, Jon Vallejo-Rodríguez, Gartze Mentxaka, Asier Fullaondo, Ainhoa Iglesias-Ara, Seth J. Field and Ana M. Zubiaga
Genes 2019, 10(3), 247; https://doi.org/10.3390/genes10030247 - 25 Mar 2019
Cited by 7 | Viewed by 3768
Abstract
The Golgi organelle duplicates its protein and lipid content to segregate evenly between two daughter cells after mitosis. However, how Golgi biogenesis is regulated during interphase remains largely unknown. Here we show that messenger RNA (mRNA) expression of GOLPH3 and GOLGA2, two [...] Read more.
The Golgi organelle duplicates its protein and lipid content to segregate evenly between two daughter cells after mitosis. However, how Golgi biogenesis is regulated during interphase remains largely unknown. Here we show that messenger RNA (mRNA) expression of GOLPH3 and GOLGA2, two genes encoding Golgi proteins, is induced specifically in G1 phase, suggesting a link between cell cycle regulation and Golgi growth. We have examined the role of E2F transcription factors, critical regulators of G1 to S progression of the cell cycle, in the expression of Golgi proteins during interphase. We show that promoter activity for GOLPH3, a Golgi protein that is also oncogenic, is induced by E2F1-3 and repressed by E2F7. Mutation of the E2F motifs present in the GOLPH3 promoter region abrogates E2F1-mediated induction of a GOLPH3 luciferase reporter construct. Furthermore, we identify a critical CREB/ATF element in the GOLPH3 promoter that is required for its steady state and ATF2-induced expression. Interestingly, depletion of GOLPH3 with small interfering RNA (siRNA) delays the G1 to S transition in synchronized U2OS cells. Taken together, our results reveal a link between cell cycle regulation and Golgi function, and suggest that E2F-mediated regulation of Golgi genes is required for the timely progression of the cell cycle. Full article
(This article belongs to the Special Issue Cell Cycle and Regulation)
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9 pages, 195 KiB  
Article
The Interaction between Sex and Hyperlipidemia on Gout Risk Is Modulated by HLA-B Polymorphic Variants in Adult Taiwanese
by Tsui-Wen Hsu, Pei-Shyuan Lee, Oswald Ndi Nfor, Chia-long Lee, Pei-Hsin Chen, Disline Manli Tantoh, Long-Yau Lin, Ming-Chih Chou, Yu-Chen Lee and Yung-Po Liaw
Genes 2019, 10(3), 246; https://doi.org/10.3390/genes10030246 - 25 Mar 2019
Cited by 4 | Viewed by 3522
Abstract
The effects of genetic variants on the interaction between hyperlipidemia and sex have not been investigated among gout patients in Taiwan. Using Taiwan Biobank and the National Health Insurance Research Database (NHIRD), we examined hyperlipidemia, sex, and their relationship with gout among Taiwanese [...] Read more.
The effects of genetic variants on the interaction between hyperlipidemia and sex have not been investigated among gout patients in Taiwan. Using Taiwan Biobank and the National Health Insurance Research Database (NHIRD), we examined hyperlipidemia, sex, and their relationship with gout among Taiwanese adults with the human leukocyte antigen B (HLA-B) genetic variants. Hyperlipidemia was present in 1437 patients with gout. Sex and hyperlipidemia had significant associations on gout risk, with hyperlipidemia showing a relatively stronger effect. Gout was present in men, with an odds ratio (OR) of 1.945 (95% confidence interval (CI) 1.568–2.411) compared to women, and in hyperlipidemic (OR = 4.032; 95% CI: 3.581–4.540) compared to non-hyperlipidemic patients. The interaction of sex and hyperlipidemia was significant for rs2523608 GG (p = 0.0402) and rs4713518 AA (p = 0.0003) genotypes. After stratification, hyperlipidemia remained a risk factor in women (OR = 4.735, 95% CI: 3.375–6.643) and men (OR = 3.640, 95% CI: 2.916–4.544) with rs2523608 GG genotype. The odds ratio in hyperlipidemic women and men with rs4713518 AA genotype was 7.454 (95% CI 5.103–10.888) and 3.585 (95% CI 2.854–4.503), respectively. Our study indicates that hyperlipidemia-sex interactions exist for gout risk in Taiwanese adults with rs2523608 GG and rs4713518 AA genotypes. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
10 pages, 1429 KiB  
Article
Sequencing and Phylogenetic Analysis of Chloroplast Genes in Freshwater Raphidophytes
by Ingrid Sassenhagen and Karin Rengefors
Genes 2019, 10(3), 245; https://doi.org/10.3390/genes10030245 - 22 Mar 2019
Cited by 2 | Viewed by 4010
Abstract
The complex evolution of chloroplasts in microalgae has resulted in highly diverse pigment profiles. Freshwater raphidophytes, for example, display a very different pigment composition to marine raphidophytes. To investigate potential differences in the evolutionary origin of chloroplasts in these two groups of raphidophytes, [...] Read more.
The complex evolution of chloroplasts in microalgae has resulted in highly diverse pigment profiles. Freshwater raphidophytes, for example, display a very different pigment composition to marine raphidophytes. To investigate potential differences in the evolutionary origin of chloroplasts in these two groups of raphidophytes, the plastid genomes of the freshwater species Gonyostomum semen and Vacuolaria virescens were sequenced. To exclusively sequence the organelle genomes, chloroplasts were manually isolated and amplified using single-cell whole-genome-amplification. Assembled and annotated chloroplast genes of the two species were phylogenetically compared to the marine raphidophyte Heterosigma akashiwo and other evolutionarily more diverse microalgae. These phylogenetic comparisons confirmed the high relatedness of all investigated raphidophyte species despite their large differences in pigment composition. Notable differences regarding the presence of light-independent protochlorophyllide oxidoreductase (LIPOR) genes among raphidophyte algae were also revealed in this study. The whole-genome amplification approach proved to be useful for isolation of chloroplast DNA from nuclear DNA. Although only approximately 50% of the genomes were covered, this was sufficient for a multiple gene phylogeny representing large parts of the chloroplast genes. Full article
(This article belongs to the Special Issue Genetics and Genomics of Phytoplankton)
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29 pages, 1675 KiB  
Review
MYC Oncogene Contributions to Release of Cell Cycle Brakes
by Lucía García-Gutiérrez, María Dolores Delgado and Javier León
Genes 2019, 10(3), 244; https://doi.org/10.3390/genes10030244 - 22 Mar 2019
Cited by 129 | Viewed by 13736
Abstract
Promotion of the cell cycle is a major oncogenic mechanism of the oncogene c-MYC (MYC). MYC promotes the cell cycle by not only activating or inducing cyclins and CDKs but also through the downregulation or the impairment of the activity of a set [...] Read more.
Promotion of the cell cycle is a major oncogenic mechanism of the oncogene c-MYC (MYC). MYC promotes the cell cycle by not only activating or inducing cyclins and CDKs but also through the downregulation or the impairment of the activity of a set of proteins that act as cell-cycle brakes. This review is focused on the role of MYC as a cell-cycle brake releaser i.e., how MYC stimulates the cell cycle mainly through the functional inactivation of cell cycle inhibitors. MYC antagonizes the activities and/or the expression levels of p15, ARF, p21, and p27. The mechanism involved differs for each protein. p15 (encoded by CDKN2B) and p21 (CDKN1A) are repressed by MYC at the transcriptional level. In contrast, MYC activates ARF, which contributes to the apoptosis induced by high MYC levels. At least in some cells types, MYC inhibits the transcription of the p27 gene (CDKN1B) but also enhances p27’s degradation through the upregulation of components of ubiquitin ligases complexes. The effect of MYC on cell-cycle brakes also opens the possibility of antitumoral therapies based on synthetic lethal interactions involving MYC and CDKs, for which a series of inhibitors are being developed and tested in clinical trials. Full article
(This article belongs to the Special Issue Cell Cycle and Regulation)
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15 pages, 3374 KiB  
Article
Droplet Digital PCR Detection of the Erythropoietin Transgene from Horse Plasma and Urine for Gene-Doping Control
by Teruaki Tozaki, Aoi Ohnuma, Masaki Takasu, Mio Kikuchi, Hironaga Kakoi, Kei-ichi Hirota, Kanichi Kusano and Shun-ichi Nagata
Genes 2019, 10(3), 243; https://doi.org/10.3390/genes10030243 - 21 Mar 2019
Cited by 34 | Viewed by 5849
Abstract
Indiscriminate genetic manipulation to improve athletic ability is a major threat to human sports and the horseracing industry, in which methods involving gene-doping, such as transgenesis, should be prohibited to ensure fairness. Therefore, development of methods to detect indiscriminate genetic manipulation are urgently [...] Read more.
Indiscriminate genetic manipulation to improve athletic ability is a major threat to human sports and the horseracing industry, in which methods involving gene-doping, such as transgenesis, should be prohibited to ensure fairness. Therefore, development of methods to detect indiscriminate genetic manipulation are urgently needed. Here, we developed a highly sensitive method to detect horse erythropoietin (EPO) transgenes using droplet digital PCR (ddPCR). We designed two TaqMan probe/primer sets, and the EPO transgene was cloned into a plasmid for use as a model. We extracted the spiked EPO transgene from horse plasma and urine via magnetic beads, followed by ddPCR amplification for absolute quantification and transgene detection. The results indicated high recovery rates (at least ~60% and ~40% in plasma and urine, respectively), suggesting successful detection of the spiked transgene at concentrations of >130 and 200 copies/mL of plasma and urine, respectively. Additionally, successful detection was achieved following intramuscular injection of 20 mg of the EPO transgene. This represents the first study demonstrating a method for detecting the EPO transgene in horse plasma and urine, with our results demonstrating its efficacy for promoting the control of gene-doping in the horseracing industry. Full article
(This article belongs to the Special Issue Equine Genetics)
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14 pages, 2042 KiB  
Article
XGBPRH: Prediction of Binding Hot Spots at Protein–RNA Interfaces Utilizing Extreme Gradient Boosting
by Lei Deng, Yuanchao Sui and Jingpu Zhang
Genes 2019, 10(3), 242; https://doi.org/10.3390/genes10030242 - 21 Mar 2019
Cited by 23 | Viewed by 3685
Abstract
Hot spot residues at protein–RNA complexes are vitally important for investigating the underlying molecular recognition mechanism. Accurately identifying protein–RNA binding hot spots is critical for drug designing and protein engineering. Although some progress has been made by utilizing various available features and a [...] Read more.
Hot spot residues at protein–RNA complexes are vitally important for investigating the underlying molecular recognition mechanism. Accurately identifying protein–RNA binding hot spots is critical for drug designing and protein engineering. Although some progress has been made by utilizing various available features and a series of machine learning approaches, these methods are still in the infant stage. In this paper, we present a new computational method named XGBPRH, which is based on an eXtreme Gradient Boosting (XGBoost) algorithm and can effectively predict hot spot residues in protein–RNA interfaces utilizing an optimal set of properties. Firstly, we download 47 protein–RNA complexes and calculate a total of 156 sequence, structure, exposure, and network features. Next, we adopt a two-step feature selection algorithm to extract a combination of 6 optimal features from the combination of these 156 features. Compared with the state-of-the-art approaches, XGBPRH achieves better performances with an area under the ROC curve (AUC) score of 0.817 and an F1-score of 0.802 on the independent test set. Meanwhile, we also apply XGBPRH to two case studies. The results demonstrate that the method can effectively identify novel energy hotspots. Full article
(This article belongs to the Section Technologies and Resources for Genetics)
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27 pages, 19633 KiB  
Article
The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data
by Hongying Ma, Sheng Wang, Guorong Zeng, Jintu Guo, Minghao Guo, Xianggui Dong, Guoying Hua, Yu Liu, Min Wang, Yao Ling, Xiangdong Ding, Chunjiang Zhao and Changxin Wu
Genes 2019, 10(3), 241; https://doi.org/10.3390/genes10030241 - 21 Mar 2019
Cited by 12 | Viewed by 4633
Abstract
The Jinjiang horse is a unique Chinese indigenous horse breed distributed in the southern coastal areas, but the ancestry of Jinjiang horses is not well understood. Here, we used Equine SNP70 Bead Array technology to genotype 301 horses representing 10 Chinese indigenous horse [...] Read more.
The Jinjiang horse is a unique Chinese indigenous horse breed distributed in the southern coastal areas, but the ancestry of Jinjiang horses is not well understood. Here, we used Equine SNP70 Bead Array technology to genotype 301 horses representing 10 Chinese indigenous horse breeds, and we integrated the published genotyped data of 352 individuals from 14 foreign horse breeds to study the relationships between Jinjiang horses and horse breeds from around the world. Principal component analysis (PCA), linkage disequilibrium (LD), runs of homozygosity (ROH) analysis, and ancestry estimating methods were conducted to study the population relationships and the ancestral sources and genetic structure of Jinjiang horses. The results showed that there is no close relationship between foreign horse breeds and Jinjiang horses, and Jinjiang horses shared a similar genetic background with Baise horses. TreeMix analysis revealed that there was gene flow from Chakouyi horses to Jinjiang horses. The ancestry analysis showed that Baise horses and Chakouyi horses are the most closely related ancestors of Jinjiang horses. In conclusion, our results showed that Jinjiang horses have a native origin and that Baise horses and Chakouyi horses were key ancestral sources of Jinjiang horses. The study also suggested that ancient trade activities and the migration of human beings had important effects on indigenous horse breeds in China. Full article
(This article belongs to the Special Issue Equine Genetics)
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15 pages, 2101 KiB  
Article
Group Lasso Regularized Deep Learning for Cancer Prognosis from Multi-Omics and Clinical Features
by Gangcai Xie, Chengliang Dong, Yinfei Kong, Jiang F. Zhong, Mingyao Li and Kai Wang
Genes 2019, 10(3), 240; https://doi.org/10.3390/genes10030240 - 21 Mar 2019
Cited by 52 | Viewed by 7680
Abstract
Accurate prognosis of patients with cancer is important for the stratification of patients, the optimization of treatment strategies, and the design of clinical trials. Both clinical features and molecular data can be used for this purpose, for instance, to predict the survival of [...] Read more.
Accurate prognosis of patients with cancer is important for the stratification of patients, the optimization of treatment strategies, and the design of clinical trials. Both clinical features and molecular data can be used for this purpose, for instance, to predict the survival of patients censored at specific time points. Multi-omics data, including genome-wide gene expression, methylation, protein expression, copy number alteration, and somatic mutation data, are becoming increasingly common in cancer studies. To harness the rich information in multi-omics data, we developed GDP (Group lass regularized Deep learning for cancer Prognosis), a computational tool for survival prediction using both clinical and multi-omics data. GDP integrated a deep learning framework and Cox proportional hazard model (CPH) together, and applied group lasso regularization to incorporate gene-level group prior knowledge into the model training process. We evaluated its performance in both simulated and real data from The Cancer Genome Atlas (TCGA) project. In simulated data, our results supported the importance of group prior information in the regularization of the model. Compared to the standard lasso regularization, we showed that group lasso achieved higher prediction accuracy when the group prior knowledge was provided. We also found that GDP performed better than CPH for complex survival data. Furthermore, analysis on real data demonstrated that GDP performed favorably against other methods in several cancers with large-scale omics data sets, such as glioblastoma multiforme, kidney renal clear cell carcinoma, and bladder urothelial carcinoma. In summary, we demonstrated that GDP is a powerful tool for prognosis of patients with cancer, especially when large-scale molecular features are available. Full article
(This article belongs to the Special Issue Computational Oncogenomics)
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18 pages, 5613 KiB  
Article
A Novel Insight into Functional Divergence of the MST Gene Family in Rice Based on Comprehensive Expression Patterns
by Xiaolong Deng, Baoguang An, Hua Zhong, Jing Yang, Weilong Kong and Yangsheng Li
Genes 2019, 10(3), 239; https://doi.org/10.3390/genes10030239 - 20 Mar 2019
Cited by 48 | Viewed by 5445
Abstract
Sugars are critical for plant growth and development as suppliers of carbon and energy, as signal molecules, or as solute molecules for osmotic homeostasis. Monosaccharide transporter (MST) genes are involved in various processes of plant growth and development as well as in response [...] Read more.
Sugars are critical for plant growth and development as suppliers of carbon and energy, as signal molecules, or as solute molecules for osmotic homeostasis. Monosaccharide transporter (MST) genes are involved in various processes of plant growth and development as well as in response to abiotic stresses. However, the evolution and their roles of MST genes in growth and development and in coping with abiotic stresses in rice are poorly known. Here, we identified 64 MST genes in rice genome, which are classified into seven subfamilies: STP, PLT, AZT, ERD, pGlcT, INT, and XTPH. MST genes are not evenly distributed between chromosomes (Chrs) with a bias to Chr 3, 4, 7, and 11, which could be a result of duplication of fragments harboring MST genes. In total, 12 duplication events were found in the rice MST family, among which, two pairs were derived from fragmental duplications and ten pairs were from tandem duplications. The synonymous and nonsynonymous substitution rates of duplicate gene pairs demonstrated that the MST family was under a strong negative selection during the evolution process. Furthermore, a comprehensive expression analysis conducted in 11 different tissues, three abiotic stresses, five hormone treatments, and three sugar treatments revealed different expression patterns of MST genes and indicated diversified functions of them. Our results suggest that MST genes play important roles not only in various abiotic stresses but also in hormone and sugar responses. The present results will provide a vital insight into the functional divergence of the MST family in the future study. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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17 pages, 618 KiB  
Review
Challenges in the Integration of Omics and Non-Omics Data
by Evangelina López de Maturana, Lola Alonso, Pablo Alarcón, Isabel Adoración Martín-Antoniano, Silvia Pineda, Lucas Piorno, M. Luz Calle and Núria Malats
Genes 2019, 10(3), 238; https://doi.org/10.3390/genes10030238 - 20 Mar 2019
Cited by 72 | Viewed by 10111
Abstract
Omics data integration is already a reality. However, few omics-based algorithms show enough predictive ability to be implemented into clinics or public health domains. Clinical/epidemiological data tend to explain most of the variation of health-related traits, and its joint modeling with omics data [...] Read more.
Omics data integration is already a reality. However, few omics-based algorithms show enough predictive ability to be implemented into clinics or public health domains. Clinical/epidemiological data tend to explain most of the variation of health-related traits, and its joint modeling with omics data is crucial to increase the algorithm’s predictive ability. Only a small number of published studies performed a “real” integration of omics and non-omics (OnO) data, mainly to predict cancer outcomes. Challenges in OnO data integration regard the nature and heterogeneity of non-omics data, the possibility of integrating large-scale non-omics data with high-throughput omics data, the relationship between OnO data (i.e., ascertainment bias), the presence of interactions, the fairness of the models, and the presence of subphenotypes. These challenges demand the development and application of new analysis strategies to integrate OnO data. In this contribution we discuss different attempts of OnO data integration in clinical and epidemiological studies. Most of the reviewed papers considered only one type of omics data set, mainly RNA expression data. All selected papers incorporated non-omics data in a low-dimensionality fashion. The integrative strategies used in the identified papers adopted three modeling methods: Independent, conditional, and joint modeling. This review presents, discusses, and proposes integrative analytical strategies towards OnO data integration. Full article
(This article belongs to the Special Issue Systems Analytics and Integration of Big Omics Data)
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14 pages, 3534 KiB  
Article
Chicken Embryonic-Stem Cells Are Permissive to Poxvirus Recombinant Vaccine Vectors
by Efstathios S. Giotis, Guillaume Montillet, Bertrand Pain and Michael A. Skinner
Genes 2019, 10(3), 237; https://doi.org/10.3390/genes10030237 - 20 Mar 2019
Cited by 12 | Viewed by 5980
Abstract
The discovery of mammalian pluripotent embryonic stem cells (ESC) has revolutionised cell research and regenerative medicine. More recently discovered chicken ESC (cESC), though less intensively studied, are increasingly popular as vaccine substrates due to a dearth of avian cell lines. Information on the [...] Read more.
The discovery of mammalian pluripotent embryonic stem cells (ESC) has revolutionised cell research and regenerative medicine. More recently discovered chicken ESC (cESC), though less intensively studied, are increasingly popular as vaccine substrates due to a dearth of avian cell lines. Information on the comparative performance of cESC with common vaccine viruses is limited. Using RNA-sequencing, we compared cESC transcriptional programmes elicited by stimulation with chicken type I interferon or infection with vaccine viruses routinely propagated in primary chicken embryo fibroblasts (CEF). We used poxviruses (fowlpox virus (FWPV) FP9, canarypox virus (CNPV), and modified vaccinia virus Ankara (MVA)) and a birnavirus (infectious bursal disease virus (IBDV) PBG98). Interferon-stimulated genes (ISGs) were induced in cESC to levels comparable to those in CEF and immortalised chicken fibroblast DF-1 cells. cESC are permissive (with distinct host transcriptional responses) to MVA, FP9, and CNPV but, surprisingly, not to PBG98. MVA, CNPV, and FP9 suppressed innate immune responses, while PBG98 induced a subset of ISGs. Dysregulation of signalling pathways (i.e., NFκB, TRAF) was observed, which might affect immune responses and viral replication. In conclusion, we show that cESC are an attractive alternative substrate to study and propagate poxvirus recombinant vaccine vectors. Full article
(This article belongs to the Special Issue Genomics of Avian Viral Infections)
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14 pages, 599 KiB  
Article
A Comparison Between Two Assays for Measuring Seminal Oxidative Stress and their Relationship with Sperm DNA Fragmentation and Semen Parameters
by Sheryl T. Homa, Anna M. Vassiliou, Jesse Stone, Aideen P. Killeen, Andrew Dawkins, Jingyi Xie, Farley Gould and Jonathan W. A. Ramsay
Genes 2019, 10(3), 236; https://doi.org/10.3390/genes10030236 - 19 Mar 2019
Cited by 71 | Viewed by 5625
Abstract
Oxidative stress (OS) is a significant cause of DNA fragmentation and is associated with poor embryo development and recurrent miscarriage. The aim of this study was to compare two different methods for assessing seminal OS and their ability to predict sperm DNA fragmentation [...] Read more.
Oxidative stress (OS) is a significant cause of DNA fragmentation and is associated with poor embryo development and recurrent miscarriage. The aim of this study was to compare two different methods for assessing seminal OS and their ability to predict sperm DNA fragmentation and abnormal semen parameters. Semen samples were collected from 520 men attending for routine diagnostic testing following informed consent. Oxidative stress was assessed using either a chemiluminescence assay to measure reactive oxygen species (ROS) or an electrochemical assay to measure oxidation reduction potential (sORP). Sperm DNA fragmentation (DFI) and sperm with immature chromatin (HDS) were assessed using sperm chromatin structure assay (SCSA). Semen analysis was performed according to WHO 2010 guidelines. Reactive oxygen species sORP and DFI are negatively correlated with sperm motility (p = 0.0012, 0.0002, <0.0001 respectively) and vitality (p < 0.0001, 0.019, <0.0001 respectively). The correlation was stronger for sORP than ROS. Reactive oxygen species (p < 0.0001), sORP (p < 0.0001), DFI (p < 0.0089) and HDS (p < 0.0001) were significantly elevated in samples with abnormal semen parameters, compared to those with normal parameters. Samples with polymorphonuclear leukocytes (PMN) have excessive ROS levels compared to those without (p < 0.0001), but sORP and DFI in this group are not significantly increased. DNA fragmentation was significantly elevated in samples with OS measured by ROS (p = 0.0052) or sORP (p = 0.004). The results demonstrate the multi-dimensional nature of oxidative stress and that neither assay can be used alone in the diagnosis of OS, especially in cases of leukocytospermia. Full article
(This article belongs to the Special Issue Male Germline Chromatin)
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11 pages, 641 KiB  
Review
Cell-Selective Regulation of CFTR Gene Expression: Relevance to Gene Editing Therapeutics
by Hannah Swahn and Ann Harris
Genes 2019, 10(3), 235; https://doi.org/10.3390/genes10030235 - 19 Mar 2019
Cited by 21 | Viewed by 6747
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene is an attractive target for gene editing approaches, which may yield novel therapeutic approaches for genetic diseases such as cystic fibrosis (CF). However, for gene editing to be effective, aspects of the three-dimensional [...] Read more.
The cystic fibrosis transmembrane conductance regulator (CFTR) gene is an attractive target for gene editing approaches, which may yield novel therapeutic approaches for genetic diseases such as cystic fibrosis (CF). However, for gene editing to be effective, aspects of the three-dimensional (3D) structure and cis-regulatory elements governing the dynamic expression of CFTR need to be considered. In this review, we focus on the higher order chromatin organization required for normal CFTR locus function, together with the complex mechanisms controlling expression of the gene in different cell types impaired by CF pathology. Across all cells, the CFTR locus is organized into an invariant topologically associated domain (TAD) established by the architectural proteins CCCTC-binding factor (CTCF) and cohesin complex. Additional insulator elements within the TAD also recruit these factors. Although the CFTR promoter is required for basal levels of expression, cis-regulatory elements (CREs) in intergenic and intronic regions are crucial for cell-specific and temporal coordination of CFTR transcription. These CREs are recruited to the promoter through chromatin looping mechanisms and enhance cell-type-specific expression. These features of the CFTR locus should be considered when designing gene-editing approaches, since failure to recognize their importance may disrupt gene expression and reduce the efficacy of therapies. Full article
(This article belongs to the Special Issue Cystic Fibrosis: Therapy and Genetics)
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11 pages, 911 KiB  
Article
Development of a DNA Barcoding-Like Approach to Detect Mustard Allergens in Wheat Flours
by Jessica Frigerio, Roberta Pellesi, Valerio Mezzasalma, Fabrizio De Mattia, Andrea Galimberti, Francesca Lambertini, Michele Suman, Sandro Zanardi, Andrea Leporati and Massimo Labra
Genes 2019, 10(3), 234; https://doi.org/10.3390/genes10030234 - 19 Mar 2019
Cited by 9 | Viewed by 4039
Abstract
The spread of food allergens is a topic of global importance due to its impact on public health. National and International regulations ask food producers and manufacturers to declare product compositions on the label, especially in case of processed raw materials. Wheat flour [...] Read more.
The spread of food allergens is a topic of global importance due to its impact on public health. National and International regulations ask food producers and manufacturers to declare product compositions on the label, especially in case of processed raw materials. Wheat flour (Triticum aestivum) can be contaminated by a wide range of species belonging to the Brassicaceae in the field or during grain harvests, storage, and processing. Among them, mustards (Brassica nigra, Brassica juncea and Sinapis alba) are well known allergenic species. Often, food quality laboratories adopt an ELISA approach to detect the presence of mustard species. However, this approach shows cross-reactivity with other non-allergenic species such as Brassica napus (rapeseed). In the last few years, DNA barcoding was proposed as a valid identification method, and it is now commonly used in the authentication of food products. This study aims to set up an easy and rapid DNA-based tool to detect mustard allergenic species. DNA barcoding (matK and ITS2) and chromosome markers (A6, B, C1 genome regions) were selected, and specific primers were validated on incurred reference food matrices. The developed test was proven to be able to distinguish mustard from rapeseed and wheat, overcoming cross-reactivity with Brassica napus. Full article
(This article belongs to the Special Issue DNA Barcoding and Metabarcoding of Complex Matrices)
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19 pages, 2988 KiB  
Article
The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria
by Matthew S. Fullmer, Matthew Ouellette, Artemis S. Louyakis, R. Thane Papke and Johann Peter Gogarten
Genes 2019, 10(3), 233; https://doi.org/10.3390/genes10030233 - 19 Mar 2019
Cited by 26 | Viewed by 6676
Abstract
Restriction–modification (RM) systems in bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, [...] Read more.
Restriction–modification (RM) systems in bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, mismatch repair, protein expression, and in biasing DNA uptake. Little is known about archaeal RM systems and DNA methylation. To elucidate further understanding for the role of RM systems and DNA methylation in Archaea, we undertook a survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria. Our results reveal that some orphan DNA methyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence. This irregular distribution is due to frequent horizontal gene transfer and gene loss, a finding suggesting that the evolution and life cycle of RM systems may be best described as that of a selfish genetic element. A putative target motif (CTAG) of one of the orphan methylases was underrepresented in all of the analyzed genomes, whereas another motif (GATC) was overrepresented in most of the haloarchaeal genomes, particularly in those that encoded the cognate orphan methylase. Full article
(This article belongs to the Special Issue Genetics of Halophilic Microorganisms)
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22 pages, 1167 KiB  
Review
Structure-Specific Endonucleases and the Resolution of Chromosome Underreplication
by Benoît Falquet and Ulrich Rass
Genes 2019, 10(3), 232; https://doi.org/10.3390/genes10030232 - 19 Mar 2019
Cited by 23 | Viewed by 5210
Abstract
Complete genome duplication in every cell cycle is fundamental for genome stability and cell survival. However, chromosome replication is frequently challenged by obstacles that impede DNA replication fork (RF) progression, which subsequently causes replication stress (RS). Cells have evolved pathways of RF protection [...] Read more.
Complete genome duplication in every cell cycle is fundamental for genome stability and cell survival. However, chromosome replication is frequently challenged by obstacles that impede DNA replication fork (RF) progression, which subsequently causes replication stress (RS). Cells have evolved pathways of RF protection and restart that mitigate the consequences of RS and promote the completion of DNA synthesis prior to mitotic chromosome segregation. If there is entry into mitosis with underreplicated chromosomes, this results in sister-chromatid entanglements, chromosome breakage and rearrangements and aneuploidy in daughter cells. Here, we focus on the resolution of persistent replication intermediates by the structure-specific endonucleases (SSEs) MUS81, SLX1-SLX4 and GEN1. Their actions and a recently discovered pathway of mitotic DNA repair synthesis have emerged as important facilitators of replication completion and sister chromatid detachment in mitosis. As RS is induced by oncogene activation and is a common feature of cancer cells, any advances in our understanding of the molecular mechanisms related to chromosome underreplication have important biomedical implications. Full article
(This article belongs to the Special Issue Chromosome Replication and Genome Integrity)
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13 pages, 3133 KiB  
Article
H3K27me3 Depletion during Differentiation Promotes Myogenic Transcription in Porcine Satellite Cells
by Sheng Wang, Yan Sun, Ruimin Ren, Junhui Xie, Xiaohuan Tian, Shuhong Zhao, Xinyun Li and Jianhua Cao
Genes 2019, 10(3), 231; https://doi.org/10.3390/genes10030231 - 19 Mar 2019
Cited by 15 | Viewed by 4764
Abstract
Background: Porcine skeletal muscle satellite cells play important roles in myogenesis and muscle regeneration. Integrated analysis of transcriptome and histone modifications would reveal epigenomic roles in promoting myogenic differentiation in swine. Methods: Porcine satellite cells (PSCs) were isolated and in-vitro cultured from newborn [...] Read more.
Background: Porcine skeletal muscle satellite cells play important roles in myogenesis and muscle regeneration. Integrated analysis of transcriptome and histone modifications would reveal epigenomic roles in promoting myogenic differentiation in swine. Methods: Porcine satellite cells (PSCs) were isolated and in-vitro cultured from newborn piglets. RNA Sequencing (RNA-Seq) and Chromatin Immunoprecipitation Sequencing (ChIP-Seq) experiments were performed using proliferating cells and terminal myotubes in order to interrogate the transcriptomic profiles, as well as the distribution of histone markers—H3K4me3, H3K27me3, and H3K27ac—and RNA polymerase II. Results: The study identified 917 differentially expressed genes during cell differentiation. The landscape of epigenetic marks was displayed on a genome-wide scale, which had globally shrunken. H3K27me3 reinforcement participated in obstructing the transcription of proliferation-related genes, while its depletion was closely related to the up-regulation of myogenic genes. Furthermore, the degree of H3K27me3 modification was dramatically reduced by 50%, and 139 myogenic genes were upregulated to promote cell differentiation. Conclusions: The depletion of H3K27me3 was shown to promote porcine satellite cell differentiation through upregulating the transcription level of myogenic genes. Our findings in this study provide new insights of the epigenomic mechanisms occurring during myogenic differentiation, and shed light on chromatin states and the dynamics underlying myogenesis. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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15 pages, 2463 KiB  
Article
Identification of Zebrafish Calcium Toolkit Genes and Their Expression in the Brain
by Iga Wasilewska, Rishikesh Kumar Gupta, Oksana Palchevska and Jacek Kuźnicki
Genes 2019, 10(3), 230; https://doi.org/10.3390/genes10030230 - 18 Mar 2019
Cited by 11 | Viewed by 4140
Abstract
Zebrafish are well-suited for in vivo calcium imaging because of the transparency of their larvae and the ability to express calcium probes in various cell subtypes. This model organism has been used extensively to study brain development, neuronal function, and network activity. However, [...] Read more.
Zebrafish are well-suited for in vivo calcium imaging because of the transparency of their larvae and the ability to express calcium probes in various cell subtypes. This model organism has been used extensively to study brain development, neuronal function, and network activity. However, only a few studies have investigated calcium homeostasis and signaling in zebrafish neurons, and little is known about the proteins that are involved in these processes. Using bioinformatics analysis and available databases, the present study identified 491 genes of the zebrafish Calcium Toolkit (CaTK). Using RNA-sequencing, we then evaluated the expression of these genes in the adult zebrafish brain and found 380 hits that belonged to the CaTK. Based on quantitative real-time polymerase chain reaction arrays, we estimated the relative mRNA levels in the brain of CaTK genes at two developmental stages. In both 5 dpf larvae and adult zebrafish, the highest relative expression was observed for tmbim4, which encodes a Golgi membrane protein. The present data on CaTK genes will contribute to future applications of zebrafish as a model for in vivo and in vitro studies of Ca2+ signaling. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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16 pages, 1909 KiB  
Review
Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices
by Laura Morello, Luca Braglia, Floriana Gavazzi, Silvia Gianì and Diego Breviario
Genes 2019, 10(3), 229; https://doi.org/10.3390/genes10030229 - 18 Mar 2019
Cited by 8 | Viewed by 4487
Abstract
The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal [...] Read more.
The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods. Full article
(This article belongs to the Special Issue DNA Barcoding and Metabarcoding of Complex Matrices)
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16 pages, 1411 KiB  
Review
Novel Insights into Plant Genome Evolution and Adaptation as Revealed through Transposable Elements and Non-Coding RNAs in Conifers
by Yang Liu and Yousry A. El-Kassaby
Genes 2019, 10(3), 228; https://doi.org/10.3390/genes10030228 - 18 Mar 2019
Cited by 7 | Viewed by 5897
Abstract
Plant genomes are punctuated by repeated bouts of proliferation of transposable elements (TEs), and these mobile bursts are followed by silencing and decay of most of the newly inserted elements. As such, plant genomes reflect TE-related genome expansion and shrinkage. In general, these [...] Read more.
Plant genomes are punctuated by repeated bouts of proliferation of transposable elements (TEs), and these mobile bursts are followed by silencing and decay of most of the newly inserted elements. As such, plant genomes reflect TE-related genome expansion and shrinkage. In general, these genome activities involve two mechanisms: small RNA-mediated epigenetic repression and long-term mutational decay and deletion, that is, genome-purging. Furthermore, the spatial relationships between TE insertions and genes are an important force in shaping gene regulatory networks, their downstream metabolic and physiological outputs, and thus their phenotypes. Such cascading regulations finally set up a fitness differential among individuals. This brief review demonstrates factual evidence that unifies most updated conceptual frameworks covering genome size, architecture, epigenetic reprogramming, and gene expression. It aims to give an overview of the impact that TEs may have on genome and adaptive evolution and to provide novel insights into addressing possible causes and consequences of intimidating genome sizes (20–30 Gb) in a taxonomic group, conifers. Full article
(This article belongs to the Special Issue Epigenetics and Adaptation)
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12 pages, 1223 KiB  
Article
Exceptional Longevity and Polygenic Risk for Cardiovascular Health
by Mary Revelas, Anbupalam Thalamuthu, Christopher Oldmeadow, Tiffany-Jane Evans, Nicola J. Armstrong, Carlos Riveros, John B. Kwok, Peter R. Schofield, Henry Brodaty, Rodney J. Scott, John R. Attia, Perminder S. Sachdev and Karen A. Mather
Genes 2019, 10(3), 227; https://doi.org/10.3390/genes10030227 - 18 Mar 2019
Cited by 7 | Viewed by 4927
Abstract
Studies investigating exceptionally long-lived (ELL) individuals, including genetic studies, have linked cardiovascular-related pathways, particularly lipid and cholesterol homeostasis, with longevity. This study explored the genetic profiles of ELL individuals (cases: n = 294, 95–106 years; controls: n = 1105, 55–65 years) by assessing [...] Read more.
Studies investigating exceptionally long-lived (ELL) individuals, including genetic studies, have linked cardiovascular-related pathways, particularly lipid and cholesterol homeostasis, with longevity. This study explored the genetic profiles of ELL individuals (cases: n = 294, 95–106 years; controls: n = 1105, 55–65 years) by assessing their polygenic risk scores (PRS) based on a genome wide association study (GWAS) threshold of p < 5 × 10−5. PRS were constructed using GWAS summary data from two exceptional longevity (EL) analyses and eight cardiovascular-related risk factors (lipids) and disease (myocardial infarction, coronary artery disease, stroke) analyses. A higher genetic risk for exceptional longevity (EL) was significantly associated with longevity in our sample (odds ratio (OR) = 1.19–1.20, p = 0.00804 and 0.00758, respectively). Two cardiovascular health PRS were nominally significant with longevity (HDL cholesterol, triglycerides), with higher PRS associated with EL, but these relationships did not survive correction for multiple testing. In conclusion, ELL individuals did not have significantly lower polygenic risk for the majority of the investigated cardiovascular health traits. Future work in larger cohorts is required to further explore the role of cardiovascular-related genetic variants in EL. Full article
(This article belongs to the Special Issue Genetic Determinants of Human Longevity)
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21 pages, 2424 KiB  
Article
Knockdown of Cytochrome P450 Genes Gh_D07G1197 and Gh_A13G2057 on Chromosomes D07 and A13 Reveals Their Putative Role in Enhancing Drought and Salt Stress Tolerance in Gossypium hirsutum
by Richard Odongo Magwanga, Pu Lu, Joy Nyangasi Kirungu, Qi Dong, Xiaoyan Cai, Zhongli Zhou, Xingxing Wang, Yuqing Hou, Yanchao Xu, Renhai Peng, Stephen Gaya Agong, Kunbo Wang and Liu Fang
Genes 2019, 10(3), 226; https://doi.org/10.3390/genes10030226 - 18 Mar 2019
Cited by 38 | Viewed by 4350
Abstract
We identified 672, 374, and 379 CYPs proteins encoded by the CYPs genes in Gossypium hirsutum, Gossypium raimondii, and Gossypium arboreum, respectively. The genes were found to be distributed in all 26 chromosomes of the tetraploid cotton, with [...] Read more.
We identified 672, 374, and 379 CYPs proteins encoded by the CYPs genes in Gossypium hirsutum, Gossypium raimondii, and Gossypium arboreum, respectively. The genes were found to be distributed in all 26 chromosomes of the tetraploid cotton, with chrA05, chrA12, and their homeolog chromosomes harboring the highest number of genes. The physiochemical properties of the proteins encoded by the CYP450 genes varied in terms of their protein lengths, molecular weight, isoelectric points (pI), and even grand hydropathy values (GRAVY). However, over 99% of the cotton proteins had GRAVY values below 0, which indicated that the majority of the proteins encoded by the CYP450 genes were hydrophilic in nature, a common property of proteins encoded by stress-responsive genes. Moreover, through the RNA interference (RNAi) technique, the expression levels of Gh_D07G1197 and Gh_A13G2057 were suppressed, and the silenced plants showed a higher concentration of hydrogen peroxide (H2O2) with a significant reduction in the concentration levels of glutathione (GSH), ascorbate peroxidase (APX), and proline compared to the wild types under drought and salt stress conditions. Furthermore, the stress-responsive genes 1-Pyrroline–5-Carboxylate Synthetase (GhP5CS), superoxide dismutase (GhSOD), and myeloblastosis (GhMYB) were downregulated in VIGS plants, but showed upregulation in the leaf tissues of the wild types under drought and salt stress conditions. In addition, CYP450-silenced cotton plants exhibited a high level of oxidative injury due to high levels of oxidant enzymes, in addition to negative effects on CMS, ELWL, RLWC, and chlorophyll content The results provide the basic foundation for future exploration of the proteins encoded by the CYP450 genes in order to understand the physiological and biochemical mechanisms in enhancing drought and salt stress tolerance in plants. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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13 pages, 1243 KiB  
Article
Gene Expression Networks Across Multiple Tissues Are Associated with Rates of Molecular Evolution in Wild House Mice
by Katya L. Mack, Megan Phifer-Rixey, Bettina Harr and Michael W. Nachman
Genes 2019, 10(3), 225; https://doi.org/10.3390/genes10030225 - 18 Mar 2019
Cited by 8 | Viewed by 4452
Abstract
Interactions between genes can influence how selection acts on sequence variation. In gene regulatory networks, genes that affect the expression of many other genes may be under stronger evolutionary constraint than genes whose expression affects fewer partners. While this has been studied for [...] Read more.
Interactions between genes can influence how selection acts on sequence variation. In gene regulatory networks, genes that affect the expression of many other genes may be under stronger evolutionary constraint than genes whose expression affects fewer partners. While this has been studied for individual tissue types, we know less about the effects of regulatory networks on gene evolution across different tissue types. We use RNA-sequencing and genomic data collected from Mus musculus domesticus to construct and compare gene co-expression networks for 10 tissue types. We identify tissue-specific expression and local regulatory variation, and we associate these components of gene expression variation with sequence polymorphism and divergence. We found that genes with higher connectivity across tissues and genes associated with a greater number of cross-tissue modules showed significantly lower genetic diversity and lower rates of protein evolution. Consistent with this pattern, “hub” genes across multiple tissues also showed evidence of greater evolutionary constraint. Using allele-specific expression, we found that genes with cis-regulatory variation had lower average connectivity and higher levels of tissue specificity. Taken together, these results are consistent with strong purifying selection acting on genes with high connectivity within and across tissues. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Gene Expression)
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23 pages, 4875 KiB  
Article
Differential Alternative Splicing Genes in Response to Boron Deficiency in Brassica napus
by Jin Gu, Wei Li, Sheliang Wang, Xiaoyan Zhang, Anne Coules, Guangda Ding, Fangsen Xu, Jian Ren, Chungui Lu and Lei Shi
Genes 2019, 10(3), 224; https://doi.org/10.3390/genes10030224 - 18 Mar 2019
Cited by 11 | Viewed by 3250
Abstract
Alternative splicing (AS) can increase transcriptome diversity, protein diversity and protein yield, and is an important mechanism to regulate plant responses to stress. Oilseed rape (Brassica napus L.), one of the main oil crops in China, shows higher sensitivity to boron (B) [...] Read more.
Alternative splicing (AS) can increase transcriptome diversity, protein diversity and protein yield, and is an important mechanism to regulate plant responses to stress. Oilseed rape (Brassica napus L.), one of the main oil crops in China, shows higher sensitivity to boron (B) deficiency than other species. Here, we demonstrated AS changes that largely increased the diversity of the mRNA expressed in response to B deficiency in B. napus. Each gene had two or more transcripts on average. A total of 33.3% genes in both Qingyou10 (QY10, B-efficient cultivar) and Westar10 (W10, B-inefficient cultivar) showed AS in both B conditions. The types of AS events were mainly intron retention, 3′ alternative splice site, 5′ alternative splice site and exon skipping. The tolerance ability of QY10 was higher than that of W10, possibly because there were far more differential alternative splicing (DAS) genes identified in QY10 at low B conditions than in W10. The number of genes with both DAS and differentially expressed (DE) was far lower than that of the genes that were either with DAS or DE in QY10 and W10, suggesting that the DAS and DE genes were independent. Four Serine/Arginine-rich (SR) splicing factors, BnaC06g14780D, BnaA01g14750D, BnaA06g15930D and BnaC01g41640D, underwent differentially alternative splicing in both cultivars. There existed gene–gene interactions between BnaC06g14780D and the genes associated with the function of B in oilseed rape at low B supply. This suggests that oilseed rape could regulate the alterative pre-mRNA splicing of SR protein related genes to increase the plant tolerance to B deficiency. Full article
(This article belongs to the Special Issue Improving Plant Nutrient Use efficiency)
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22 pages, 1623 KiB  
Review
Centromere Repeats: Hidden Gems of the Genome
by Gabrielle Hartley and Rachel J. O’Neill
Genes 2019, 10(3), 223; https://doi.org/10.3390/genes10030223 - 16 Mar 2019
Cited by 87 | Viewed by 12019
Abstract
Satellite DNAs are now regarded as powerful and active contributors to genomic and chromosomal evolution. Paired with mobile transposable elements, these repetitive sequences provide a dynamic mechanism through which novel karyotypic modifications and chromosomal rearrangements may occur. In this review, we discuss the [...] Read more.
Satellite DNAs are now regarded as powerful and active contributors to genomic and chromosomal evolution. Paired with mobile transposable elements, these repetitive sequences provide a dynamic mechanism through which novel karyotypic modifications and chromosomal rearrangements may occur. In this review, we discuss the regulatory activity of satellite DNA and their neighboring transposable elements in a chromosomal context with a particular emphasis on the integral role of both in centromere function. In addition, we discuss the varied mechanisms by which centromeric repeats have endured evolutionary processes, producing a novel, species-specific centromeric landscape despite sharing a ubiquitously conserved function. Finally, we highlight the role these repetitive elements play in the establishment and functionality of de novo centromeres and chromosomal breakpoints that underpin karyotypic variation. By emphasizing these unique activities of satellite DNAs and transposable elements, we hope to disparage the conventional exemplification of repetitive DNA in the historically-associated context of ‘junk’. Full article
(This article belongs to the Special Issue Repetitive DNA Sequences)
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28 pages, 1538 KiB  
Review
The Genetic Variability of APOE in Different Human Populations and Its Implications for Longevity
by Paolo Abondio, Marco Sazzini, Paolo Garagnani, Alessio Boattini, Daniela Monti, Claudio Franceschi, Donata Luiselli and Cristina Giuliani
Genes 2019, 10(3), 222; https://doi.org/10.3390/genes10030222 - 15 Mar 2019
Cited by 90 | Viewed by 14771
Abstract
Human longevity is a complex phenotype resulting from the combinations of context-dependent gene-environment interactions that require analysis as a dynamic process in a cohesive ecological and evolutionary framework. Genome-wide association (GWAS) and whole-genome sequencing (WGS) studies on centenarians pointed toward the inclusion of [...] Read more.
Human longevity is a complex phenotype resulting from the combinations of context-dependent gene-environment interactions that require analysis as a dynamic process in a cohesive ecological and evolutionary framework. Genome-wide association (GWAS) and whole-genome sequencing (WGS) studies on centenarians pointed toward the inclusion of the apolipoprotein E (APOE) polymorphisms ε2 and ε4, as implicated in the attainment of extreme longevity, which refers to their effect in age-related Alzheimer’s disease (AD) and cardiovascular disease (CVD). In this case, the available literature on APOE and its involvement in longevity is described according to an anthropological and population genetics perspective. This aims to highlight the evolutionary history of this gene, how its participation in several biological pathways relates to human longevity, and which evolutionary dynamics may have shaped the distribution of APOE haplotypes across the globe. Its potential adaptive role will be described along with implications for the study of longevity in different human groups. This review also presents an updated overview of the worldwide distribution of APOE alleles based on modern day data from public databases and ancient DNA samples retrieved from literature in the attempt to understand the spatial and temporal frame in which present-day patterns of APOE variation evolved. Full article
(This article belongs to the Special Issue Genetic Determinants of Human Longevity)
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23 pages, 2096 KiB  
Review
DNA Replication Timing Enters the Single-Cell Era
by Ichiro Hiratani and Saori Takahashi
Genes 2019, 10(3), 221; https://doi.org/10.3390/genes10030221 - 15 Mar 2019
Cited by 10 | Viewed by 6007
Abstract
In mammalian cells, DNA replication timing is controlled at the level of megabase (Mb)-sized chromosomal domains and correlates well with transcription, chromatin structure, and three-dimensional (3D) genome organization. Because of these properties, DNA replication timing is an excellent entry point to explore genome [...] Read more.
In mammalian cells, DNA replication timing is controlled at the level of megabase (Mb)-sized chromosomal domains and correlates well with transcription, chromatin structure, and three-dimensional (3D) genome organization. Because of these properties, DNA replication timing is an excellent entry point to explore genome regulation at various levels and a variety of studies have been carried out over the years. However, DNA replication timing studies traditionally required at least tens of thousands of cells, and it was unclear whether the replication domains detected by cell population analyses were preserved at the single-cell level. Recently, single-cell DNA replication profiling methods became available, which revealed that the Mb-sized replication domains detected by cell population analyses were actually well preserved in individual cells. In this article, we provide a brief overview of our current knowledge on DNA replication timing regulation in mammals based on cell population studies, outline the findings from single-cell DNA replication profiling, and discuss future directions and challenges. Full article
(This article belongs to the Special Issue DNA Replication Timing: Where, When, How and Why?)
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