Editor’s Choice Articles

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to readers, or important in the respective research area. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

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13 pages, 3223 KiB  
Article
BcTFIIIA Negatively Regulates Turnip Mosaic Virus Infection through Interaction with Viral CP and VPg Proteins in Pak Choi (Brassica campestris ssp. chinensis)
by Rujia Zhang, Changwei Zhang, Shanwu Lyu, Huiyuan Wu, Mengguo Yuan, Zhiyuan Fang, Fangfang Li and Xilin Hou
Genes 2022, 13(7), 1209; https://doi.org/10.3390/genes13071209 - 6 Jul 2022
Cited by 1 | Viewed by 2289
Abstract
TFIIIA is a zinc-finger transcription factor that is involved in post-transcriptional regulation during development. Here, the BcTFIIIA gene was isolated from pak choi. Sequence analysis showed that BcTFIIIA encodes 383 amino acids (aa) with an open reading frame (ORF) of 1152 base pairs [...] Read more.
TFIIIA is a zinc-finger transcription factor that is involved in post-transcriptional regulation during development. Here, the BcTFIIIA gene was isolated from pak choi. Sequence analysis showed that BcTFIIIA encodes 383 amino acids (aa) with an open reading frame (ORF) of 1152 base pairs (bp). We investigated the subcellular location of BcTFIIIA and found the localized protein in the nucleus. BcTFIIIA was suppressed when the pak choi was infected by the turnip mosaic virus (TuMV). The BcTFIIIA mRNA expression level in a resistant variety was higher than that in a sensitive variety, as determined by qRT-PCR analysis. Yeast two hybrid (Y2H) assay and bimolecular fluorescence complementation (BiFC) suggested that BcTFIIIA interacts with TuMV CP and VPg in vivo, respectively, and in vitro. A virus-induced gene silencing (VIGS) experiment showed that the silencing of BcTFIIIA gene expression in pak choi promoted the accumulation of TuMV. These results suggest that BcTFIIIA negatively regulates viral infection through the interaction with TuMV CP and VPg. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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7 pages, 1591 KiB  
Case Report
Methionine Adenosyltransferase I/III Deficiency Detected by Newborn Screening
by Vanessa Hübner, Luciana Hannibal, Nils Janzen, Sarah Catharina Grünert and Peter Freisinger
Genes 2022, 13(7), 1163; https://doi.org/10.3390/genes13071163 - 27 Jun 2022
Viewed by 2670
Abstract
Methionine adenosyltransferase I/III deficiency is an inborn error of metabolism due to mutations in the MAT1A gene. It is the most common cause of hypermethioninemia in newborn screening. Heterozygotes are often asymptomatic. In contrast, homozygous or compound heterozygous individuals can develop severe neurological [...] Read more.
Methionine adenosyltransferase I/III deficiency is an inborn error of metabolism due to mutations in the MAT1A gene. It is the most common cause of hypermethioninemia in newborn screening. Heterozygotes are often asymptomatic. In contrast, homozygous or compound heterozygous individuals can develop severe neurological symptoms. Less than 70 cases with biallelic variants have been reported worldwide. A methionine-restricted diet is recommended if methionine levels are above 500–600 µmol/L. In this study, we report on a female patient identified with elevated methionine concentrations in a pilot newborn screening program. The patient carries a previously described variant c.1132G>A (p.Gly378Ser) in homozygosity. It is located at the C-terminus of MAT1A. In silico analysis suggests impaired protein stability by β-turn disruption. On a methionine-restricted diet, her serum methionine concentration ranged between 49–605 µmol/L (median 358 µmol/L). Her clinical course was characterized by early-onset muscular hypotonia, mild developmental delay, delayed myelination and mild periventricular diffusion interference in MRI. At 21 months, the girl showed age-appropriate neurological development, but progressive diffusion disturbances in MRI. Little is known about the long-term outcome of this disorder and the necessity of treatment. Our case demonstrates that neurological symptoms can be transient and even patients with initial neurologic manifestations can show normal development under dietary management. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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11 pages, 1410 KiB  
Article
Structural Analysis of microRNAs in Myeloid Cancer Reveals Consensus Motifs
by Senol Dogan, Emrulla Spahiu and Anis Cilic
Genes 2022, 13(7), 1152; https://doi.org/10.3390/genes13071152 - 26 Jun 2022
Cited by 1 | Viewed by 3052
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that function in post-transcriptional gene silencing and mRNA regulation. Although the number of nucleotides of miRNAs ranges from 17 to 27, they are mostly made up of 22 nucleotides. The expression of miRNAs changes significantly in cancer, [...] Read more.
MicroRNAs (miRNAs) are short non-coding RNAs that function in post-transcriptional gene silencing and mRNA regulation. Although the number of nucleotides of miRNAs ranges from 17 to 27, they are mostly made up of 22 nucleotides. The expression of miRNAs changes significantly in cancer, causing protein alterations in cancer cells by preventing some genes from being translated into proteins. In this research, a structural analysis of 587 miRNAs that are differentially expressed in myeloid cancer was carried out. Length distribution studies revealed a mean and median of 22 nucleotides, with an average of 21.69 and a variance of 1.65. We performed nucleotide analysis for each position where Uracil was the most observed nucleotide and Adenine the least observed one with 27.8% and 22.6%, respectively. There was a higher frequency of Adenine at the beginning of the sequences when compared to Uracil, which was more frequent at the end of miRNA sequences. The purine content of each implicated miRNA was also assessed. A novel motif analysis script was written to detect the most frequent 3–7 nucleotide (3–7n) long motifs in the miRNA dataset. We detected CUG (42%) as the most frequent 3n motif, CUGC (15%) as a 4n motif, AGUGC (6%) as a 5n motif, AAGUGC (4%) as a 6n motif, and UUUAGAG (4%) as a 7n motif. Thus, in the second part of our study, we further characterized the motifs by analyzing whether these motifs align at certain consensus sequences in our miRNA dataset, whether certain motifs target the same genes, and whether these motifs are conserved within other species. This thorough structural study of miRNA sequences provides a novel strategy to study the implications of miRNAs in health and disease. A better understanding of miRNA structure is crucial to developing therapeutic settings. Full article
(This article belongs to the Section RNA)
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15 pages, 3548 KiB  
Article
Research on Potential Network Markers and Signaling Pathways in Type 2 Diabetes Based on Conditional Cell-Specific Network
by Yuke Xie, Zhizhong Cui, Nan Wang and Peiluan Li
Genes 2022, 13(7), 1155; https://doi.org/10.3390/genes13071155 - 26 Jun 2022
Cited by 2 | Viewed by 2553
Abstract
Traditional methods concerning type 2 diabetes (T2D) are limited to grouped cells instead of each single cell, and thus the heterogeneity of single cells is erased. Therefore, it is still challenging to study T2D based on a single-cell and network perspective. In this [...] Read more.
Traditional methods concerning type 2 diabetes (T2D) are limited to grouped cells instead of each single cell, and thus the heterogeneity of single cells is erased. Therefore, it is still challenging to study T2D based on a single-cell and network perspective. In this study, we construct a conditional cell-specific network (CCSN) for each single cell for the GSE86469 dataset which is a single-cell transcriptional set from nondiabetic (ND) and T2D human islet samples, and obtain a conditional network degree matrix (CNDM). Since beta cells are the key cells leading to T2D, we search for hub genes in CCSN of beta cells and find that ATP6AP2 is essential for regulation and storage of insulin, and the renin-angiotensin system involving ATP6AP2 is related to most pathological processes leading to diabetic nephropathy. The communication between beta cells and other endocrine cells is performed and three gene pairs with obvious interaction are found. In addition, different expression genes (DEGs) are found based on CNDM and the gene expression matrix (GEM), respectively. Finally, ‘dark’ genes are identified, and enrichment analysis shows that NFATC2 is involved in the VEGF signaling pathway and indirectly affects the production of Prostacyclin (PGI2), which may be a potential biomarker for diabetic nephropathy. Full article
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14 pages, 2658 KiB  
Article
QTL Mapping for Age-Related Eye Pigmentation in the Pink-Eyed Dilution Castaneus Mutant Mouse
by Takaya Nakano, Momoko Takenaka, Makoto Sugiyama and Akira Ishikawa
Genes 2022, 13(7), 1138; https://doi.org/10.3390/genes13071138 - 24 Jun 2022
Viewed by 2841
Abstract
Pink-eyed dilution castaneus (Oca2p-cas) is a mutant gene on mouse chromosome 7 that arose spontaneously in wild Mus musculus castaneus. Homozygotes for Oca2p-cas exhibit pink eyes and a light gray coat throughout life. In an ordinary [...] Read more.
Pink-eyed dilution castaneus (Oca2p-cas) is a mutant gene on mouse chromosome 7 that arose spontaneously in wild Mus musculus castaneus. Homozygotes for Oca2p-cas exhibit pink eyes and a light gray coat throughout life. In an ordinary mutant strain carrying Oca2p-cas, we previously discovered a novel spontaneous mutation that gradually increases melanin pigmentation in the eyes and coat with aging, and we developed a novel mutant strain that was fixed for the novel phenotype. The purpose of this study was to map major quantitative trait loci (QTLs) for the novel pigmentation phenotype and for expression levels of four important melanogenesis genes, microphthalmia-associated transcription factor (Mitf), tyrosinase (Tyr), tyrosinase-related protein-1 (Tyrp1) and dopachrome tautomerase (Dct). We developed 69 DNA markers and created 303 F2 mice from two reciprocal crosses between novel and ordinary mutant strains. The QTL analysis using a selective genotyping strategy revealed a significant QTL for eye pigmentation between 34 and 64 Mb on chromosome 13. This QTL explained approximately 20% of the phenotypic variance. The QTL allele derived from the novel strain increased pigmentation. Although eye pigmentation was positively correlated with Dct expression, no expression QTLs were found, suggesting that the pigmentation QTL on chromosome 13 may not be directly in the pathway of any of the four melanogenesis genes. This study is the first step toward identifying a causal gene for the novel spontaneous phenotype in mice and is expected to discover a new regulatory mechanism for complex melanin biosynthesis during aging. Full article
(This article belongs to the Special Issue From QTL Mapping to QTG and QTN Identification)
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9 pages, 212 KiB  
Review
From First to Second: How Stickler’s Diagnostic Genetics Has Evolved to Match Sequencing Technologies
by Howard Martin, Allan J. Richards and Martin P. Snead
Genes 2022, 13(7), 1123; https://doi.org/10.3390/genes13071123 - 23 Jun 2022
Viewed by 1742
Abstract
Diagnostic genetics within the United Kingdom National Health Service (NHS) has undergone many stepwise improvements in technology since the completion of the human genome project in 2003. Although Sanger sequencing has remained a cornerstone of the diagnostic sequencing arena, the human genome reference [...] Read more.
Diagnostic genetics within the United Kingdom National Health Service (NHS) has undergone many stepwise improvements in technology since the completion of the human genome project in 2003. Although Sanger sequencing has remained a cornerstone of the diagnostic sequencing arena, the human genome reference sequence has enabled next-generation sequencing (more accurately named ‘second-generation sequencing’), to rapidly surpass it in scale and potential. This mini review discusses such developments from the viewpoint of the Stickler’s higher specialist service, detailing the considerations and improvements to diagnostic sequencing implemented since 2003. Full article
(This article belongs to the Special Issue Genetics in Stickler Syndrome)
17 pages, 9746 KiB  
Article
Characterization of Immune-Based Molecular Subtypes and Prognostic Model in Prostate Adenocarcinoma
by Li Guo, Yihao Kang, Daoliang Xia, Yujie Ren, Xueni Yang, Yangyang Xiang, Lihua Tang, Dekang Ren, Jiafeng Yu, Jun Wang and Tingming Liang
Genes 2022, 13(6), 1087; https://doi.org/10.3390/genes13061087 - 18 Jun 2022
Cited by 1 | Viewed by 2818
Abstract
Prostate adenocarcinoma (PRAD), also named prostate cancer, the most common visceral malignancy, is diagnosed in male individuals. Herein, in order to obtain immune-based subtypes, we performed an integrative analysis to characterize molecular subtypes based on immune-related genes, and further discuss the potential features [...] Read more.
Prostate adenocarcinoma (PRAD), also named prostate cancer, the most common visceral malignancy, is diagnosed in male individuals. Herein, in order to obtain immune-based subtypes, we performed an integrative analysis to characterize molecular subtypes based on immune-related genes, and further discuss the potential features and differences between identified subtypes. Simultaneously, we also construct an immune-based risk model to assess cancer prognosis. Our findings showed that the two subtypes, C1 and C2, could be characterized, and the two subtypes showed different characteristics that could clearly describe the heterogeneity of immune microenvironments. The C2 subtype presented a better survival rate than that in the C1 subtype. Further, we constructed an immune-based prognostic model based on four screened abnormally expressed genes, and they were selected as predictors of the robust prognostic model (AUC = 0.968). Our studies provide reference for characterization of molecular subtypes and immunotherapeutic agents against prostate cancer, and the developed robust and useful immune-based prognostic model can contribute to cancer prognosis and provide reference for the individualized treatment plan and health resource utilization. These findings further promote the development and application of precision medicine in prostate cancer. Full article
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3 pages, 182 KiB  
Editorial
Male Reproduction: Regulation, Differentiation and Epigenetics
by Massimo Venditti and Sergio Minucci
Genes 2022, 13(6), 1001; https://doi.org/10.3390/genes13061001 - 2 Jun 2022
Viewed by 1828
Abstract
The production of good-quality spermatozoa (SPZ) is one of the most intricate and far from being completely understood developmental processes during postnatal life [...] Full article
(This article belongs to the Special Issue Male Reproduction: Regulation, Differentiation and Epigenetics)
9 pages, 1094 KiB  
Article
Genetic Determination of the Amount of White Spotting: A Case Study in Siberian Cats
by Agnieszka Górska, Wioleta Drobik-Czwarno, Agata Górska and Joanna Bryś
Genes 2022, 13(6), 1006; https://doi.org/10.3390/genes13061006 - 2 Jun 2022
Viewed by 8418
Abstract
The current hypothesis, along with the opinion of the breeders, is that a cat with two copies of the white spotting allele (SS) has white on more than half of its body, while a cat with only one copy (Ss [...] Read more.
The current hypothesis, along with the opinion of the breeders, is that a cat with two copies of the white spotting allele (SS) has white on more than half of its body, while a cat with only one copy (Ss) has white on less than half of its body. The present study was based on the analysis of two large pedigree databases of Siberian cats (23,905 individuals in PawPeds and 21,650 individuals in Felis Polonia database). The distribution of the amount of white spotting in the offspring of cats with different amounts of white was investigated. Significant differences compared to expected distributions were observed. In many cases the amount of white in cats that were supposed to be homozygous was less than 50% of the body, while in many supposedly heterozygous cats a very large amount of white (over 50%) was observed. This phenomenon was also presented on the verified examples of the specific families excluding possible errors in determining the amount of white by the breeder. The collected evidence suggests that there are other factors involved in the inheritance of the amount of white in cats and the current hypothesis should be revised. Full article
(This article belongs to the Special Issue Animal Domestication and Breeding)
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13 pages, 2754 KiB  
Article
Genome-Wide RNA Sequencing Analysis in Human Dermal Fibroblasts Exposed to Low-Dose Ultraviolet A Radiation
by Jinyun Wang, Satoshi Yano, Kun Xie, Yoshihisa Ohata and Taichi Hara
Genes 2022, 13(6), 974; https://doi.org/10.3390/genes13060974 - 29 May 2022
Cited by 2 | Viewed by 4523
Abstract
Ultraviolet A (UVA) radiation can pass through the epidermis and reach the dermal skin layer, contributing to photoaging, DNA damage, and photocarcinogenesis in dermal fibroblasts. High-dose UVA exposure induces erythema, whereas low-dose, long-term UVA exposure causes skin damage and cell senescence. Biomarkers for [...] Read more.
Ultraviolet A (UVA) radiation can pass through the epidermis and reach the dermal skin layer, contributing to photoaging, DNA damage, and photocarcinogenesis in dermal fibroblasts. High-dose UVA exposure induces erythema, whereas low-dose, long-term UVA exposure causes skin damage and cell senescence. Biomarkers for evaluating damage caused by low-dose UVA in fibroblasts are lacking, making it difficult to develop therapeutic agents for skin aging and aging-associated diseases. We performed RNA-sequencing to investigate gene and pathway alterations in low-dose UVA-irradiated human skin-derived NB1RGB primary fibroblasts. Differentially expressed genes were identified and subjected to Gene Ontology and reactome pathway analysis, which revealed enrichment in genes in the senescence-associated secretory phenotype, apoptosis, respiratory electron transport, and transcriptional regulation by tumor suppressor p53 pathways. Insulin-like growth factor binding protein 7 (IGFBP7) showed the lowest p-value in RNA-sequencing analysis and was associated with the senescence-associated secretory phenotype. Protein–protein interaction analysis revealed that Fos proto-oncogene had a high-confidence network with IGFBP7 as transcription factor of the IGFBP7 gene among SASP hit genes, which were validated using RT-qPCR. Because of their high sensitivity to low-dose UVA radiation, Fos and IGFBP7 show potential as biomarkers for evaluating the effect of low-dose UVA radiation on dermal fibroblasts. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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26 pages, 3468 KiB  
Article
Characterization, Selection, and Trans-Species Polymorphism in the MHC Class II of Heermann’s Gull (Charadriiformes)
by Misael Daniel Mancilla-Morales, Enriqueta Velarde, Araceli Contreras-Rodríguez, Zulema Gómez-Lunar, Jesús A. Rosas-Rodríguez, Joseph Heras, José G. Soñanez-Organis and Enrico A. Ruiz
Genes 2022, 13(5), 917; https://doi.org/10.3390/genes13050917 - 20 May 2022
Viewed by 3599
Abstract
The major histocompatibility complex (MHC) enables vertebrates to cope with pathogens and maintain healthy populations, thus making it a unique set of loci for addressing ecology and evolutionary biology questions. The aim of our study was to examine the variability of Heermann’s Gull [...] Read more.
The major histocompatibility complex (MHC) enables vertebrates to cope with pathogens and maintain healthy populations, thus making it a unique set of loci for addressing ecology and evolutionary biology questions. The aim of our study was to examine the variability of Heermann’s Gull MHC class II (MHCIIB) and compare these loci with other Charadriiformes. Fifty-nine MHCIIB haplotypes were recovered from sixty-eight Heermann’s Gulls by cloning, of them, twelve were identified as putative true alleles, forty-five as unique alleles, and two as pseudogenes. Intra and interspecific relationships indicated at least two loci in Heermann’s Gull MHCIIB and trans-species polymorphism among Charadriiformes (coinciding with the documented evidence of two ancient avian MHCIIB lineages, except in the Charadriidae family). Additionally, sites under diversifying selection revealed a better match with peptide-binding sites inferred in birds than those described in humans. Despite the negative anthropogenic activity reported on Isla Rasa, Heermann’s Gull showed MHCIIB variability consistent with population expansion, possibly due to a sudden growth following conservation efforts. Duplication must play an essential role in shaping Charadriiformes MHCIIB variability, buffering selective pressures through balancing selection. These findings suggest that MHC copy number and protected islands can contribute to seabird conservation. Full article
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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13 pages, 793 KiB  
Article
Array Comparative Genomic Hybridisation and Droplet Digital PCR Uncover Recurrent Copy Number Variation of the TTN Segmental Duplication Region
by Lydia Sagath, Vilma-Lotta Lehtokari, Katarina Pelin and Kirsi Kiiski
Genes 2022, 13(5), 905; https://doi.org/10.3390/genes13050905 - 19 May 2022
Cited by 1 | Viewed by 2542
Abstract
Intragenic segmental duplication regions are potential hotspots for recurrent copy number variation and possible pathogenic aberrations. Two large sarcomeric genes, nebulin and titin, both contain such segmental duplication regions. Using our custom Comparative Genomic Hybridisation array, we have previously shown that a gain [...] Read more.
Intragenic segmental duplication regions are potential hotspots for recurrent copy number variation and possible pathogenic aberrations. Two large sarcomeric genes, nebulin and titin, both contain such segmental duplication regions. Using our custom Comparative Genomic Hybridisation array, we have previously shown that a gain or loss of more than one copy of the repeated block of the nebulin triplicate region constitutes a recessive pathogenic mutation. Using targeted array-CGH, similar copy number variants can be detected in the segmental duplication region of titin. Due to the limitations of the array-CGH methodology and the repetitiveness of the region, the exact copy numbers of the blocks could not be determined. Therefore, we developed complementary custom Droplet Digital PCR assays for the titin segmental duplication region to confirm true variation. Our combined methods show that the titin segmental duplication region is subject to recurrent copy number variation. Gains and losses were detected in samples from healthy individuals as well as in samples from patients with different muscle disorders. The copy number variation observed in our cohort is likely benign, but pathogenic copy number variants in the segmental duplication region of titin cannot be excluded. Further investigations are needed, however, this region should no longer be neglected in genetic analyses. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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24 pages, 332 KiB  
Article
The Skin We Live in: Pigmentation Traits and Tanning Behaviour in British Young Adults, an Observational and Genetically-Informed Study
by Carolina Bonilla and Cilia Mejia-Lancheros
Genes 2022, 13(5), 896; https://doi.org/10.3390/genes13050896 - 17 May 2022
Cited by 1 | Viewed by 3045
Abstract
Skin cancer incidence has been increasing worldwide, representing a particularly high burden for populations of European ancestry. Outdoor and indoor tanning using ultraviolet (UV) radiation devices are major risk factors for skin cancer. While tanning behaviours can be modified by targeted interventions to [...] Read more.
Skin cancer incidence has been increasing worldwide, representing a particularly high burden for populations of European ancestry. Outdoor and indoor tanning using ultraviolet (UV) radiation devices are major risk factors for skin cancer. While tanning behaviours can be modified by targeted interventions to reduce skin cancer rates, there is insufficient evidence on the motivations for tanning preferences and their relationship with pigmentation phenotypes. The present observational and genetically-informed study investigates motives for tanning and the role that pigmentation phenotypes play on outdoor and indoor tanning behaviour in British young adults. This study included 3722 participants from the Avon Longitudinal Study of Parents and Children in South West England, with data on pigmentation features, tanning ability and preferences, and SNP genotypes. Liking to tan and outdoor tanning were strongly influenced by pigmentary traits and tanning ability. However, the association of these phenotypes with UV indoor tanning was weaker. Our results provide evidence to support the implementation of skin cancer preventative interventions that consider individual biological characteristics and motives for undergoing outdoor and indoor tanning. Full article
(This article belongs to the Special Issue Feature Papers in Human Genomics and Genetic Diseases)
5 pages, 205 KiB  
Editorial
Genetics of Hearing Impairment
by Hannie Kremer and Ignacio del Castillo
Genes 2022, 13(5), 852; https://doi.org/10.3390/genes13050852 - 11 May 2022
Cited by 2 | Viewed by 2353
Abstract
The inner ear is a complex structure at the cellular and molecular levels [...] Full article
(This article belongs to the Special Issue Genetics of Hearing Impairment)
26 pages, 2954 KiB  
Article
Gene-Based Methods for Estimating the Degree of the Skewness of X Chromosome Inactivation
by Meng-Kai Li, Yu-Xin Yuan, Bin Zhu, Kai-Wen Wang, Wing Kam Fung and Ji-Yuan Zhou
Genes 2022, 13(5), 827; https://doi.org/10.3390/genes13050827 - 6 May 2022
Viewed by 2573
Abstract
Skewed X chromosome inactivation (XCI-S) has been reported to be associated with some X-linked diseases, and currently several methods have been proposed to estimate the degree of the XCI-S (denoted as γ) for a single locus. However, no method has been available [...] Read more.
Skewed X chromosome inactivation (XCI-S) has been reported to be associated with some X-linked diseases, and currently several methods have been proposed to estimate the degree of the XCI-S (denoted as γ) for a single locus. However, no method has been available to estimate γ for genes. Therefore, in this paper, we first propose the point estimate and the penalized point estimate of γ for genes, and then derive its confidence intervals based on the Fieller’s and penalized Fieller’s methods, respectively. Further, we consider the constraint condition of γ[0, 2] and propose the Bayesian methods to obtain the point estimates and the credible intervals of γ, where a truncated normal prior and a uniform prior are respectively used (denoted as GBN and GBU). The simulation results show that the Bayesian methods can avoid the extreme point estimates (0 or 2), the empty sets, the noninformative intervals ([0, 2]) and the discontinuous intervals to occur. GBN performs best in both the point estimation and the interval estimation. Finally, we apply the proposed methods to the Minnesota Center for Twin and Family Research data for their practical use. In summary, in practical applications, we recommend using GBN to estimate γ of genes. Full article
(This article belongs to the Special Issue Statistical Genetics in Human Diseases)
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13 pages, 24956 KiB  
Article
Novel Role of AaMYBC1 in Regulating Actinidia arguta Vine Architecture by Elongating Internode Based on Multi-Omics Analysis of Transgenic Tobacco
by Yukuo Li, Hailei Huang, Muhammad Abid, Hong Gu, Zhongping Cheng, Jinbao Fang and Xiujuan Qi
Genes 2022, 13(5), 817; https://doi.org/10.3390/genes13050817 - 3 May 2022
Cited by 1 | Viewed by 2288
Abstract
The internode length affects the status of fruiting branches and shapes the vine architecture. MYB TFs (transcription factors) have been widely studied and reported to control many biological processes including secondary metabolism, abiotic stresses, growth and development, etc. However, the roles of MYB [...] Read more.
The internode length affects the status of fruiting branches and shapes the vine architecture. MYB TFs (transcription factors) have been widely studied and reported to control many biological processes including secondary metabolism, abiotic stresses, growth and development, etc. However, the roles of MYB TFs in regulating internode length remain poorly understood. Here, we demonstrated that a secondary metabolism-related R2R3-MYB TF AaMYBC1 from Actinidia arguta was involved in the regulation of internode length by combined analysis of transcriptome and metabolome of transgenic tobacco plants. The metabolome analysis of OE (over-expressed tobacco) and WT (wild-typed tobacco) showed that there were a total of 1000 metabolites, 176 of which had significant differences. A key metabolite pme1651 annotated as indole 3-acetic acid belonged to phytohormone that was involved in internode length regulation. The RNA-seq analysis presented 446 differentially expressed genes (DEGs) between OE and WT, 14 of which were common DEGs in KEGG and GO enrichment. Through the combined analysis of metabolome and transcriptome in transgenic and wild-type tobacco, three key genes including two SAUR and a GH3 gene were possibly involved in internode elongation. Finally, a regulatory module was deduced to show the role of AaMYBC1 in internode elongation. Our results proposed a molecular mechanism of AaMYBC1 regulating internode length by mediated auxin signaling, implying the potential role in regulating the vine architecture. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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18 pages, 9698 KiB  
Article
Molecular Evolutionary Rate Predicts Intraspecific Genetic Polymorphism and Species-Specific Selection
by Jiaqi Wu, Takahiro Yonezawa and Hirohisa Kishino
Genes 2022, 13(4), 708; https://doi.org/10.3390/genes13040708 - 17 Apr 2022
Viewed by 3000
Abstract
It is unknown what determines genetic diversity and how genetic diversity is associated with various biological traits. In this work, we provide insight into these issues. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual human, chimpanzee, gorilla, mouse, [...] Read more.
It is unknown what determines genetic diversity and how genetic diversity is associated with various biological traits. In this work, we provide insight into these issues. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual human, chimpanzee, gorilla, mouse, and dog/wolf genomes, we found that intraspecific genetic diversity can be predicted by long-term molecular evolutionary rates rather than de novo mutation rates. This relationship was established during the early stage of mammalian evolution. Moreover, we developed a method to detect fluctuations of species-specific selection on genes based on the deviations of intraspecific genetic diversity predicted from long-term rates. We showed that the evolution of epithelial cells, rather than connective tissue, mainly contributed to morphological evolution of different species. For humans, evolution of the immune system and selective sweeps caused by infectious diseases are the most representative examples of adaptive evolution. Full article
(This article belongs to the Special Issue Genetic Structure of Human Populations)
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27 pages, 19141 KiB  
Article
A Penalization Method for Estimating Heterogeneous Covariate Effects in Cancer Genomic Data
by Ziye Luo, Yuzhao Zhang and Yifan Sun
Genes 2022, 13(4), 702; https://doi.org/10.3390/genes13040702 - 15 Apr 2022
Viewed by 2233
Abstract
In high-throughput profiling studies, extensive efforts have been devoted to searching for the biomarkers associated with the development and progression of complex diseases. The heterogeneity of covariate effects associated with the outcomes across subjects has been noted in the literature. In this paper, [...] Read more.
In high-throughput profiling studies, extensive efforts have been devoted to searching for the biomarkers associated with the development and progression of complex diseases. The heterogeneity of covariate effects associated with the outcomes across subjects has been noted in the literature. In this paper, we consider a scenario where the effects of covariates change smoothly across subjects, which are ordered by a known auxiliary variable. To this end, we develop a penalization-based approach, which applies a penalization technique to simultaneously select important covariates and estimate their unique effects on the outcome variables of each subject. We demonstrate that, under the appropriate conditions, our method shows selection and estimation consistency. Additional simulations demonstrate its superiority compared to several competing methods. Furthermore, applying the proposed approach to two The Cancer Genome Atlas datasets leads to better prediction performance and higher selection stability. Full article
(This article belongs to the Special Issue Application of Bioinformatics in Human Cancers)
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17 pages, 4303 KiB  
Article
hMSH5 Regulates NHEJ and Averts Excessive Nucleotide Alterations at Repair Joints
by Aneesa T. Al-Soodani, Xiling Wu, Nicole C. Kelp, Alexander J. Brown, Steven A. Roberts and Chengtao Her
Genes 2022, 13(4), 673; https://doi.org/10.3390/genes13040673 - 11 Apr 2022
Cited by 1 | Viewed by 3128
Abstract
Inappropriate repair of DNA double-strand breaks (DSBs) leads to genomic instability, cell death, or malignant transformation. Cells minimize these detrimental effects by selectively activating suitable DSB repair pathways in accordance with their underlying cellular context. Here, we report that hMSH5 down-regulates NHEJ and [...] Read more.
Inappropriate repair of DNA double-strand breaks (DSBs) leads to genomic instability, cell death, or malignant transformation. Cells minimize these detrimental effects by selectively activating suitable DSB repair pathways in accordance with their underlying cellular context. Here, we report that hMSH5 down-regulates NHEJ and restricts the extent of DSB end processing before rejoining, thereby reducing “excessive” deletions and insertions at repair joints. RNAi-mediated knockdown of hMSH5 led to large nucleotide deletions and longer insertions at the repair joints, while at the same time reducing the average length of microhomology (MH) at repair joints. Conversely, hMSH5 overexpression reduced end-joining activity and increased RPA foci formation (i.e., more stable ssDNA at DSB ends). Furthermore, silencing of hMSH5 delayed 53BP1 chromatin spreading, leading to increased end resection at DSB ends. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Microorganisms, Plants and Mammalian Systems)
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9 pages, 1052 KiB  
Article
Integrated Quantitative Neuro-Transcriptome Analysis of Several Brain Areas in Human Trisomy 21
by Alejandra Rodríguez-Ortiz, Julio César Montoya-Villegas, Felipe García-Vallejo and Yecid Mina-Paz
Genes 2022, 13(4), 628; https://doi.org/10.3390/genes13040628 - 1 Apr 2022
Viewed by 2369
Abstract
Background: Although Down syndrome (DS) is the most frequent human chromosomal disorder and it causes mainly intellectual disability, its clinical presentation is complex and variable. Objective: We aimed to analyze and compare the transcriptome disruption in several brain areas from individuals with DS [...] Read more.
Background: Although Down syndrome (DS) is the most frequent human chromosomal disorder and it causes mainly intellectual disability, its clinical presentation is complex and variable. Objective: We aimed to analyze and compare the transcriptome disruption in several brain areas from individuals with DS and euploid controls as a new approach to consider a global systemic differential disruption of gene expression beyond chromosome 21. Methods: We used data from a DNA microarray experiment with ID GSE59630 previously deposited in the GEO DataSet of NCBI database. The array contained log2 values of 17,537 human genes expressed in several aeras of the human brain. We calculated the differential gene expression (Z-ratio) of all genes. Results: We found several differences in gene expression along the DS brain transcriptome, not only in the genes located at chromosome 21 but in other chromosomes. Moreover, we registered the lowest Z-ratio correlation between the age ranks of 16–22 weeks of gestation and 39–42 years (R2 = 0.06) and the highest Z-ratio correlation between the age ranks of 30–39 years and 40–42 years (R2 = 0.89). The analysis per brain areas showed that the hippocampus and the cerebellar cortex had the most different gene expression pattern when compared to the brain as a whole. Conclusions: Our results support the hypothesis of a systemic imbalance of brain protein homeostasis, or proteostasis network of cognitive and neuroplasticity process, as new model to explain the important effect on the neurophenotype of trisomy that occur not only in the loci of chromosome 21 but also in genes located in other chromosomes. Full article
(This article belongs to the Special Issue Epigenetics in Brain Development and Neurodevelopmental Disorders)
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9 pages, 1170 KiB  
Communication
Effectiveness of Two Universal Angiosperm Probe Sets Tested In Silico for Caryophyllids Taxa with Emphasis on Cacti Species
by Delil A. Chincoya and Sofía Solórzano
Genes 2022, 13(4), 570; https://doi.org/10.3390/genes13040570 - 24 Mar 2022
Cited by 1 | Viewed by 2480
Abstract
In angiosperms, huge advances in massive DNA sequencing technologies have impacted phylogenetic studies. Probe sets have been developed with the purpose of recovering hundreds of orthologous loci of targeted DNA sequences (TDS) across different plant lineages. We tested in silico the effectiveness of [...] Read more.
In angiosperms, huge advances in massive DNA sequencing technologies have impacted phylogenetic studies. Probe sets have been developed with the purpose of recovering hundreds of orthologous loci of targeted DNA sequences (TDS) across different plant lineages. We tested in silico the effectiveness of two universal probe sets in the whole available genomes of Caryophyllids, emphasizing phylogenetic issues in cacti species. A total of 870 TDS (517 TDS from Angiosperm v.1 and 353 from Angiosperms353) were individually tested in nine cacti species and Amaranthus hypochondriacus (external group) with ≥17 Gbp of available DNA data. The effectiveness was measured by the total number of orthologous loci recovered and their length, the percentage of loci discarded by paralogy, and the proportion of informative sites (PIS) in the alignments. The results showed that, on average, Angiosperms353 was better than Angiosperm v.1 for cacti species, since the former obtained an average of 275.6 loci that represent 123,687 bp, 2.48% of paralogous loci, and 4.32% of PIS in alignments, whereas the latter recovered 148.4 loci (37,683 bp), 10.38% of paralogous loci, and 3.49% of PIS. We recommend the use of predesigned universal probe sets for Caryophyllids, since these recover a high number of orthologous loci that resolve phylogenetic relationships. Full article
(This article belongs to the Special Issue Cactaceae Genetics and Genomics)
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9 pages, 1547 KiB  
Brief Report
Identification of Frameshift Variants in POLH Gene Causing Xeroderma Pigmentosum in Two Consanguineous Pakistani Families
by Ghazala Y. Zamani, Ranjha Khan, Noreen Karim, Zubair M. Ahmed and Muhammad Naeem
Genes 2022, 13(3), 543; https://doi.org/10.3390/genes13030543 - 19 Mar 2022
Viewed by 3310
Abstract
Xeroderma pigmentosum (XP) is a rare autosomal recessive genetic disorder characterized by severe sensitivity of skin to sunlight and an increased risk of skin cancer. XP variant (XPV), a milder subtype, is caused by variants in the POLH gene. POLH encodes an error-prone [...] Read more.
Xeroderma pigmentosum (XP) is a rare autosomal recessive genetic disorder characterized by severe sensitivity of skin to sunlight and an increased risk of skin cancer. XP variant (XPV), a milder subtype, is caused by variants in the POLH gene. POLH encodes an error-prone DNA-polymerase eta (pol eta) which performs translesion synthesis past ultraviolet photoproducts. The current study documents the clinical and genetic investigations of two large consanguineous Pakistani families affected with XPV. In family 1, whole exome sequencing (WES) revealed a novel frameshift variant, c.1723dupG (p.(Val575Glyfs*4)), of POLH, which is predicted to cause frameshift and premature truncation of the encoded enzyme. Indeed, our ex vivo studies in HEK293T cells confirmed the truncation of the encoded protein due to the c.1723dupG variant. In family 2, Sanger sequencing of POLH exons, revealed a recurrent nonsense variant, c.437dupA (p.Tyr146*). POLH forms a hetero-tetrameric POLZ complex with REV3L, REV7, POLD2 and POLD3. Next, we performed in silico analysis of POLH and other POLZ complex genes expression in publicly available single cell mRNAseq datasets from adult human healthy and aging skin. We found overlapping expression of POLH, REV3L and POLD2 in multiple cell types including differentiated and undifferentiated keratinocytes, pericytes and melanocytes in healthy skin. However, in aging human skin, POLH expression is reduced in compare to its POLZ complex partners. Insights from our study will facilitate counseling regarding the molecular and phenotypic landscape of POLH-related XPV. Full article
(This article belongs to the Special Issue Molecular Basis of Rare Diseases)
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16 pages, 1480 KiB  
Article
Transcriptomics of Wet Skin Biopsies Predict Early Radiation-Induced Hematological Damage in a Mouse Model
by Abdulnaser Alkhalil, John Clifford, Stacy Ann Miller, Aarti Gautam, Marti Jett, Rasha Hammamieh, Lauren T. Moffatt and Jeffrey W. Shupp
Genes 2022, 13(3), 538; https://doi.org/10.3390/genes13030538 - 18 Mar 2022
Viewed by 2907
Abstract
The lack of an easy and fast radiation-exposure testing method with a dosimetric ability complicates triage and treatment in response to a nuclear detonation, radioactive material release, or clandestine exposure. The potential of transcriptomics in radiation diagnosis and prognosis were assessed here using [...] Read more.
The lack of an easy and fast radiation-exposure testing method with a dosimetric ability complicates triage and treatment in response to a nuclear detonation, radioactive material release, or clandestine exposure. The potential of transcriptomics in radiation diagnosis and prognosis were assessed here using wet skin (blood/skin) biopsies obtained at hour 2 and days 4, 7, 21, and 28 from a mouse radiation model. Analysis of significantly differentially transcribed genes (SDTG; p ≤ 0.05 and FC ≥ 2) during the first post-exposure week identified the glycoprotein 6 (GP-VI) signaling, the dendritic cell maturation, and the intrinsic prothrombin activation pathways as the top modulated pathways with stable inactivation after lethal exposures (20 Gy) and intermittent activation after sublethal (1, 3, 6 Gy) exposure time points (TPs). Interestingly, these pathways were inactivated in the late TPs after sublethal exposure in concordance with a delayed deleterious effect. Modulated transcription of a variety of collagen types, laminin, and peptidase genes underlay the modulated functions of these hematologically important pathways. Several other SDTGs related to platelet and leukocyte development and functions were identified. These results outlined genetic determinants that were crucial to clinically documented radiation-induced hematological and skin damage with potential countermeasure applications. Full article
(This article belongs to the Collection Feature Papers in ‘Animal Genetics and Genomics’)
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10 pages, 2059 KiB  
Article
Crlz-1 Homozygous Null Knockout Mouse Embryos Are Lethally Stopped in Their Early Development
by Seung-Young Choi, Joo-Hyun Pi, So-Eun Jeong and Chang-Joong Kang
Genes 2022, 13(3), 511; https://doi.org/10.3390/genes13030511 - 14 Mar 2022
Viewed by 2621
Abstract
Although the conditional gene knockout (KO) is a better choice for observing its phenotype in a specific cell, tissue, and/or organ, the simple null gene KO could nevertheless be attempted initially to scan its overall phenotypes at the level of the whole-body system, [...] Read more.
Although the conditional gene knockout (KO) is a better choice for observing its phenotype in a specific cell, tissue, and/or organ, the simple null gene KO could nevertheless be attempted initially to scan its overall phenotypes at the level of the whole-body system, especially for a new gene such as Crlz-1. Therefore, with a hope to glean phenotypic clues for Crlz-1 at the whole-body system, we attempted to generate its null KO mice. Contrary to our original desire, Crlz-1 homozygous null KO mice were not born. However, in the chasing of their homozygous KO embryos, they were found to be lethally impaired from early development, remaining in a state of small globular mass without ever leading to a body shape, indicating the critical role of Crlz-1 as a Wnt target gene for the proliferation and/or differentiation of cells during early mouse embryonic development. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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8 pages, 3208 KiB  
Communication
First Description of Inheritance of a Postzygotic OPA1 Mosaic Variant
by Svenja Alter, Navid Farassat, Sebastian Küchlin, Wolf A. Lagrèze and Judith Fischer
Genes 2022, 13(3), 478; https://doi.org/10.3390/genes13030478 - 8 Mar 2022
Viewed by 2314
Abstract
Optic atrophy 1 (MIM #165500) is caused by pathogenic variants in the gene OPA1 (OPA1 MITOCHONDRIAL DYNAMIN-LIKE GTPase, MIM *605290) and is inherited in an autosomal dominant manner. We describe a 6-year-old male patient with severe early onset manifestation of optic [...] Read more.
Optic atrophy 1 (MIM #165500) is caused by pathogenic variants in the gene OPA1 (OPA1 MITOCHONDRIAL DYNAMIN-LIKE GTPase, MIM *605290) and is inherited in an autosomal dominant manner. We describe a 6-year-old male patient with severe early onset manifestation of optic atrophy, whose parents are subjectively asymptomatic. OPA1-sequence analysis revealed the heterozygous missense variant NM_015560.3:c.806C>T, p.(Ser269Phe) in the patient. Segregation analysis of the parents showed that the mother carried a low-grade postzygotic mosaic of this variant, which apparently also involves germline cells. In line with this, ophthalmological investigation of the mother showed subclinical manifestation of optic atrophy 1. This is the first report of an OPA1 postzygotic mosaic that was inherited to offspring. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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25 pages, 3377 KiB  
Article
Functional Similarities of Protein-Coding Genes in Topologically Associating Domains and Spatially-Proximate Genomic Regions
by Chenguang Zhao, Tong Liu and Zheng Wang
Genes 2022, 13(3), 480; https://doi.org/10.3390/genes13030480 - 8 Mar 2022
Cited by 1 | Viewed by 2907
Abstract
Topologically associating domains (TADs) are the structural and functional units of the genome. However, the functions of protein-coding genes existing in the same or different TADs have not been fully investigated. We compared the functional similarities of protein-coding genes existing in the same [...] Read more.
Topologically associating domains (TADs) are the structural and functional units of the genome. However, the functions of protein-coding genes existing in the same or different TADs have not been fully investigated. We compared the functional similarities of protein-coding genes existing in the same TAD and between different TADs, and also in the same gap region (the region between two consecutive TADs) and between different gap regions. We found that the protein-coding genes from the same TAD or gap region are more likely to share similar protein functions, and this trend is more obvious with TADs than the gap regions. We further created two types of gene–gene spatial interaction networks: the first type is based on Hi-C contacts, whereas the second type is based on both Hi-C contacts and the relationship of being in the same TAD. A graph auto-encoder was applied to learn the network topology, reconstruct the two types of networks, and predict the functions of the central genes/nodes based on the functions of the neighboring genes/nodes. It was found that better performance was achieved with the second type of network. Furthermore, we detected long-range spatially-interactive regions based on Hi-C contacts and calculated the functional similarities of the gene pairs from these regions. Full article
(This article belongs to the Special Issue 3D Reconstruction of Genome Structures)
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9 pages, 2880 KiB  
Article
enChIP-Seq Analyzer: A Software Program to Analyze and Interpret enChIP-Seq Data for the Detection of Physical Interactions between Genomic Regions
by Ashita Sarudate, Toshitsugu Fujita, Takahiro Nakayama and Hodaka Fujii
Genes 2022, 13(3), 472; https://doi.org/10.3390/genes13030472 - 7 Mar 2022
Viewed by 2548
Abstract
Accumulating evidence suggests that the physical interactions between genomic regions play critical roles in the regulation of genome functions, such as transcription and epigenetic regulation. Various methods to detect the physical interactions between genomic regions have been developed. We recently developed a method [...] Read more.
Accumulating evidence suggests that the physical interactions between genomic regions play critical roles in the regulation of genome functions, such as transcription and epigenetic regulation. Various methods to detect the physical interactions between genomic regions have been developed. We recently developed a method to search for genomic regions interacting with a locus of interest in a non-biased manner that combines pull-down of the locus using engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) and next-generation sequencing (NGS) analysis (enChIP-Seq). The clustered regularly interspaced short palindromic repeats (CRISPR) system, consisting of a nuclease-dead form of Cas9 (dCas9) and a guide RNA (gRNA), or transcription activator-like (TAL) proteins, can be used for enChIP. In enChIP-Seq, it is necessary to compare multiple datasets of enChIP-Seq data to unambiguously detect specific interactions. However, it is not always easy to analyze enChIP-Seq datasets to subtract non-specific interactions or identify common interactions. To facilitate such analysis, we developed the enChIP-Seq analyzer software. It enables easy extraction of common signals as well as subtraction of non-specific signals observed in negative control samples, thereby streamlining extraction of specific enChIP-Seq signals. enChIP-Seq analyzer will help users analyze enChIP-Seq data and identify physical interactions between genomic regions. Full article
(This article belongs to the Section Bioinformatics)
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22 pages, 1056 KiB  
Article
Simulation Research on the Methods of Multi-Gene Region Association Analysis Based on a Functional Linear Model
by Shijing Li, Fujie Zhou, Jiayu Shen, Hui Zhang and Yongxian Wen
Genes 2022, 13(3), 455; https://doi.org/10.3390/genes13030455 - 2 Mar 2022
Viewed by 2348
Abstract
Genome-wide association analysis is an important approach to identify genetic variants associated with complex traits. Complex traits are not only affected by single gene loci, but also by the interaction of multiple gene loci. Studies of association between gene regions and quantitative traits [...] Read more.
Genome-wide association analysis is an important approach to identify genetic variants associated with complex traits. Complex traits are not only affected by single gene loci, but also by the interaction of multiple gene loci. Studies of association between gene regions and quantitative traits are of great significance in revealing the genetic mechanism of biological development. There have been a lot of studies on single-gene region association analysis, but the application of functional linear models in multi-gene region association analysis is still less. In this paper, a functional multi-gene region association analysis test method is proposed based on the functional linear model. From the three directions of common multi-gene region method, multi-gene region weighted method and multi-gene region loci weighted method, that test method is studied combined with computer simulation. The following conclusions are obtained through computer simulation: (a) The functional multi-gene region association analysis test method has higher power than the functional single gene region association analysis test method; (b) The functional multi-gene region weighted method performs better than the common functional multi-gene region method; (c) the functional multi-gene region loci weighted method is the best method for association analysis on three directions of the common multi-gene region method; (d) the performance of the Step method and Multi-gene region loci weighted Step for multi-gene regions is the best in general. Functional multi-gene region association analysis test method can theoretically provide a feasible method for the study of complex traits affected by multiple genes. Full article
(This article belongs to the Section Bioinformatics)
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3 pages, 179 KiB  
Editorial
Investigations on Nuclear DNA Content and DNA Synthesis in Plants and Fungi Using Flow Cytometry and Fluorescence Microscopy
by Elwira Sliwinska
Genes 2022, 13(3), 417; https://doi.org/10.3390/genes13030417 - 25 Feb 2022
Viewed by 1780
Abstract
The twenty-first century has been an era of extensive genome exploration and modifications, using advanced methods such as genome sequencing and editing [...] Full article
20 pages, 10456 KiB  
Article
Cloning of the Human MORG1 Promoter: Differential Regulation by Hypoxia and Prolyl-Hydroxylase Inhibitors
by Tzvetanka Bondeva and Gunter Wolf
Genes 2022, 13(3), 427; https://doi.org/10.3390/genes13030427 - 25 Feb 2022
Viewed by 2068
Abstract
MAPK-organizer 1 (MORG1) is a molecular scaffold for prolyl-hydroxylase-3 containing a domain (PHD3) protein linking MORG1 to mechanisms of adaptation in hypoxic conditions. In this paper, we report the cloning of the promoter region of the murine and human MORG1 gene. Among other [...] Read more.
MAPK-organizer 1 (MORG1) is a molecular scaffold for prolyl-hydroxylase-3 containing a domain (PHD3) protein linking MORG1 to mechanisms of adaptation in hypoxic conditions. In this paper, we report the cloning of the promoter region of the murine and human MORG1 gene. Among other transcriptional factors binding sites, we identified that both (mouse and human) promoter regions contained several putative hypoxia-inducible factor binding motifs. Analyses of the human MORG1 promoter by reporter assays revealed that hypoxia and pharmacological inhibitors of prolyl-hydroxylases under in vitro conditions in HEK 293 cells differentially regulate the MORG1 promoter reporter activity. The exposure of the cells to 10% hypoxia showed inhibition of MORG1 promotor activity at 6 and 12 h, but stimulation after 24 h while treated with prolyl-hydroxylase inhibitors led to a time-independent MORG1 promoter activation. Mutational analyses of the individual HIF binding sites on human MORG1 promoter suggest that the binding sites work in a complex corporation because single mutations were not sufficient to abolish completely the MORG1 reporter activation by PHD inhibitors. Our data provide the first evidence that not only MORG1 regulate HIF stabilization through a PHD complex, but also that, vice versa, HIFs control MORG1 expression directly or indirectly by a complex regulatory mechanism. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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15 pages, 13317 KiB  
Article
Characterization and Functional Study of FAM49B Reveals Its Effect on Cell Proliferation in HEK293T Cells
by Yijian Chen, Yuyan Jiang, Jihui Lao, Yankuan Zhou, Lida Su and Xiao Huang
Genes 2022, 13(2), 388; https://doi.org/10.3390/genes13020388 - 21 Feb 2022
Cited by 2 | Viewed by 3151
Abstract
FAM49B/Fam49b is a member of the Fam49 (Family with sequence similarity 49) gene family, which is characterized by the conserved domain, DUF1394 (Domain of Unknown Function 1394). It has also been named CYRI-B (CYFIP related RAC1 interactor B), implicating its important function of [...] Read more.
FAM49B/Fam49b is a member of the Fam49 (Family with sequence similarity 49) gene family, which is characterized by the conserved domain, DUF1394 (Domain of Unknown Function 1394). It has also been named CYRI-B (CYFIP related RAC1 interactor B), implicating its important function of regulating RAC1-driven cytoskeleton remolding. In this study, to further investigate its functions and mechanisms affecting cell behaviors, HEK293T cells (where FAM49B is highly expressed) were used to establish a FAM49B knockout cell line by CRISPR/Cas9 genome editing technology. Our data have clearly revealed that there are triple alleles of FAM49B in the genome of HEK293T cells. Meanwhile, the proliferation deficiency of the FAM49B KO HEK293T cell line and the significantly changed cell proliferation related gene expression profiles, such as CCND1, have been uncovered. At the same time, the existence of isoform 3 has been confirmed in HEK293T cells. Our studies have suggested that FAM49B may also affect cell proliferation via Cyclins, besides its influence on the cytoskeleton. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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15 pages, 679 KiB  
Article
Leveraging Gene-Level Prediction as Informative Covariate in Hypothesis Weighting Improves Power for Rare Variant Association Studies
by Ying Ji, Rui Chen, Quan Wang, Qiang Wei, Ran Tao and Bingshan Li
Genes 2022, 13(2), 381; https://doi.org/10.3390/genes13020381 - 19 Feb 2022
Viewed by 2885
Abstract
Gene-based rare variant association studies (RVASs) have low power due to the infrequency of rare variants and the large multiple testing burden. To correct for multiple testing, traditional false discovery rate (FDR) procedures which depend solely on P-values are often used. Recently, Independent [...] Read more.
Gene-based rare variant association studies (RVASs) have low power due to the infrequency of rare variants and the large multiple testing burden. To correct for multiple testing, traditional false discovery rate (FDR) procedures which depend solely on P-values are often used. Recently, Independent Hypothesis Weighting (IHW) was developed to improve the detection power while maintaining FDR control by leveraging prior information for each hypothesis. Here, we present a framework to increase power of gene-based RVASs by incorporating prior information using IHW. We first build supervised machine learning models to assign each gene a prediction score that measures its disease risk, using the input of multiple biological features, fed with high-confidence risk genes and local background genes selected near GWAS significant loci as the training set. Then we use the prediction scores as covariates to prioritize RVAS results via IHW. We demonstrate the effectiveness of this framework through applications to RVASs in schizophrenia and autism spectrum disorder. We found sizeable improvements in the number of significant associations compared to traditional FDR approaches, and independent evidence supporting the relevance of the genes identified by our framework but not traditional FDR, demonstrating the potential of our framework to improve power of gene-based RVASs. Full article
(This article belongs to the Special Issue Statistical Genetics in Human Diseases)
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8 pages, 1609 KiB  
Article
FDDM1 and FDDM2, Two SGS3-like Proteins, Function as a Complex to Affect DNA Methylation in Arabidopsis
by Shengjun Li, Weilong Yang, Yunfeng Liu, Guangyong Li, Xiang Liu, Yaling Liu, James R. Alfano, Chi Zhang and Bin Yu
Genes 2022, 13(2), 339; https://doi.org/10.3390/genes13020339 - 12 Feb 2022
Viewed by 2478
Abstract
DNA methylation is an important epigenetic modification required for the specific regulation of gene expression and the maintenance of genome stability in plants and animals. However, the mechanism of DNA demethylation remains largely unknown. Here, we show that two SGS3-like proteins, FACTOR OF [...] Read more.
DNA methylation is an important epigenetic modification required for the specific regulation of gene expression and the maintenance of genome stability in plants and animals. However, the mechanism of DNA demethylation remains largely unknown. Here, we show that two SGS3-like proteins, FACTOR OF DNA DEMETHYLATION 1 (FDDM1) and FDDM2, negatively affect the DNA methylation levels at ROS1-dependend DNA loci in Arabidopsis. FDDM1 binds dsRNAs with 5′ overhangs through its XS (rice gene X and SGS3) domain and forms a heterodimer with FDDM2 through its XH (rice gene X Homology) domain. A lack of FDDM1 or FDDM2 increased DNA methylation levels at several ROS1-dependent DNA loci. However, FDDM1 and FDDM2 may not have an additive effect on DNA methylation levels. Moreover, the XS and XH domains are required for the function of FDDM1. Taken together, these results suggest that FDDM1 and FDDM2 act as a heterodimer to positively modulate DNA demethylation. Our finding extends the function of plant-specific SGS3-like proteins. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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23 pages, 4197 KiB  
Article
Whole Genome DNA Methylation Profiling of D2 Medium Spiny Neurons in Mouse Nucleus Accumbens Using Two Independent Library Preparation Methods
by Yuxiang Li, Haiyang Xu, Javed M. Chitaman and Jian Feng
Genes 2022, 13(2), 306; https://doi.org/10.3390/genes13020306 - 6 Feb 2022
Cited by 2 | Viewed by 3889
Abstract
DNA methylation plays essential roles in various cellular processes. Next-generation sequencing has enabled us to study the functional implication of DNA methylation across the whole genome. However, this approach usually requires a substantial amount of genomic DNA, which limits its application to defined [...] Read more.
DNA methylation plays essential roles in various cellular processes. Next-generation sequencing has enabled us to study the functional implication of DNA methylation across the whole genome. However, this approach usually requires a substantial amount of genomic DNA, which limits its application to defined cell types within a discrete brain region. Here, we applied two separate protocols, Accel-NGS Methyl-Seq (AM-seq) and Enzymatic Methyl-seq (EM-seq), to profile the methylome of D2 dopamine receptor-expressing medium spiny neurons (D2-MSNs) in mouse nucleus accumbens (NAc). Using 40 ng DNA extracted from FACS-isolated D2-MSNs, we found that both methods yielded comparably high-quality methylome data. Additionally, we identified numerous unmethylated regions (UMRs) as cell type-specific regulatory regions. By comparing the NAc D2-MSN methylome with the published methylomes of mouse prefrontal cortex excitatory neurons and neural progenitor cells (NPCs), we identified numerous differentially methylated CpG and non-CpG regions. Our study not only presents a comparison of these two low-input DNA whole genome methylation profiling protocols, but also provides a resource of DNA methylome of mouse accumbal D2-MSNs, a neuron type that has critical roles in addiction and other neuropsychiatric disorders. Full article
(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)
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25 pages, 3321 KiB  
Article
Balanced Polymorphism at the Pgm-1 Locus of the Pompeii Worm Alvinella pompejana and Its Variant Adaptability Is Only Governed by Two QE Mutations at Linked Sites
by Alexis Bioy, Anne-Sophie Le Port, Emeline Sabourin, Marie Verheye, Patrice Piccino, Baptiste Faure, Stéphane Hourdez, Jean Mary and Didier Jollivet
Genes 2022, 13(2), 206; https://doi.org/10.3390/genes13020206 - 24 Jan 2022
Cited by 2 | Viewed by 3113
Abstract
The polychaete Alvinella pompejana lives exclusively on the walls of deep-sea hydrothermal chimneys along the East Pacific Rise (EPR), and displays specific adaptations to withstand the high temperatures and hypoxia associated with this highly variable habitat. Previous studies have revealed the existence of [...] Read more.
The polychaete Alvinella pompejana lives exclusively on the walls of deep-sea hydrothermal chimneys along the East Pacific Rise (EPR), and displays specific adaptations to withstand the high temperatures and hypoxia associated with this highly variable habitat. Previous studies have revealed the existence of a balanced polymorphism on the enzyme phosphoglucomutase associated with thermal variations, where allozymes 90 and 100 exhibit different optimal activities and thermostabilities. Exploration of the mutational landscape of phosphoglucomutase 1 revealed the maintenance of four highly divergent allelic lineages encoding the three most frequent electromorphs over the geographic range of A. pompejana. This polymorphism is only governed by two linked amino acid replacements, located in exon 3 (E155Q and E190Q). A two-niche model of selection, including ‘cold’ and ‘hot’ conditions, represents the most likely scenario for the long-term persistence of these isoforms. Using directed mutagenesis and the expression of the three recombinant variants allowed us to test the additive effect of these two mutations on the biochemical properties of this enzyme. Our results are coherent with those previously obtained from native proteins, and reveal a thermodynamic trade-off between protein thermostability and catalysis, which is likely to have maintained these functional phenotypes prior to the geographic separation of populations across the Equator about 1.2 million years ago. Full article
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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12 pages, 851 KiB  
Article
Expanding the Clinical Phenotype of 19q Interstitial Deletions: A New Case with 19q13.32-q13.33 Deletion and Short Review of the Literature
by Elena-Silvia Shelby, Michael Morris, Liliana Pădure, Andrada Mirea, Relu Cocoș, Alexandru Cărămizaru, Simona Șerban-Sosoi, Andrei Pîrvu and Ioana Streață
Genes 2022, 13(2), 212; https://doi.org/10.3390/genes13020212 - 24 Jan 2022
Cited by 2 | Viewed by 4315
Abstract
19q13 microdeletion syndrome is a very rare genetic disease characterized by pre- and postnatal growth retardation, intellectual disability, expressive language impairment, ectodermal dysplasia, and slender habitus. Since the description of the first case in 1998, less than 30 cases have been reported worldwide. [...] Read more.
19q13 microdeletion syndrome is a very rare genetic disease characterized by pre- and postnatal growth retardation, intellectual disability, expressive language impairment, ectodermal dysplasia, and slender habitus. Since the description of the first case in 1998, less than 30 cases have been reported worldwide. This article aims to review the knowledge gathered so far on this subject and to present the case of a 10-year-old girl admitted to the National University Center for Children Neurorehabilitation “Dr. Nicolae Robanescu” in November of 2018 who presented a slender habitus, growth retardation, facial dysmorphism, skeletal abnormalities, and ectodermal dysplasia. Array-CGH analysis revealed a 1.53 Mb deletion in the 19q13.32-q13.33 region. MLPA for the FKRP gene revealed that the microdeletion was de novo. The patient’s phenotype overlapped with the clinical features of 19q13 microdeletion syndrome. To our knowledge, this is the first case of 19q13 microdeletion syndrome to ever be reported in Romania. We believe our case presents additional features that have never been previously reported in this syndrome, namely, dilatation of the third ventricle and subependymal cyst, left iris coloboma, and tracheomalacia. Moreover, unlike the other 19q13 microdeletion cases that presented with dystonia, our patient also presented dystonia but, interestingly, without having haploinsufficiency of the KMT2B gene. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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17 pages, 7896 KiB  
Article
MtWRP1, a Novel Fabacean Specific Gene, Regulates Root Nodulation and Plant Growth in Medicago truncatula
by Wei Chen, Yingjun Chi, Jinglong Zhang, Binqiang Bai, Xiaomin Ji and Yixin Shen
Genes 2022, 13(2), 193; https://doi.org/10.3390/genes13020193 - 22 Jan 2022
Viewed by 2915
Abstract
Fabaceans symbiotically interact with nitrogen-fixing rhizobacteria to form root nodules. Some fabacean specific proteins play important roles in the symbiosis. WRKY-related Protein (WRP) is a novel fabacean specific protein, whose functions have not been well characterized. In this study, MtWRP1 was functionally characterized [...] Read more.
Fabaceans symbiotically interact with nitrogen-fixing rhizobacteria to form root nodules. Some fabacean specific proteins play important roles in the symbiosis. WRKY-related Protein (WRP) is a novel fabacean specific protein, whose functions have not been well characterized. In this study, MtWRP1 was functionally characterized in Medicago truncatula. It contains a WRKY domain at C-terminal and a novel transmembrane (TM) domain at N-terminal, and its WRKY domain was highly similar to the N-terminal WRKY domain of the group I WRKY proteins. The TM domain was highly homologous to the eukaryotic cytochrome b561 (Cytb561) proteins from birds. Subcellular localization revealed that MtWRP1 was targeted to the Golgi apparatus through the novel TM domain. MtWRP1 was highly expressed in roots and nodules, suggesting its possible roles in the regulation of root growth and nodulation. Both MtWRP1-overexpression transgenic M. truncatula and MtWRP1 mutants showed altered root nodulation and plant growth performance. Specifically, the formation of root nodules was significantly reduced in the absence of MtWRP1. These results demonstrated that MtWRP1 plays critical roles in root nodulation and plant growth. Full article
(This article belongs to the Special Issue Mining the Excellent Functional Genes of Forage)
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13 pages, 25329 KiB  
Article
Identification and Functional Analysis of the Regulatory Elements in the pHSPA6 Promoter
by Shuyu Jiao, Chunyan Bai, Chunyun Qi, Heyong Wu, Lanxin Hu, Feng Li, Kang Yang, Chuheng Zhao, Hongsheng Ouyang, Daxin Pang, Xiaochun Tang and Zicong Xie
Genes 2022, 13(2), 189; https://doi.org/10.3390/genes13020189 - 21 Jan 2022
Cited by 2 | Viewed by 3320
Abstract
Functional and expressional research of heat shock protein A6 (HSPA6) suggests that the gene is of great value for neurodegenerative diseases, biosensors, cancer, etc. Based on the important value of pigs in agriculture and biomedicine and to advance knowledge of this little-studied HSPA [...] Read more.
Functional and expressional research of heat shock protein A6 (HSPA6) suggests that the gene is of great value for neurodegenerative diseases, biosensors, cancer, etc. Based on the important value of pigs in agriculture and biomedicine and to advance knowledge of this little-studied HSPA member, the stress-sensitive sites in porcine HSPA6 (pHSPA6) were investigated following different stresses. Here, two heat shock elements (HSEs) and a conserved region (CR) were identified in the pHSPA6 promoter by a CRISPR/Cas9-mediated precise gene editing strategy. Gene expression data showed that sequence disruption of these regions could significantly reduce the expression of pHSPA6 under heat stress. Stimulation studies indicated that these regions responded not only to heat stress but also to copper sulfate, MG132, and curcumin. Further mechanism studies showed that downregulated pHSPA6 could significantly affect some important members of the HSP family that are involved in HSP40, HSP70, and HSP90. Overall, our results provide a new approach for investigating gene expression and regulation that may contribute to gene regulatory mechanisms, drug target selection, and breeding stock selection. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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15 pages, 3862 KiB  
Article
Research on Frequent Itemset Mining of Imaging Genetics GWAS in Alzheimer’s Disease
by Hong Liang, Luolong Cao, Yue Gao, Haoran Luo, Xianglian Meng, Ying Wang, Jin Li and Wenjie Liu
Genes 2022, 13(2), 176; https://doi.org/10.3390/genes13020176 - 19 Jan 2022
Cited by 1 | Viewed by 2718
Abstract
As an efficient method, genome-wide association study (GWAS) is used to identify the association between genetic variation and pathological phenotypes, and many significant genetic variations founded by GWAS are closely associated with human diseases. However, it is not enough to mine only a [...] Read more.
As an efficient method, genome-wide association study (GWAS) is used to identify the association between genetic variation and pathological phenotypes, and many significant genetic variations founded by GWAS are closely associated with human diseases. However, it is not enough to mine only a single marker effect variation on complex biological phenotypes. Mining highly correlated single nucleotide polymorphisms (SNP) is more meaningful for the study of Alzheimer's disease (AD). In this paper, we used two frequent pattern mining (FPM) framework, the FP-Growth and Eclat algorithms, to analyze the GWAS results of functional magnetic resonance imaging (fMRI) phenotypes. Moreover, we applied the definition of confidence to FP-Growth and Eclat to enhance the FPM framework. By calculating the conditional probability of identified SNPs, we obtained the corresponding association rules to provide support confidence between these important SNPs. The resulting SNPs showed close correlation with hippocampus, memory, and AD. The experimental results also demonstrate that our framework is effective in identifying SNPs and provide candidate SNPs for further research. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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