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Volume 10
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Genes, Volume 10, Issue 11 (November 2019) – 112 articles

Cover Story (view full-size image): Globally, we find ourselves in the midst of a biodiversity crisis and in need of conservation tools to help preserve the species that remain. Advances in sequencing technologies and reduction in sequencing costs have given rise to the era of genomics. Whole-genome data can provide answers to a variety of crucial conservation questions including understanding demography and population structure, minimising inbreeding, maximising adaptive potential, and identifying the basis of important phenotypic traits. Incorporation of genomic data to assist in the recovery of threatened species is vital; however, it is often unclear how reference genomes facilitate the use of genomics in management practice. In this review we use the Tasmanian devil as a model to demonstrate specific examples of how a reference genome can aid management actions in the conservation of threatened species. View this paper.
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14 pages, 1688 KiB  
Article
Coding and Non-Coding RNA Abnormalities in Bipolar Disorder
by Jurjen J. Luykx, Fabrizio Giuliani, Giuliano Giuliani and Jan Veldink
Genes 2019, 10(11), 946; https://doi.org/10.3390/genes10110946 - 19 Nov 2019
Cited by 23 | Viewed by 3957
Abstract
The molecular mechanisms underlying bipolar disorder (BPD) have remained largely unknown. Postmortem brain tissue studies comparing BPD patients with healthy controls have produced a heterogeneous array of potentially implicated protein-coding RNAs. We hypothesized that dysregulation of not only coding, but multiple classes of [...] Read more.
The molecular mechanisms underlying bipolar disorder (BPD) have remained largely unknown. Postmortem brain tissue studies comparing BPD patients with healthy controls have produced a heterogeneous array of potentially implicated protein-coding RNAs. We hypothesized that dysregulation of not only coding, but multiple classes of RNA (coding RNA, long non-coding (lnc) RNA, circular (circ) RNA, and/or alternative splicing) underlie the pathogenesis of BPD. Using non-polyadenylated libraries we performed RNA sequencing in postmortem human medial frontal gyrus tissue from BPD patients and healthy controls. Twenty genes, some of which not previously implicated in BPD, were differentially expressed (DE). PCR validation and replication confirmed the implication of these DE genes. Functional in silico analyses identified enrichment of angiogenesis, vascular system development and histone H3-K4 demethylation. In addition, ten lncRNA transcripts were differentially expressed. Furthermore, an overall increased number of alternative splicing events in BPD was detected, as well as an increase in the number of genes carrying alternative splicing events. Finally, a large reservoir of circRNAs populating brain tissue not affected by BPD is described, while in BPD altered levels of two circular transcripts, cNEBL and cEPHA3, are reported. cEPHA3, hitherto unlinked to BPD, is implicated in developmental processes in the central nervous system. Although we did not perform replication analyses of non-coding RNA findings, our findings hint that RNA dysregulation in BPD is not limited to coding regions, opening avenues for future pharmacological investigations and biomarker research. Full article
(This article belongs to the Special Issue Genetics of Psychiatric Disorders)
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10 pages, 504 KiB  
Article
Genome-Wide Association Study of Body Mass Index and Body Fat in Mexican-Mestizo Children
by Paula Costa-Urrutia, Valentina Colistro, Angélica Saraí Jiménez-Osorio, Helios Cárdenas-Hernández, Jacqueline Solares-Tlapechco, Miryam Ramirez-Alcántara, Julio Granados, Iván de Jesús Ascencio-Montiel and Martha Eunice Rodríguez-Arellano
Genes 2019, 10(11), 945; https://doi.org/10.3390/genes10110945 - 19 Nov 2019
Cited by 18 | Viewed by 4632
Abstract
Background: Childhood obesity is a major health problem in Mexico. Obesity prevalence estimated by body mass index (BMI) is almost half than that estimated by percent body fat (%BF) in the Childhood Obesity pediatric cohort (COIPIS). Objective. We performed a genome-wide association study [...] Read more.
Background: Childhood obesity is a major health problem in Mexico. Obesity prevalence estimated by body mass index (BMI) is almost half than that estimated by percent body fat (%BF) in the Childhood Obesity pediatric cohort (COIPIS). Objective. We performed a genome-wide association study (GWAS) of BMI and %BF in 828 children from the COIPIS to identify markers of predisposition to high values for both phenotypes used for obesity classification. Methods: For the GWAS we used the LAT Axiom 1, Affymetrix and 2.5 million single loci from the 1000 Genomes Phase 3 imputation panel. We used a linear model, adjusted by age, sex, and Amerindian ancestry assuming an additive inheritance model. Results. Genome-wide significance (p ≤ 5.0 × 10−8) and 80% of statistical power was reached for associations of two loci in two genes (CERS3 and CYP2E1) to BMI. Also, 11 loci in six genes (ANKS1B, ARNTL2, KCNS3, LMNB1, SRGAP3, TRPC7) reached genome-wide significance for associations to %BF, though not 80% of statistical power. Discussion: None of the SNPs were previously reported as being associated to BMI or %BF. In addition, different loci were found for BMI and %BF. These results highlight the importance of gaining deeper understanding of genetic markers of predisposition to high values for the phenotypes used for obesity diagnosis. Full article
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18 pages, 6292 KiB  
Article
Dissecting the Regulatory Network of Leaf Premature Senescence in Maize (Zea mays L.) Using Transcriptome Analysis of ZmELS5 Mutant
by Mao Chai, Zhanyong Guo, Xia Shi, Yingbo Li, Jihua Tang and Zhanhui Zhang
Genes 2019, 10(11), 944; https://doi.org/10.3390/genes10110944 - 19 Nov 2019
Cited by 11 | Viewed by 4245
Abstract
Leaf premature senescence largely determines maize (Zea mays L.) grain yield and quality. A natural recessive premature-senescence mutant was selected from the breeding population, and near-isogenic lines were constructed using Jing24 as the recurrent parent. In the near-isogenic lines, the dominant homozygous [...] Read more.
Leaf premature senescence largely determines maize (Zea mays L.) grain yield and quality. A natural recessive premature-senescence mutant was selected from the breeding population, and near-isogenic lines were constructed using Jing24 as the recurrent parent. In the near-isogenic lines, the dominant homozygous material was wild-type (WT), and the recessive material of early leaf senescence was the premature-senescence-type ZmELS5. To identify major genes and regulatory mechanisms involved in leaf senescence, a transcriptome analysis of the ZmELS5 and WT near-isogenic lines (NILs) was performed. A total of 8796 differentially expressed transcripts were identified between ZmELS5 and WT, including 3811 up-regulated and 4985 down-regulated transcripts. By combining gene ontology, Kyoto Encyclopedia of Genes and Genomes, gene set, and transcription factor enrichment analyses, key differentially expressed genes were screened. The senescence regulatory network was predicted based on these key differentially expressed genes, which indicated that the senescence process is mainly regulated by bHLH, WRKY, and AP2/EREBP family transcription factors, leading to the accumulations of jasmonic acid and ethylene. This causes stress responses and reductions in the chlorophyll a/b-binding protein activity level. Then, decreased ATP synthase activity leads to increased photosystem II photodamage, ultimately leading to leaf senescence. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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17 pages, 3026 KiB  
Article
Analysis of Soybean Somatic Embryogenesis Using Chromosome Segment Substitution Lines and Transcriptome Sequencing
by Si-Nan Li, Peng Cheng, Yun-Qi Bai, Yan Shi, Jing-Yao Yu, Rui-Chao Li, Run-Nan Zhou, Zhan-Guo Zhang, Xiao-Xia Wu and Qing-Shan Chen
Genes 2019, 10(11), 943; https://doi.org/10.3390/genes10110943 - 19 Nov 2019
Cited by 4 | Viewed by 3141
Abstract
Soybean is an important cash crop that is widely used as a source of vegetable protein and edible oil. The regeneration ability of soybean directly affects the application of biotechnology. In this study, we used the exogenous hormone 2,4-D to treat immature embryos. [...] Read more.
Soybean is an important cash crop that is widely used as a source of vegetable protein and edible oil. The regeneration ability of soybean directly affects the application of biotechnology. In this study, we used the exogenous hormone 2,4-D to treat immature embryos. Different levels of somatic incidence were selected from the chromosome segment substitution lines (CSSLs) constructed by SN14 and ZYD00006. Transcriptome sequencing of extreme materials was performed, and 2666 differentially expressed genes were obtained. At the same time, a difference table was generated by combining the data on CSSL rearrangement. In the extreme materials, a total of 93 differentially expressed genes were predicted and were then analyzed by cluster analysis and Gene Ontology (GO) annotation. After screening and annotating the target genes, three differentially expressed genes with hormone pathways were identified. The expression patterns of the target genes were verified by real-time quantitative PCR (qRT-PCR). Haplotype polymorphism detection and linkage disequilibrium analysis were performed on the candidate gene Glyma.09g248200. This study provided more information on the regulation network of soybean somatic embryogenesis and regeneration processes, and further identified important genes in the soybean regeneration process and provided a theoretical basis for accelerating the application of biotechnology to soybean for improving its breeding efficiency. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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16 pages, 883 KiB  
Article
SNP-Based Genetic Risk Score Modeling Suggests No Increased Genetic Susceptibility of the Roma Population to Type 2 Diabetes Mellitus
by Nardos Abebe Werissa, Peter Piko, Szilvia Fiatal, Zsigmond Kosa, Janos Sandor and Roza Adany
Genes 2019, 10(11), 942; https://doi.org/10.3390/genes10110942 - 19 Nov 2019
Cited by 23 | Viewed by 4111
Abstract
Background: In a previous survey, an elevated fasting glucose level (FG) and/or known type 2 diabetes mellitus (T2DM) were significantly more frequent in the Roma population than in the Hungarian general population. We assessed whether the distribution of 16 single nucleotide polymorphisms (SNPs) [...] Read more.
Background: In a previous survey, an elevated fasting glucose level (FG) and/or known type 2 diabetes mellitus (T2DM) were significantly more frequent in the Roma population than in the Hungarian general population. We assessed whether the distribution of 16 single nucleotide polymorphisms (SNPs) with unequivocal effects on the development of T2DM contributes to this higher prevalence. Methods: Genetic risk scores, unweighted (GRS) and weighted (wGRS), were computed and compared between the study populations. Associations between GRSs and FG levels and T2DM status were investigated in separate and combined study populations. Results: The Hungarian general population carried a greater genetic risk for the development of T2DM (GRSGeneral = 15.38 ± 2.70 vs. GRSRoma = 14.80 ± 2.68, p < 0.001; wGRSGeneral = 1.41 ± 0.32 vs. wGRSRoma = 1.36 ± 0.31, p < 0.001). In the combined population models, GRSs and wGRSs showed significant associations with elevated FG (p < 0.001) and T2DM (p < 0.001) after adjusting for ethnicity, age, sex, body mass index (BMI), high-density Lipoprotein Cholesterol (HDL-C), and triglyceride (TG). In these models, the effect of ethnicity was relatively strong on both outcomes (FG levels: βethnicity = 0.918, p < 0.001; T2DM status: ORethnicity = 2.484, p < 0.001). Conclusions: The higher prevalence of elevated FG and/or T2DM among Roma does not seem to be directly linked to their increased genetic load but rather to their environmental/cultural attributes. Interventions targeting T2DM prevention among Roma should focus on harmful environmental exposures related to their unhealthy lifestyle. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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33 pages, 2615 KiB  
Review
Evolving Role of RING1 and YY1 Binding Protein in the Regulation of Germ-Cell-Specific Transcription
by Izabella Bajusz, Surya Henry, Enikő Sutus, Gergő Kovács and Melinda K. Pirity
Genes 2019, 10(11), 941; https://doi.org/10.3390/genes10110941 - 19 Nov 2019
Cited by 13 | Viewed by 5538
Abstract
Separation of germline cells from somatic lineages is one of the earliest decisions of embryogenesis. Genes expressed in germline cells include apoptotic and meiotic factors, which are not transcribed in the soma normally, but a number of testis-specific genes are active in numerous [...] Read more.
Separation of germline cells from somatic lineages is one of the earliest decisions of embryogenesis. Genes expressed in germline cells include apoptotic and meiotic factors, which are not transcribed in the soma normally, but a number of testis-specific genes are active in numerous cancer types. During germ cell development, germ-cell-specific genes can be regulated by specific transcription factors, retinoic acid signaling and multimeric protein complexes. Non-canonical polycomb repressive complexes, like ncPRC1.6, play a critical role in the regulation of the activity of germ-cell-specific genes. RING1 and YY1 binding protein (RYBP) is one of the core members of the ncPRC1.6. Surprisingly, the role of Rybp in germ cell differentiation has not been defined yet. This review is focusing on the possible role of Rybp in this process. By analyzing whole-genome transcriptome alterations of the Rybp-/- embryonic stem (ES) cells and correlating this data with experimentally identified binding sites of ncPRC1.6 subunits and retinoic acid receptors in ES cells, we propose a model how germ-cell-specific transcription can be governed by an RYBP centered regulatory network, underlining the possible role of RYBP in germ cell differentiation and tumorigenesis. Full article
(This article belongs to the Special Issue Transcriptional Regulation of Early Embryogenesis)
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9 pages, 3189 KiB  
Review
Biogenesis of Developmental Master Regulatory 27nt-RNAs in Stylonychia—Can Coding RNA Turn into Non-Coding?
by Jan Postberg, Patrick Philipp Weil and Anton Pembaur
Genes 2019, 10(11), 940; https://doi.org/10.3390/genes10110940 - 18 Nov 2019
Cited by 2 | Viewed by 2835
Abstract
In the ciliate Stylonychia, somatic macronuclei differentiate from germline micronuclei during sexual reproduction, accompanied by developmental sequence reduction. Concomitantly, over 95% of micronuclear sequences adopt a heterochromatin structure characterized by the histone variant H3.4 and H3K27me3. RNAi-related genes and histone variants dominate the [...] Read more.
In the ciliate Stylonychia, somatic macronuclei differentiate from germline micronuclei during sexual reproduction, accompanied by developmental sequence reduction. Concomitantly, over 95% of micronuclear sequences adopt a heterochromatin structure characterized by the histone variant H3.4 and H3K27me3. RNAi-related genes and histone variants dominate the list of developmentally expressed genes. Simultaneously, 27nt-ncRNAs that match sequences retained in new macronuclei are synthesized and bound by PIWI1. Recently, we proposed a mechanistic model for ‘RNA-induced DNA replication interference’ (RIRI): during polytene chromosome formation PIWI1/27nt-RNA-complexes target macronucleus-destined sequences (MDS) by base-pairing and temporarily cause locally stalled replication. At polytene chromosomal segments with ongoing replication, H3.4K27me3-nucleosomes become selectively deposited, thus dictating the prospective heterochromatin structure of these areas. Consequently, these micronucleus-specific sequences become degraded, whereas 27nt-RNA-covered sites remain protected. However, the biogenesis of the 27nt-RNAs remains unclear. It was proposed earlier that in stichotrichous ciliates 27nt-RNA precursors could derive from telomere-primed bidirectional transcription of nanochromosomes and subsequent Dicer-like (DCL) activity. As a minimalistic explanation, we propose here that the 27nt-RNA precursor could rather be mRNA or pre-mRNA and that the transition of coding RNA from parental macronuclei to non-coding RNAs, which act in premature developing macronuclei, could involve RNA-dependent RNA polymerase (RDRP) activity creating dsRNA intermediates prior to a DCL-dependent pathway. Interestingly, by such mechanism the partition of a parental somatic genome and possibly also the specific nanochromosome copy numbers could be vertically transmitted to the differentiating nuclei of the offspring. Full article
(This article belongs to the Special Issue Ciliate Genetics and Epigenetics)
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13 pages, 1659 KiB  
Article
Transcriptomic Analysis Reveals Involvement of the Macrophage Migration Inhibitory Factor Gene Network in Duchenne Muscular Dystrophy
by Salvo Danilo Lombardo, Emanuela Mazzon, Katia Mangano, Maria Sofia Basile, Eugenio Cavalli, Santa Mammana, Paolo Fagone, Ferdinando Nicoletti and Maria Cristina Petralia
Genes 2019, 10(11), 939; https://doi.org/10.3390/genes10110939 - 18 Nov 2019
Cited by 16 | Viewed by 3657
Abstract
Duchenne muscular dystrophy (DMD) is a progressive hereditary muscular disease with X-linked recessive inheritance, that leads patients to premature death. The loss of dystrophin determines membrane instability, causing cell damage and inflammatory response. Macrophage migration inhibitory factor (MIF) is a cytokine that exerts [...] Read more.
Duchenne muscular dystrophy (DMD) is a progressive hereditary muscular disease with X-linked recessive inheritance, that leads patients to premature death. The loss of dystrophin determines membrane instability, causing cell damage and inflammatory response. Macrophage migration inhibitory factor (MIF) is a cytokine that exerts pleiotropic properties and is implicated in the pathogenesis of a variety of diseases. Recently, converging data from independent studies have pointed to a possible role of MIF in dystrophic muscle disorders, including DMD. In the present study, we have investigated the modulation of MIF and MIF-related genes in degenerative muscle disorders, by making use of publicly available whole-genome expression datasets. We show here a significant enrichment of MIF and related genes in muscle samples from DMD patients, as well as from patients suffering from Becker’s disease and limb-girdle muscular dystrophy type 2B. On the other hand, transcriptomic analysis of in vitro differentiated myotubes from healthy controls and DMD patients revealed no significant alteration in the expression levels of MIF-related genes. Finally, by analyzing DMD samples as a time series, we show that the modulation of the genes belonging to the MIF network is an early event in the DMD muscle and does not change with the increasing age of the patients, Overall, our analysis suggests that MIF may play a role in vivo during muscle degeneration, likely promoting inflammation and local microenvironment reaction. Full article
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24 pages, 5841 KiB  
Article
Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds
by Rabiul Islam, Yefang Li, Xuexue Liu, Haile Berihulay, Adam Abied, Gebremedhin Gebreselassie, Qing Ma and Yuehui Ma
Genes 2019, 10(11), 938; https://doi.org/10.3390/genes10110938 - 17 Nov 2019
Cited by 45 | Viewed by 6486
Abstract
Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with [...] Read more.
Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat. Full article
(This article belongs to the Special Issue Genomics of Sexual Development and Reproduction in Mammals)
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18 pages, 3969 KiB  
Article
NF-YA Overexpression in Lung Cancer: LUSC
by Eugenia Bezzecchi, Mirko Ronzio, Diletta Dolfini and Roberto Mantovani
Genes 2019, 10(11), 937; https://doi.org/10.3390/genes10110937 - 17 Nov 2019
Cited by 27 | Viewed by 4952
Abstract
The CCAAT box is recognized by the trimeric transcription factor NF-Y, whose NF-YA subunit is present in two major splicing isoforms, NF-YAl (“long”) and NF-YAs (“short”). Little is known about the expression levels of NF-Y subunits in tumors, and nothing in lung cancer. [...] Read more.
The CCAAT box is recognized by the trimeric transcription factor NF-Y, whose NF-YA subunit is present in two major splicing isoforms, NF-YAl (“long”) and NF-YAs (“short”). Little is known about the expression levels of NF-Y subunits in tumors, and nothing in lung cancer. By interrogating RNA-seq TCGA and GEO datasets, we found that, unlike NF-YB/NF-YC, NF-YAs is overexpressed in lung squamous cell carcinomas (LUSC). The ratio of the two isoforms changes from normal to cancer cells, with NF-YAs becoming predominant in the latter. NF-YA increased expression correlates with common proliferation markers. We partitioned all 501 TCGA LUSC tumors in the four molecular cohorts and verified that NF-YAs is similarly overexpressed. We analyzed global and subtype-specific RNA-seq data and found that CCAAT is the most abundant DNA matrix in promoters of genes overexpressed in all subtypes. Enriched Gene Ontology terms are cell-cycle and signaling. Survival curves indicate a worse clinical outcome for patients with increasing global amounts of NF-YA; same with hazard ratios with very high and, surprisingly, very low NF-YAs/NF-YAl ratios. We then analyzed gene expression in this latter cohort and identified a different, pro-migration signature devoid of CCAAT. We conclude that overexpression of the NF-Y regulatory subunit in LUSC has the scope of increasing CCAAT-dependent, proliferative (NF-YAshigh) or CCAAT-less, pro-migration (NF-YAlhigh) genes. The data further reinstate the importance of analysis of single isoforms of TFs involved in tumor development. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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15 pages, 3586 KiB  
Article
A Bi-Exponential Repair Algorithm for Radiation-Induced Double-Strand Breaks: Application to Simulation of Chromosome Aberrations
by Ianik Plante, Tony Slaba, Zarana Shavers and Megumi Hada
Genes 2019, 10(11), 936; https://doi.org/10.3390/genes10110936 - 16 Nov 2019
Cited by 14 | Viewed by 2795
Abstract
Background: Radiation induces DNA double-strand breaks (DSBs), and chromosome aberrations (CA) form during the DSBs repair process. Several methods have been used to model the repair kinetics of DSBs including the bi-exponential model, i.e., N(t) = N1exp(−t/τ1) + N [...] Read more.
Background: Radiation induces DNA double-strand breaks (DSBs), and chromosome aberrations (CA) form during the DSBs repair process. Several methods have been used to model the repair kinetics of DSBs including the bi-exponential model, i.e., N(t) = N1exp(−t/τ1) + N2exp(−t/τ2), where N(t) is the number of breaks at time t, and N1, N2, τ1 and τ2 are parameters. This bi-exponential fit for DSB decay suggests that some breaks are repaired rapidly and other, more complex breaks, take longer to repair. Methods: The bi-exponential repair kinetics model is implemented into a recent simulation code called RITCARD (Radiation Induced Tracks, Chromosome Aberrations, Repair, and Damage). RITCARD simulates the geometric configuration of human chromosomes, radiation-induced breaks, their repair, and the creation of various categories of CAs. The bi-exponential repair relies on a computational algorithm that is shown to be mathematically exact. To categorize breaks as complex or simple, a threshold for the local (voxel) dose was used. Results: The main findings are: i) the curves for the kinetics of restitution of DSBs are mostly independent of dose; ii) the fraction of unrepaired breaks increases with the linear energy transfer (LET) of the incident radiation; iii) the simulated dose–response curves for simple reciprocal chromosome exchanges that are linear-quadratic; iv) the alpha coefficient of the dose–response curve peaks at about 100 keV/µm. Full article
(This article belongs to the Special Issue DNA Damage and Repair after Radiation)
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30 pages, 1172 KiB  
Review
Zebrafish Models of Cancer—New Insights on Modeling Human Cancer in a Non-Mammalian Vertebrate
by Martina Hason and Petr Bartůněk
Genes 2019, 10(11), 935; https://doi.org/10.3390/genes10110935 - 15 Nov 2019
Cited by 120 | Viewed by 15500
Abstract
Zebrafish (Danio rerio) is a valuable non-mammalian vertebrate model widely used to study development and disease, including more recently cancer. The evolutionary conservation of cancer-related programs between human and zebrafish is striking and allows extrapolation of research outcomes obtained in fish [...] Read more.
Zebrafish (Danio rerio) is a valuable non-mammalian vertebrate model widely used to study development and disease, including more recently cancer. The evolutionary conservation of cancer-related programs between human and zebrafish is striking and allows extrapolation of research outcomes obtained in fish back to humans. Zebrafish has gained attention as a robust model for cancer research mainly because of its high fecundity, cost-effective maintenance, dynamic visualization of tumor growth in vivo, and the possibility of chemical screening in large numbers of animals at reasonable costs. Novel approaches in modeling tumor growth, such as using transgene electroporation in adult zebrafish, could improve our knowledge about the spatial and temporal control of cancer formation and progression in vivo. Looking at genetic as well as epigenetic alterations could be important to explain the pathogenesis of a disease as complex as cancer. In this review, we highlight classic genetic and transplantation models of cancer in zebrafish as well as provide new insights on advances in cancer modeling. Recent progress in zebrafish xenotransplantation studies and drug screening has shown that zebrafish is a reliable model to study human cancer and could be suitable for evaluating patient-derived xenograft cell invasiveness. Rapid, large-scale evaluation of in vivo drug responses and kinetics in zebrafish could undoubtedly lead to new applications in personalized medicine and combination therapy. For all of the above-mentioned reasons, zebrafish is approaching a future of being a pre-clinical cancer model, alongside the mouse. However, the mouse will continue to be valuable in the last steps of pre-clinical drug screening, mostly because of the highly conserved mammalian genome and biological processes. Full article
(This article belongs to the Special Issue Animal Modeling in Cancer)
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17 pages, 7502 KiB  
Article
Cytogenetic Analysis Did Not Reveal Differentiated Sex Chromosomes in Ten Species of Boas and Pythons (Reptilia: Serpentes)
by Barbora Augstenová, Sofia Mazzoleni, Alexander Kostmann, Marie Altmanová, Daniel Frynta, Lukáš Kratochvíl and Michail Rovatsos
Genes 2019, 10(11), 934; https://doi.org/10.3390/genes10110934 - 15 Nov 2019
Cited by 13 | Viewed by 5367
Abstract
Homologous and differentiated ZZ/ZW sex chromosomes (or derived multiple neo-sex chromosomes) were often described in caenophidian snakes, but sex chromosomes were unknown until recently in non-caenophidian snakes. Previous studies revealed that two species of boas (Boa imperator, B. constrictor) and [...] Read more.
Homologous and differentiated ZZ/ZW sex chromosomes (or derived multiple neo-sex chromosomes) were often described in caenophidian snakes, but sex chromosomes were unknown until recently in non-caenophidian snakes. Previous studies revealed that two species of boas (Boa imperator, B. constrictor) and one species of python (Python bivittatus) independently evolved XX/XY sex chromosomes. In addition, heteromorphic ZZ/ZW sex chromosomes were recently revealed in the Madagascar boa (Acrantophis sp. cf. dumerili) and putatively also in the blind snake Myriopholis macrorhyncha. Since the evolution of sex chromosomes in non-caenophidian snakes seems to be more complex than previously thought, we examined ten species of pythons and boas representing the families Boidae, Calabariidae, Candoiidae, Charinidae, Pythonidae, and Sanziniidae by conventional and molecular cytogenetic methods, aiming to reveal their sex chromosomes. Our results show that all examined species do not possess sex-specific differences in their genomes detectable by the applied cytogenetic methods, indicating the presence of poorly differentiated sex chromosomes or even the absence of sex chromosomes. Interestingly, fluorescence in situ hybridization with telomeric repeats revealed extensive distribution of interstitial telomeric repeats in eight species, which are likely a consequence of intra-chromosomal rearrangements. Full article
(This article belongs to the Special Issue Chromosome-Centric View of the Genome Organization and Evolution)
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19 pages, 3937 KiB  
Article
Enriching Human Interactome with Functional Mutations to Detect High-Impact Network Modules Underlying Complex Diseases
by Hongzhu Cui, Suhas Srinivasan and Dmitry Korkin
Genes 2019, 10(11), 933; https://doi.org/10.3390/genes10110933 - 15 Nov 2019
Cited by 9 | Viewed by 4740
Abstract
Rapid progress in high-throughput -omics technologies moves us one step closer to the datacalypse in life sciences. In spite of the already generated volumes of data, our knowledge of the molecular mechanisms underlying complex genetic diseases remains limited. Increasing evidence shows that biological [...] Read more.
Rapid progress in high-throughput -omics technologies moves us one step closer to the datacalypse in life sciences. In spite of the already generated volumes of data, our knowledge of the molecular mechanisms underlying complex genetic diseases remains limited. Increasing evidence shows that biological networks are essential, albeit not sufficient, for the better understanding of these mechanisms. The identification of disease-specific functional modules in the human interactome can provide a more focused insight into the mechanistic nature of the disease. However, carving a disease network module from the whole interactome is a difficult task. In this paper, we propose a computational framework, Discovering most IMpacted SUbnetworks in interactoMe (DIMSUM), which enables the integration of genome-wide association studies (GWAS) and functional effects of mutations into the protein–protein interaction (PPI) network to improve disease module detection. Specifically, our approach incorporates and propagates the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) on PPIs to implicate the genes that are most likely influenced by the disruptive mutations, and to identify the module with the greatest functional impact. Comparison against state-of-the-art seed-based module detection methods shows that our approach could yield modules that are biologically more relevant and have stronger association with the studied disease. We expect for our method to become a part of the common toolbox for the disease module analysis, facilitating the discovery of new disease markers. Full article
(This article belongs to the Special Issue Current Advances in Network Biology for Disease Understanding)
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26 pages, 4861 KiB  
Review
Cell-Specific DNA Methylation Signatures in Asthma
by Andrée-Anne Hudon Thibeault and Catherine Laprise
Genes 2019, 10(11), 932; https://doi.org/10.3390/genes10110932 - 15 Nov 2019
Cited by 28 | Viewed by 5577
Abstract
Asthma is a complex trait, often associated with atopy. The genetic contribution has been evidenced by familial occurrence. Genome-wide association studies allowed for associating numerous genes with asthma, as well as identifying new loci that have a minor contribution to its phenotype. Considering [...] Read more.
Asthma is a complex trait, often associated with atopy. The genetic contribution has been evidenced by familial occurrence. Genome-wide association studies allowed for associating numerous genes with asthma, as well as identifying new loci that have a minor contribution to its phenotype. Considering the role of environmental exposure on asthma development, an increasing amount of literature has been published on epigenetic modifications associated with this pathology and especially on DNA methylation, in an attempt to better understand its missing heritability. These studies have been conducted in different tissues, but mainly in blood or its peripheral mononuclear cells. However, there is growing evidence that epigenetic changes that occur in one cell type cannot be directly translated into another one. In this review, we compare alterations in DNA methylation from different cells of the immune system and of the respiratory tract. The cell types in which data are obtained influences the global status of alteration of DNA methylation in asthmatic individuals compared to control (an increased or a decreased DNA methylation). Given that several genes were cell-type-specific, there is a great need for comparative studies on DNA methylation from different cells, but from the same individuals in order to better understand the role of epigenetics in asthma pathophysiology. Full article
(This article belongs to the Special Issue Genetic Susceptibility to Allergic Conditions: A Focus on Epigenetic Mechanisms)
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17 pages, 2268 KiB  
Article
HisCoM-PAGE: Hierarchical Structural Component Models for Pathway Analysis of Gene Expression Data
by Lydia Mok, Yongkang Kim, Sungyoung Lee, Sungkyoung Choi, Seungyeoun Lee, Jin-Young Jang and Taesung Park
Genes 2019, 10(11), 931; https://doi.org/10.3390/genes10110931 - 14 Nov 2019
Cited by 6 | Viewed by 4234
Abstract
Although there have been several analyses for identifying cancer-associated pathways, based on gene expression data, most of these are based on single pathway analyses, and thus do not consider correlations between pathways. In this paper, we propose a hierarchical structural component model for [...] Read more.
Although there have been several analyses for identifying cancer-associated pathways, based on gene expression data, most of these are based on single pathway analyses, and thus do not consider correlations between pathways. In this paper, we propose a hierarchical structural component model for pathway analysis of gene expression data (HisCoM-PAGE), which accounts for the hierarchical structure of genes and pathways, as well as the correlations among pathways. Specifically, HisCoM-PAGE focuses on the survival phenotype and identifies its associated pathways. Moreover, its application to real biological data analysis of pancreatic cancer data demonstrated that HisCoM-PAGE could successfully identify pathways associated with pancreatic cancer prognosis. Simulation studies comparing the performance of HisCoM-PAGE with other competing methods such as Gene Set Enrichment Analysis (GSEA), Global Test, and Wald-type Test showed HisCoM-PAGE to have the highest power to detect causal pathways in most simulation scenarios. Full article
(This article belongs to the Special Issue Selected Papers from the 15th International Conference on Bioinformatics (BIOINFO 2019))
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16 pages, 7080 KiB  
Article
Increased Leaf Nicotine Content by Targeting Transcription Factor Gene Expression in Commercial Flue-Cured Tobacco (Nicotiana tabacum L.)
by Hai Liu, Tatyana I. Kotova and Michael P. Timko
Genes 2019, 10(11), 930; https://doi.org/10.3390/genes10110930 - 14 Nov 2019
Cited by 14 | Viewed by 4471
Abstract
Nicotine, the most abundant pyridine alkaloid in cultivated tobacco (Nicotiana tabacum L.), is a potent inhibitor of insect and animal herbivory and a neurostimulator of human brain function. Nicotine biosynthesis is controlled developmentally and can be induced by abiotic and biotic stressors [...] Read more.
Nicotine, the most abundant pyridine alkaloid in cultivated tobacco (Nicotiana tabacum L.), is a potent inhibitor of insect and animal herbivory and a neurostimulator of human brain function. Nicotine biosynthesis is controlled developmentally and can be induced by abiotic and biotic stressors via a jasmonic acid (JA)-mediated signal transduction mechanism involving members of the APETALA 2/ethylene-responsive factor (AP2/ERF) and basic helix-loop-helix (bHLH) transcription factor (TF) families. AP2/ERF and bHLH TFs work combinatorically to control nicotine biosynthesis and its subsequent accumulation in tobacco leaves. Here, we demonstrate that overexpression of the tobacco NtERF32, NtERF221/ORC1, and NtMYC2a TFs leads to significant increases in nicotine accumulation in T2 transgenic K326 tobacco plants before topping. Up to 9-fold higher nicotine production was achieved in transgenics overexpressing NtERF221/ORC1 under the control of a constitutive GmUBI3 gene promoter compared to wild-type plants. The constitutive 2XCaMV35S promoter and a novel JA-inducible 4XGAG promoter were less effective in driving high-level nicotine formation. Methyljasmonic acid (MeJA) treatment further elevated nicotine production in all transgenic lines. Our results show that targeted manipulation of NtERF221/ORC1 is an effective strategy for elevating leaf nicotine levels in commercial tobacco for use in the preparation of reduced risk tobacco products for smoking replacement therapeutics. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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18 pages, 4401 KiB  
Article
Genomic Variance and Transcriptional Comparisons Reveal the Mechanisms of Leaf Color Affecting Palatability and Stressed Defense in Tea Plant
by Xuewen Wang, Ben-ying Liu, Qingshi Zhao, Xuemei Sun, Youyong Li, Zhifen Duan, Xinli Miao, Shan Luo and Jianbin Li
Genes 2019, 10(11), 929; https://doi.org/10.3390/genes10110929 - 14 Nov 2019
Cited by 18 | Viewed by 3893
Abstract
Leaves are one of the most important organs of plants, and yet, the association between leaf color and consumable traits remains largely unclear. Tea leaves are an ideal study system with which to investigate the mechanism of how leaf coloration affects palatability, since [...] Read more.
Leaves are one of the most important organs of plants, and yet, the association between leaf color and consumable traits remains largely unclear. Tea leaves are an ideal study system with which to investigate the mechanism of how leaf coloration affects palatability, since tea is made from the leaves of the crop Camellia sinensis. Our genomic resequencing analysis of a tea cultivar ZiJuan (ZJ) with purple leaves and altered flavor revealed genetic variants when compared with the green-leaf, wild type cultivar YunKang(YK). RNA-Seq based transcriptomic comparisons of the bud and two youngest leaves in ZJ and YK identified 93%, 9% and 5% expressed genes that were shared in YK- and ZJ-specific cultivars, respectively. A comparison of both transcript abundance and particular metabolites revealed that the high expression of gene UFGT for anthocyanin biosynthesis is responsible for purple coloration, which competes with the intermediates for catechin-like flavanol biosynthesis. Genes with differential expression are enriched in response to stress, heat and defense, and are casually correlated with the environmental stress of ZJ plant origin in the Himalayas. In addition, the highly expressed C4H and LDOX genes for synthesizing flavanol precursors, ZJ-specific CLH1 for degrading chlorophyll, alternatively spliced C4H and FDR and low photosynthesis also contributed to the altered color and flavor of ZJ. Thus, our study provides a better molecular understanding of the effect of purple coloration on leaf flavor, and helps to guide future engineering improvement of palatability. Full article
(This article belongs to the Special Issue Recent Advances in Orphan Crop Genetics and Genomics)
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15 pages, 589 KiB  
Review
Cdx2 Animal Models Reveal Developmental Origins of Cancers
by Kallayanee Chawengsaksophak
Genes 2019, 10(11), 928; https://doi.org/10.3390/genes10110928 - 14 Nov 2019
Cited by 12 | Viewed by 3886
Abstract
The Cdx2 homeobox gene is important in assigning positional identity during the finely orchestrated process of embryogenesis. In adults, regenerative responses to tissues damage can require a replay of these same developmental pathways. Errors in reassigning positional identity during regeneration can cause metaplasias—normal [...] Read more.
The Cdx2 homeobox gene is important in assigning positional identity during the finely orchestrated process of embryogenesis. In adults, regenerative responses to tissues damage can require a replay of these same developmental pathways. Errors in reassigning positional identity during regeneration can cause metaplasias—normal tissue arising in an abnormal location—and this in turn, is a well-recognized cancer risk factor. In animal models, a gain of Cdx2 function can elicit a posterior shift in tissue identity, modeling intestinal-type metaplasias of the esophagus (Barrett’s esophagus) and stomach. Conversely, loss of Cdx2 function can elicit an anterior shift in tissue identity, inducing serrated-type lesions expressing gastric markers in the colon. These metaplasias are major risk factors for the later development of esophageal, stomach and colon cancer. Leukemia, another cancer in which Cdx2 is ectopically expressed, may have mechanistic parallels with epithelial cancers in terms of stress-induced reprogramming. This review will address how animal models have refined our understanding of the role of Cdx2 in these common human cancers. Full article
(This article belongs to the Special Issue Animal Modeling in Cancer)
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18 pages, 3711 KiB  
Review
The Critical Role of Hypoxic Microenvironment and Epigenetic Deregulation in Esophageal Cancer Radioresistance
by Catarina Macedo-Silva, Vera Miranda-Gonçalves, Rui Henrique, Carmen Jerónimo and Isabel Bravo
Genes 2019, 10(11), 927; https://doi.org/10.3390/genes10110927 - 14 Nov 2019
Cited by 24 | Viewed by 5046
Abstract
Esophageal cancer (EC) is the seventh most common cancer worldwide and the sixth leading cause of death, according to Globocan 2018. Despite efforts made for therapeutic advances, EC remains highly lethal, portending a five-year overall survival of just 15–20%. Hence, the discovery of [...] Read more.
Esophageal cancer (EC) is the seventh most common cancer worldwide and the sixth leading cause of death, according to Globocan 2018. Despite efforts made for therapeutic advances, EC remains highly lethal, portending a five-year overall survival of just 15–20%. Hence, the discovery of new molecular targets that might improve therapeutic efficacy is urgently needed. Due to high proliferative rates and also the limited oxygen and nutrient diffusion in tumors, the development of hypoxic regions and consequent activation of hypoxia-inducible factors (HIFs) are a common characteristic of solid tumors, including EC. Accordingly, HIF-1α, involved in cell cycle deregulation, apoptosis, angiogenesis induction and proliferation in cancer, constitutes a predictive marker of resistance to radiotherapy (RT). Deregulation of epigenetic mechanisms, including aberrant DNA methylation and histone modifications, have emerged as critical factors in cancer development and progression. Recently, interactions between epigenetic enzymes and HIF-1α transcription factors have been reported. Thus, further insight into hypoxia-induced epigenetic alterations in EC may allow the identification of novel therapeutic targets and predictive biomarkers, impacting on patient survival and quality of life. Full article
(This article belongs to the Special Issue DNA Damage and Repair after Radiation)
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13 pages, 2681 KiB  
Article
CNV Detection from Circulating Tumor DNA in Late Stage Non-Small Cell Lung Cancer Patients
by Hao Peng, Lan Lu, Zisong Zhou, Jian Liu, Dadong Zhang, Kejun Nan, Xiaochen Zhao, Fugen Li, Lei Tian, Hua Dong and Yu Yao
Genes 2019, 10(11), 926; https://doi.org/10.3390/genes10110926 - 14 Nov 2019
Cited by 36 | Viewed by 6241
Abstract
While methods for detecting SNVs and indels in circulating tumor DNA (ctDNA) with hybridization capture-based next-generation sequencing (NGS) have been available, copy number variations (CNVs) detection is more challenging. Here, we present a method enabling CNV detection from a 150-gene panel using a [...] Read more.
While methods for detecting SNVs and indels in circulating tumor DNA (ctDNA) with hybridization capture-based next-generation sequencing (NGS) have been available, copy number variations (CNVs) detection is more challenging. Here, we present a method enabling CNV detection from a 150-gene panel using a very low amount of ctDNA. First, a read depth-based CNV estimation method without a paired blood sample was developed and cfDNA sequencing data from healthy people were used to build a panel of normal (PoN) model. Then, in silico and in vitro simulations were performed to define the limit of detection (LOD) for EGFR, ERBB2, and MET. Compared to the WES results of the 48 samples, the concordance rate for EGFR, ERBB2, and MET CNVs was 78%, 89.6%, and 92.4%, respectively. In another cohort profiled with the 150-gene panel from 5980 lung cancer ctDNA samples, we detected the three genes’ amplification with comparable population frequency with other cohorts. One lung adenocarcinoma patient with MET amplification detected by our method reached partial response to crizotinib. These findings show that our ctDNA CNV detection pipeline can detect CNVs with high specificity and concordance, which enables CNV calling in a non-invasive way for cancer patients when tissues are not available. Full article
(This article belongs to the Special Issue Selected Papers from the International Conference on Intelligent Biology and Medicine (ICIBM 2019))
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19 pages, 1931 KiB  
Review
Tomato Natural Resistance Genes in Controlling the Root-Knot Nematode
by Ahmed H. El-Sappah, Islam M. M., Hamada H. El-awady, Shi Yan, Shiming Qi, Jingyi Liu, Guo-ting Cheng and Yan Liang
Genes 2019, 10(11), 925; https://doi.org/10.3390/genes10110925 - 14 Nov 2019
Cited by 71 | Viewed by 11014
Abstract
The root-knot nematode (RKN) is one of the most dangerous and widespread types of nematodes affecting tomatoes. There are few methods for controlling nematodes in tomatoes. Nature resistance genes (R-genes) are important in conferring resistance against nematodes. These genes that confer resistance to [...] Read more.
The root-knot nematode (RKN) is one of the most dangerous and widespread types of nematodes affecting tomatoes. There are few methods for controlling nematodes in tomatoes. Nature resistance genes (R-genes) are important in conferring resistance against nematodes. These genes that confer resistance to the RKN have already been identified as Mi-1, Mi-2, Mi-3, Mi-4, Mi-5, Mi-6, Mi-7, Mi-8, Mi-9, and Mi-HT. Only five of these genes have been mapped. The major problem is that their resistance breaks down at high temperatures. Some of these genes still work at high temperatures. In this paper, the mechanism and characteristics of these natural resistance genes are summarized. Other difficulties in using these genes in the resistance and how to improve them are also mentioned. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)
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12 pages, 1403 KiB  
Article
Global Vectors Representation of Protein Sequences and Its Application for Predicting Self-Interacting Proteins with Multi-Grained Cascade Forest Model
by Zhan-Heng Chen, Zhu-Hong You, Wen-Bo Zhang, Yan-Bin Wang, Li Cheng and Daniyal Alghazzawi
Genes 2019, 10(11), 924; https://doi.org/10.3390/genes10110924 - 12 Nov 2019
Cited by 9 | Viewed by 2588
Abstract
Self-interacting proteins (SIPs) is of paramount importance in current molecular biology. There have been developed a number of traditional biological experiment methods for predicting SIPs in the past few years. However, these methods are costly, time-consuming and inefficient, and often limit their usage [...] Read more.
Self-interacting proteins (SIPs) is of paramount importance in current molecular biology. There have been developed a number of traditional biological experiment methods for predicting SIPs in the past few years. However, these methods are costly, time-consuming and inefficient, and often limit their usage for predicting SIPs. Therefore, the development of computational method emerges at the times require. In this paper, we for the first time proposed a novel deep learning model which combined natural language processing (NLP) method for potential SIPs prediction from the protein sequence information. More specifically, the protein sequence is de novo assembled by k-mers. Then, we obtained the global vectors representation for each protein sequences by using natural language processing (NLP) technique. Finally, based on the knowledge of known self-interacting and non-interacting proteins, a multi-grained cascade forest model is trained to predict SIPs. Comprehensive experiments were performed on yeast and human datasets, which obtained an accuracy rate of 91.45% and 93.12%, respectively. From our evaluations, the experimental results show that the use of amino acid semantics information is very helpful for addressing the problem of sequences containing both self-interacting and non-interacting pairs of proteins. This work would have potential applications for various biological classification problems. Full article
(This article belongs to the Section Technologies and Resources for Genetics)
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27 pages, 2028 KiB  
Article
Proteomics Recapitulates Ovarian Proteins Relevant to Puberty and Fertility in Brahman Heifers (Bos indicus L.)
by Muhammad S. Tahir, Loan T. Nguyen, Benjamin L. Schulz, Gry A. Boe-Hansen, Milton G. Thomas, Stephen S. Moore, Li Yieng Lau and Marina R. S. Fortes
Genes 2019, 10(11), 923; https://doi.org/10.3390/genes10110923 - 12 Nov 2019
Cited by 15 | Viewed by 3958
Abstract
High fertility and early puberty in Bos indicus heifers are desirable and genetically correlated traits in beef production. The hypothalamus–pituitary–ovarian (HPO) axis synthesizes steroid hormones, which contribute to the shift from the pre-pubertal state into the post-pubertal state and influence subsequent fertility. Understanding [...] Read more.
High fertility and early puberty in Bos indicus heifers are desirable and genetically correlated traits in beef production. The hypothalamus–pituitary–ovarian (HPO) axis synthesizes steroid hormones, which contribute to the shift from the pre-pubertal state into the post-pubertal state and influence subsequent fertility. Understanding variations in abundance of proteins that govern steroid synthesis and ovarian signaling pathways remains crucial to understanding puberty and fertility. We used whole ovaries of six pre-pubertal and six post-pubertal Brahman heifers to conduct differential abundance analyses of protein profiles between the two physiological states. Extracted proteins were digested into peptides followed by identification and quantification with massspectrometry (MS) by sequential window acquisition of all instances of theoretical fragment ion mass spectrometry (SWATH-MS). MS and statistical analysis identified 566 significantly differentially abundant (DA) proteins (adjusted p < 0.05), which were then analyzed for gene ontology and pathway enrichment. Our data indicated an up-regulation of steroidogenic proteins contributing to progesterone synthesis at luteal phase post-puberty. Proteins related to progesterone signaling, TGF-β, retinoic acid, extracellular matrix, cytoskeleton, and pleiotrophin signaling were DA in this study. The DA proteins probably relate to the formation and function of the corpus luteum, which is only present after ovulation, post-puberty. Some DA proteins might also be related to granulosa cells signaling, which regulates oocyte maturation or arrest in ovaries prior to ovulation. Ten DA proteins were coded by genes previously associated with reproductive traits according to the animal quantitative trait loci (QTL) database. In conclusion, the DA proteins and their pathways were related to ovarian activity in Bos indicus cattle. The genes that code for these proteins may explain some known QTLs and could be targeted in future genetic studies. Full article
(This article belongs to the Special Issue Genomics of Sexual Development and Reproduction in Mammals)
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10 pages, 493 KiB  
Article
A Weighted Genomic Relationship Matrix Based on Fixation Index (FST) Prioritized SNPs for Genomic Selection
by Ling-Yun Chang, Sajjad Toghiani, El Hamidi Hay, Samuel E. Aggrey and Romdhane Rekaya
Genes 2019, 10(11), 922; https://doi.org/10.3390/genes10110922 - 12 Nov 2019
Cited by 7 | Viewed by 3730
Abstract
A dramatic increase in the density of marker panels has been expected to increase the accuracy of genomic selection (GS), unfortunately, little to no improvement has been observed. By including all variants in the association model, the dimensionality of the problem should be [...] Read more.
A dramatic increase in the density of marker panels has been expected to increase the accuracy of genomic selection (GS), unfortunately, little to no improvement has been observed. By including all variants in the association model, the dimensionality of the problem should be dramatically increased, and it could undoubtedly reduce the statistical power. Using all Single nucleotide polymorphisms (SNPs) to compute the genomic relationship matrix (G) does not necessarily increase accuracy as the additive relationships can be accurately estimated using a much smaller number of markers. Due to these limitations, variant prioritization has become a necessity to improve accuracy. The fixation index (FST) as a measure of population differentiation has been used to identify genome segments and variants under selection pressure. Using prioritized variants has increased the accuracy of GS. Additionally, FST can be used to weight the relative contribution of prioritized SNPs in computing G. In this study, relative weights based on FST scores were developed and incorporated into the calculation of G and their impact on the estimation of variance components and accuracy was assessed. The results showed that prioritizing SNPs based on their FST scores resulted in an increase in the genetic similarity between training and validation animals and improved the accuracy of GS by more than 5%. Full article
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13 pages, 1303 KiB  
Article
Wnt-11 Expression Promotes Invasiveness and Correlates with Survival in Human Pancreatic Ductal Adeno Carcinoma
by Dafydd A. Dart, Damla E Arisan, Sioned Owen, Chunyi Hao, Wen G. Jiang and Pinar Uysal-Onganer
Genes 2019, 10(11), 921; https://doi.org/10.3390/genes10110921 - 11 Nov 2019
Cited by 11 | Viewed by 3429
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest forms of cancer, proving difficult to manage clinically. Wnt-11, a developmentally regulated gene producing a secreted protein, has been associated with various carcinomas but has not previously been studied in PDAC. The present study [...] Read more.
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest forms of cancer, proving difficult to manage clinically. Wnt-11, a developmentally regulated gene producing a secreted protein, has been associated with various carcinomas but has not previously been studied in PDAC. The present study aimed to elucidate these aspects first in vitro and then in a clinical setting in vivo. Molecular analyses of Wnt-11 expression as well as other biomarkers involved qRT-PCR, RNA-seq and siRNA. Proliferation was measured by MTT; invasiveness was quantified by Boyden chamber (Matrigel) assay. Wnt-11 mRNA was present in three different human PDAC cell lines. Wnt-11 loss affected epithelial-mesenchymal transition and expression of neuronal and stemness biomarkers associated with metastasis. Indeed, silencing Wnt-11 in Panc-1 cells significantly inhibited their Matrigel invasiveness without affecting their proliferative activity. Consistently with the in vitro data, human biopsies of PDAC showed significantly higher Wnt-11 mRNA levels compared with matched adjacent tissues. Expression was significantly upregulated during PDAC progression (TNM stage I to II) and maintained (TNM stages III and IV). Wnt-11 is expressed in PDAC in vitro and in vivo and plays a significant role in the pathophysiology of the disease; this evidence leads to the conclusion that Wnt-11 could serve as a novel, functional biomarker PDAC. Full article
(This article belongs to the Special Issue Wnt Signaling in Development, Regeneration and Cancer)
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17 pages, 4671 KiB  
Article
RNA Sequencing Reveals That Both Abiotic and Biotic Stress-Responsive Genes are Induced during Expression of Steroidal Glycoalkaloid in Potato Tuber Subjected to Light Exposure
by Weina Zhang, Cunwu Zuo, Zhongjian Chen, Yichen Kang and Shuhao Qin
Genes 2019, 10(11), 920; https://doi.org/10.3390/genes10110920 - 11 Nov 2019
Cited by 11 | Viewed by 4530
Abstract
Steroidal glycoalkaloids (SGAs), which are widely produced by potato, even in other Solanaceae plants, are a class of potentially toxic compounds, but are beneficial to host resistance. However, changes of the other metabolic process along with SGA accumulation are still poorly understood and [...] Read more.
Steroidal glycoalkaloids (SGAs), which are widely produced by potato, even in other Solanaceae plants, are a class of potentially toxic compounds, but are beneficial to host resistance. However, changes of the other metabolic process along with SGA accumulation are still poorly understood and researched. Based on RNA sequencing (RNA-seq) and bioinformatics analysis, the global gene expression profiles of potato variety Helan 15 (Favorita) was investigated at four-time points during light exposure. The data was further verified by using quantitative Real-time PCR (qRT-PCR). When compared to the control group, 1288, 1592, 1737, and 1870 differentially expressed genes (DEGs) were detected at 6 h, 24 h, 48 h, and 8 d, respectively. The results of both RNAseq and qRT-PCR showed that SGA biosynthetic genes were up-regulated in the potato tuber under light exposure. Functional enrichment analysis revealed that genes related to PS light reaction and Protein degradation were significantly enriched in most time points of light exposure. Additionally, enriched Bins included Receptor kinases, Secondary metabolic process in flavonoids, Abiotic stress, and Biotic stress in the early stage of light exposure, but PS Calvin cycle, RNA regulation of transcription, and UDP glucosyl and glucoronyl transferases in the later stage. Most of the DEGs involved in PS light reaction and Abiotic stress were up-regulated at all four time points, whereas DEGs that participated in biotic stresses were mainly up-regulated at the later stage (48 h and 8 d). Cis-element prediction and co-expression assay were used to confirm the expressional correlation between genes that are responsible for SGA biosynthesis and disease resistance. In conclusion, the expressions of genes involved in PS light reaction, Abiotic stress, and Biotic stress were obviously aroused during the accumulation of SGAs induced by light exposure. Moreover, an increased defense response might contribute to the potato resistance to the infection by phytopathogenic microorganisms. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)
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10 pages, 1083 KiB  
Article
X-Linked Emery–Dreifuss Muscular Dystrophy: Study Of X-Chromosome Inactivation and Its Relation with Clinical Phenotypes in Female Carriers
by Emanuela Viggiano, Agnieszka Madej-Pilarczyk, Nicola Carboni, Esther Picillo, Manuela Ergoli, Stefania del Gaudio, Michal Marchel, Gerardo Nigro, Alberto Palladino and Luisa Politano
Genes 2019, 10(11), 919; https://doi.org/10.3390/genes10110919 - 11 Nov 2019
Cited by 7 | Viewed by 3070
Abstract
X-linked Emery–Dreifuss muscular dystrophy (EDMD1) affects approximately 1:100,000 male births. Female carriers are usually asymptomatic but, in some cases, they may present clinical symptoms after age 50 at cardiac level, especially in the form of conduction tissue anomalies. The aim of this study [...] Read more.
X-linked Emery–Dreifuss muscular dystrophy (EDMD1) affects approximately 1:100,000 male births. Female carriers are usually asymptomatic but, in some cases, they may present clinical symptoms after age 50 at cardiac level, especially in the form of conduction tissue anomalies. The aim of this study was to evaluate the relation between heart involvement in symptomatic EDMD1 carriers and the X-chromosome inactivation (XCI) pattern. The XCI pattern was determined on the lymphocytes of 30 symptomatic and asymptomatic EDMD1 female carriers—25 familial and 5 sporadic cases—seeking genetic advice using the androgen receptor (AR) methylation-based assay. Carriers were subdivided according to whether they were above or below 50 years of age. A variance analysis was performed to compare the XCI pattern between symptomatic and asymptomatic carriers. The results show that 20% of EDMD1 carriers had cardiac symptoms, and that 50% of these were ≥50 years of age. The XCI pattern was similar in both symptomatic and asymptomatic carriers. Conclusions: Arrhythmias in EDMD1 carriers poorly correlate on lymphocytes to a skewed XCI, probably due to (a) the different embryological origin of cardiac conduction tissue compared to lymphocytes or (b) the preferential loss of atrial cells replaced by fibrous tissue. Full article
(This article belongs to the Special Issue Selected Papers from the International Workshop on Fragile X and Other Neurodevelopmental Disorders)
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11 pages, 2257 KiB  
Article
Restrictive Cardiomyopathy is Caused by a Novel Homozygous Desmin (DES) Mutation p.Y122H Leading to a Severe Filament Assembly Defect
by Andreas Brodehl, Seyed Ahmad Pour Hakimi, Caroline Stanasiuk, Sandra Ratnavadivel, Doris Hendig, Anna Gaertner, Brenda Gerull, Jan Gummert, Lech Paluszkiewicz and Hendrik Milting
Genes 2019, 10(11), 918; https://doi.org/10.3390/genes10110918 - 11 Nov 2019
Cited by 52 | Viewed by 4838
Abstract
Here, we present a small Iranian family, where the index patient received a diagnosis of restrictive cardiomyopathy (RCM) in combination with atrioventricular (AV) block. Genetic analysis revealed a novel homozygous missense mutation in the DES gene (c.364T > C; p.Y122H), which is absent [...] Read more.
Here, we present a small Iranian family, where the index patient received a diagnosis of restrictive cardiomyopathy (RCM) in combination with atrioventricular (AV) block. Genetic analysis revealed a novel homozygous missense mutation in the DES gene (c.364T > C; p.Y122H), which is absent in human population databases. The mutation is localized in the highly conserved coil-1 desmin subdomain. In silico, prediction tools indicate a deleterious effect of the desmin (DES) mutation p.Y122H. Consequently, we generated an expression plasmid encoding the mutant and wildtype desmin formed, and analyzed the filament formation in vitro in cardiomyocytes derived from induced pluripotent stem cells and HT-1080 cells. Confocal microscopy revealed a severe filament assembly defect of mutant desmin supporting the pathogenicity of the DES mutation, p.Y122H, whereas the wildtype desmin formed regular intermediate filaments. According to the guidelines of the American College of Medical Genetics and Genomics, we classified this mutation, therefore, as a novel pathogenic mutation. Our report could point to a recessive inheritance of the DES mutation, p.Y122H, which is important for the genetic counseling of similar families with restrictive cardiomyopathy caused by DES mutations. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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15 pages, 1448 KiB  
Article
A Novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data
by Ruizheng Tian, Cunhuan Zhang, Yixiao Huang, Xin Guo and Maohua Chen
Genes 2019, 10(11), 917; https://doi.org/10.3390/genes10110917 - 11 Nov 2019
Cited by 5 | Viewed by 2962
Abstract
Traditional methods for developing polymorphic microsatellite loci without reference sequences are time-consuming and labor-intensive, and the polymorphisms of simple sequence repeat (SSR) loci developed from expressed sequence tag (EST) databases are generally poor. To address this issue, in this study, we developed a [...] Read more.
Traditional methods for developing polymorphic microsatellite loci without reference sequences are time-consuming and labor-intensive, and the polymorphisms of simple sequence repeat (SSR) loci developed from expressed sequence tag (EST) databases are generally poor. To address this issue, in this study, we developed a new software (PSSRdt) and established an effective method for directly obtaining polymorphism details of SSR loci by analyzing diverse transcriptome data. The new method includes three steps, raw data processing, PSSRdt application, and loci extraction and verification. To test the practicality of the method, we successfully obtained 1940 potential polymorphic SSRs from the transcript dataset combined with 44 pea aphid transcriptomes. Fifty-two SSR loci obtained by the new method were selected for validating the polymorphic characteristics by genotyping in pea aphid individuals. The results showed that over 92% of SSR loci were polymorphic and 73.1% of loci were highly polymorphic. Our new software and method provide an innovative approach to microsatellite development based on RNA-seq data, and open a new path for the rapid mining of numerous loci with polymorphism to add to the body of research on microsatellites. Full article
(This article belongs to the Section Technologies and Resources for Genetics)
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