Genetic and Clinical Analyses of 13 Chinese Families With Cystine Urolithiasis and Identification of 15 Novel Pathogenic Variants in SLC3A1 and SLC7A9
ConclusionAll 13 pediatric CU families harbored SLC3A1 or/and SLC7A9 rare variants. A total of 15 novel pathogenic variants in SLC3A1 and SLC7A9 were identified. This study expanded the known mutational spectrum of CU in the Chinese population. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 18, 2020 Category: Genetics & Stem Cells Source Type: research

Identification of Multigene Biomarker for Shrimp White Feces Syndrome by Full-Length Transcriptome Sequencing
The pacific white shrimp, Litopenaeus vannamei, with the largest shrimp industry production in the world, is currently threatened by a severe disease, white feces syndrome (WFS), which cause devastating losses globally, while its causal agents remain largely unknown. Herein, compared to the Control shrimp by metagenomic analysis, we firstly investigated that the altered functions of intestinal microbial community in WFS shrimp were the enrichment of bacterial chemotaxis and flagellar assembly pathways, hinting at a potential role of pathogenic bacteria for growth and development, which might be related to WFS occurrence. S...
Source: Frontiers in Genetics - February 18, 2020 Category: Genetics & Stem Cells Source Type: research

NanoGBS: A Miniaturized Procedure for GBS Library Preparation
High-throughput reduced-representation sequencing (RRS)-based genotyping methods, such as genotyping-by-sequencing (GBS), have provided attractive genotyping solutions in numerous species. Here, we present NanoGBS, a miniaturized and eco-friendly method for GBS library construction. Using acoustic droplet ejection (ADE) technology, NanoGBS libraries were constructed in tenfold smaller volumes compared to standard methods (StdGBS) and leading to a reduced use of plastics of up to 90%. A high-quality DNA library and SNP catalogue were obtained with extensive overlap (96%) in SNP loci and 100% agreement in genotype calls comp...
Source: Frontiers in Genetics - February 18, 2020 Category: Genetics & Stem Cells Source Type: research

The Cytochrome P450 Monooxygenase Inventory of Grapevine (Vitis vinifera L.): Genome-Wide Identification, Evolutionary Characterization and Expression Analysis
In this study, a sum of 236 VvCYPs, divided into 46 families and clustered into nine clans, have been identified based on bioinformatics analyses in grapevine genome. The characteristics of both exon–intron organizations and motif structures further supported the close evolutionary relationships of VvCYP superfamily as well as the reliability of phylogenetic analysis. The gene number-based hierarchical cluster of CYP subfamilies of different plants demonstrated that the loss of CYP families seems to be limited to single species or single taxa. Promoter analysis elucidated various cis-regulatory elements related to ph...
Source: Frontiers in Genetics - February 18, 2020 Category: Genetics & Stem Cells Source Type: research

Whole Transcriptome Analysis of Mesenchyme Tissue in Sika Deer Antler Revealed the CeRNAs Regulatory Network Associated With Antler Development
In this study, we analyzed the time series expression data of nine samples from mesenchyme layer in three male sika deer in the early period of the antler with a saddle-like appearance (30 days), the rapid growth period of the antler with two branches (60 days), and the final period of the antler with three branches (90 days). Whole Transcriptome sequencing results show that in the 30 d versus 60 d group, 1,464 genes, 85 long noncoding RNAs (lncRNAs), and 61 miRNAs were identified as differentially expressed; 1,748 genes, 138 lncRNAs, and 78 miRNAs were identified as differentially expressed in 30d versus 90d group; and 81...
Source: Frontiers in Genetics - February 18, 2020 Category: Genetics & Stem Cells Source Type: research

Integrative Clustering Reveals a Novel Subtype of Soft Tissue Sarcoma With Poor Prognosis
ConclusionIntegrative clustering analysis revealed that the STSs could be clustered into three sub-clusters. The ceRNA network, especially the subnetwork LncRNA (KCNQ1OT1)-miRNA (has-miR-29c-3p)-mRNA (JARID2, CDK8, DNMT3A, TET1) was a promising therapeutic target for the STS sub-cluster associated with a poor prognosis. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 17, 2020 Category: Genetics & Stem Cells Source Type: research

New Insights Into Chromomere Organization Provided by Lampbrush Chromosome Microdissection and High-Throughput Sequencing
Giant lampbrush chromosomes (LBCs) typical for growing oocytes of various animal species are characterized by a specific chromomere-loop appearance and massive transcription. Chromomeres represent universal units of chromatin packaging at LBC stage. While quite good progress has been made in investigation of LBCs structure and function, chromomere organization still remains poorly understood. To extend our knowledge on chromomere organization, we applied microdissection to chicken LBCs. In particular, 31 and 5 individual chromomeres were dissected one by one along the macrochromosome 4 and one microchromosome, respectively...
Source: Frontiers in Genetics - February 17, 2020 Category: Genetics & Stem Cells Source Type: research

Identification of Specific Long Non-Coding Ribonucleic Acid Signatures and Regulatory Networks in Prostate Cancer in Fine-Needle Aspiration Biopsies
Prostate cancer (PCa) is one of the most common tumors in men and can be lethal, especially if left untreated. A substantial majority of PCa patients not only are diagnosed based on fine needle aspiration (FNA) biopsies, but their treatment choices are also largely driven by the pathological findings obtained with these FNA specimens. It is widely believed that lncRNAs have strong biological significance, but their specific functions and regulatory networks have not been elucidated. LncRNAs may serve as key players and regulators of PCa carcinogenesis and could be novel biomarkers of this cancer. To identify potential mark...
Source: Frontiers in Genetics - February 14, 2020 Category: Genetics & Stem Cells Source Type: research

WGCNA Co-Expression Network Analysis Reveals ILF3-AS1 Functions as a CeRNA to Regulate PTBP1 Expression by Sponging miR-29a in Gastric Cancer
Gastric cancer (GC) is one of the most common types of human cancers worldwide. However, the detail mechanisms underlying GC progression remained to be investigated. The present study identified 2823 differently expressed mRNAs and 441 differently expressed lncRNAs in GC. WGCNA was conducted to identify highly correlated lncRNAs and mRNAs. Bioinformatics analysis observed that these dysregulated lncRNAs were significantly associated with the regulation of angiogenesis, cell division, cell-cell adhesion, blood vessel development, adaptive immune response, gastric acid secretion, immune response. Co-expression analysis ident...
Source: Frontiers in Genetics - February 14, 2020 Category: Genetics & Stem Cells Source Type: research

Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle
Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp–4,477,860 bp in size), cover...
Source: Frontiers in Genetics - February 14, 2020 Category: Genetics & Stem Cells Source Type: research

The Sole Mycobacterium smegmatis MazF Toxin Targets tRNALys to Impart Highly Selective, Codon-Dependent Proteome Reprogramming
Survival of mycobacteria, both free-living and host-dependent pathogenic species, is dependent on their ability to evade being killed by the stresses they routinely encounter. Toxin-antitoxin (TA) systems are unique to bacteria and archaea and are thought to function as stress survival proteins. Here, we study the activity of the endoribonuclease toxin derived from the MazEF TA system in Mycobacterium smegmatis, designated MazEF-ms. We first enlisted a specialized RNA-seq method, 5’ RNA-seq, to identify the primary RNA target(s) of the MazF-ms toxin. Just two tRNA species, tRNALys-UUU and tRNALys-CUU, were targeted f...
Source: Frontiers in Genetics - February 14, 2020 Category: Genetics & Stem Cells Source Type: research

Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas
The domestic pig (Sus scrofa) is both an economically important livestock species and a model for biomedical research. Two highly contiguous pig reference genomes have recently been released. To support functional annotation of the pig genomes and comparative analysis with large human transcriptomic data sets, we aimed to create a pig gene expression atlas. To achieve this objective, we extended a previous approach developed for the chicken. We downloaded RNAseq data sets from public repositories, down-sampled to a common depth, and quantified expression against a reference transcriptome using the mRNA quantitation tool, K...
Source: Frontiers in Genetics - February 14, 2020 Category: Genetics & Stem Cells Source Type: research

An Information Entropy-Based Approach for Computationally Identifying Histone Lysine Butyrylation
Butyrylation plays a crucial role in the cellular processes. Due to limit of techniques, it is a challenging task to identify histone butyrylation sites on a large scale. To fill the gap, we propose an approach based on information entropy and machine learning for computationally identifying histone butyrylation sites. The proposed method achieves 0.92 of area under the receiver operating characteristic (ROC) curve over the training set by 3-fold cross validation and 0.80 over the testing set by independent test. Feature analysis implies that amino acid residues in the down/upstream of butyrylation sites would exhibit spec...
Source: Frontiers in Genetics - February 14, 2020 Category: Genetics & Stem Cells Source Type: research

Spinal Muscular Atrophy in the Black South African Population: A Matter of Rearrangement?
This study emphasizes the lack of understanding of the architecture of the SMN region as well as the cause of SMA in the black SA population. These factors need to be taken into account when counseling and performing diagnostic testing in black populations. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 13, 2020 Category: Genetics & Stem Cells Source Type: research

Holistic Optimization of Bioinformatic Analysis Pipeline for Detection and Quantification of 2 ′-O-Methylations in RNA by RiboMethSeq
A major trend in the epitranscriptomics field over the last 5 years has been the high-throughput analysis of RNA modifications by a combination of specific chemical treatment(s), followed by library preparation and deep sequencing. Multiple protocols have been described for several important RNA modifications, such as 5-methylcytosine (m5C), pseudouridine (ψ), 1-methyladenosine (m1A), and 2′-O-methylation (Nm). One commonly used method is the alkaline cleavage-based RiboMethSeq protocol, where positions of reads' 5'-ends are used to distinguish nucleotides protected by ribose methylation. This method was successf...
Source: Frontiers in Genetics - February 13, 2020 Category: Genetics & Stem Cells Source Type: research

In Situ Genetic Evaluation of European Larch Across Climatic Regions Using Marker-Based Pedigree Reconstruction
Sustainable and efficient forestry in a rapidly changing climate is a daunting task. The sessile nature of trees makes adaptation to climate change challenging; thereby, ecological services and economic potential are under risk. Current long-term and costly gene resources management practices have been primarily directed at a few economically important species and are confined to defined ecological boundaries. Here, we present a novel in situ gene-resource management approach that conserves forest biodiversity and improves productivity and adaptation through utilizing basic forest regeneration installations located across ...
Source: Frontiers in Genetics - February 13, 2020 Category: Genetics & Stem Cells Source Type: research

Corrigendum: Associations Between Behavioral Effects of Bisphenol A and DNA Methylation in Zebrafish Embryos
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 12, 2020 Category: Genetics & Stem Cells Source Type: research

epiCOLOC: Integrating Large-Scale and Context-Dependent Epigenomics Features for Comprehensive Colocalization Analysis
High-throughput genome-wide epigenomic assays, such as ChIP-seq, DNase-seq and ATAC-seq, have profiled a huge number of functional elements across numerous human tissues/cell types, which provide an unprecedented opportunity to interpret human genome and disease in context-dependent manner. Colocalization analysis determines whether genomic features are functionally related to a given search and will facilitate identifying the underlying biological functions characterizing intricate relationships with queries for genomic regions. Existing colocalization methods leveraged diverse assumptions and background models to assess ...
Source: Frontiers in Genetics - February 12, 2020 Category: Genetics & Stem Cells Source Type: research

MicroRNA-206 Regulation of Skin Pigmentation in Koi Carp (Cyprinus carpio L.)
MicroRNAs (miRNAs) are ∼22 nucleotide non-coding RNA molecules that act as crucial roles in plenty of biological processes. However, the molecular and cellular mechanisms of miRNAs to regulate skin color differentiation and pigmentation in fish have not been fully understood. Herein, we revealed that miR-206, a skin-enriched miRNA, regulates melanocortin 1 receptor (Mc1r, a key regulator of melanogenesis) expression by binding to its 3'-untranslated (UTR) region through bioinformatics and luciferase reporter assay in koi carp (Cyprinus carpio L.). The analysis of spatial and temporal expression patterns suggested that ...
Source: Frontiers in Genetics - February 12, 2020 Category: Genetics & Stem Cells Source Type: research

Epigenetic Modifications May Regulate the Activation of the Hypopharyngeal Gland of Honeybees (Apis Mellifera) During Winter
DNA methylation is an epigenetic modification primarily responsible for individual phenotypic variation. This modification has been reported to play an important role in caste, brain plasticity, and body development in honeybees (Apis mellifera). Here, we report the DNA methylation profile of honeybee hypopharyngeal glands, from atrophy in winter to arousal in the following spring, through the use of whole-genome bisulfite sequencing. Consistent with previous studies in other Apis species, we found low methylation levels of the hypopharyngeal gland genome that were mostly of the CG type. Notably, we observed a strong prefe...
Source: Frontiers in Genetics - February 12, 2020 Category: Genetics & Stem Cells Source Type: research

Radial Organization in the Mammalian Nucleus
In eukaryotic cells, most of the genetic material is contained within a highly specialized organelle—the nucleus. A large body of evidence indicates that, within the nucleus, chromatinized DNA is spatially organized at multiple length scales. The higher-order organization of chromatin is crucial for proper execution of multiple genome functions, including DNA replication and transcription. Here, we review our current knowledge on the spatial organization of chromatin in the nucleus of mammalian cells, focusing in particular on how chromatin is radially arranged with respect to the nuclear lamina. We then discuss the ...
Source: Frontiers in Genetics - February 12, 2020 Category: Genetics & Stem Cells Source Type: research

Integrated Analysis of Large-Scale Omics Data Revealed Relationship Between Tissue Specificity and Evolutionary Dynamics of Small RNAs in Maize (Zea mays)
The evolutionary dynamics and tissue specificity of protein-coding genes are well documented in plants. However, the evolutionary consequences of small RNAs (sRNAs) on tissue-specific functions remain poorly understood. Here, we performed integrated analysis of 195 deeply sequenced sRNA libraries of maize B73, representing more than 10 tissues, and identified a comprehensive list of 419 maize microRNA (miRNA) genes, 271 of which were newly discovered in this study. We further characterized the evolutionary dynamics and tissue specificity of miRNA genes and corresponding miRNA isoforms (isomiRs). Our analysis revealed that ...
Source: Frontiers in Genetics - February 11, 2020 Category: Genetics & Stem Cells Source Type: research

Mutation in Fbxo11 Leads to Altered Immune Cell Content in Jeff Mouse Model of Otitis Media
The Jeff mouse mutant carries a mutation in the F-box only 11 gene (Fbxo11) and heterozygous animals display conductive deafness due to the development of otitis media (OM). The Fbxo11 locus is also associated with chronic otitis media with effusion (COME) and recurrent OM in humans. The Jeff mutation affects the ability of FBXO11 to stabilize p53 that leads to perturbation in the TGF-beta/Smad2 signaling pathway important in immunity and inflammation. In the current study, we evaluated the effect of the Jeff mutation on the immune cell content using multicolor flow cytometry. In blood of Jeff heterozygotes, we observed a ...
Source: Frontiers in Genetics - February 11, 2020 Category: Genetics & Stem Cells Source Type: research

Systematic Nucleotide Exchange Analysis of ESTs From the Human Cancer Genome Project Report: Origins of 347 Unknown ESTs Indicate Putative Transcription of Non-Coding Genomic Regions
Expressed sequence tags (ESTs) provide an imprint of cellular RNA diversity irrespectively of sequence homology with template genomes. NCBI databases include many unknown RNAs from various normal and cancer cells. These are usually ignored assuming sequencing artefacts or contamination due to their lack of sequence homology with template DNA. Here, we report genomic origins of 347 ESTs previously assumed artefacts/unknown, from the FAPESP/LICR Human Cancer Genome Project. EST template detection uses systematic nucleotide exchange analyses called swinger transformations. Systematic nucleotide exchanges replace systematicall...
Source: Frontiers in Genetics - February 11, 2020 Category: Genetics & Stem Cells Source Type: research

Neonatal Alcohol Exposure in Mice Induces Select Differentiation- and Apoptosis-Related Chromatin Changes Both Independent of and Dependent on Sex
Prenatal alcohol exposure (PAE) affects many aspects of physiology and behavior, including brain development. Specifically, ethanol can influence expression of genes important for brain growth, including chromatin modifiers. Ethanol can also increase apoptotic cell death in the brain and alter epigenetic profiles such as modifications to histones and DNA methylation. Although differential sex outcomes and disruptions to the function of multiple brain regions have been reported in fetal alcohol spectrum disorder (FASD), the majority of our knowledge on molecular epigenetic and apoptotic dysregulation in PAE is based on data...
Source: Frontiers in Genetics - February 11, 2020 Category: Genetics & Stem Cells Source Type: research

Identification of the Prognosis-Related lncRNAs and Genes in Gastric Cancer
In this study, using TCGA data, we identified 585 long noncoding RNAs (lncRNAs) and 927 protein-coding genes (PCGs) correlated with the overall survival rate of gastric cancer. Functional enrichment analysis revealed that the prognostic genes positively correlated with death rates were enriched in pathways, including gap junction, focal adhesion, cell adhesion molecules (CAMs), and neuroactive ligand-receptor interaction, that are involved in the tumor microenvironment and cell-cell communications, suggesting that their dysregulation may promote the tumor progression. To evaluate the performance of the prognostic genes in ...
Source: Frontiers in Genetics - February 11, 2020 Category: Genetics & Stem Cells Source Type: research

Genetic Variation Related to High Elevation Adaptation Revealed by Common Garden Experiments in Pinus yunnanensis
Local adaptation, adaptation to specialized niches and environmental clines have been extensively reported for forest trees. Investigation of the adaptive genetic variation is crucial for forest resource management and breeding, especially in the context of global climate change. Here, we utilized a Pinus yunnanensis common garden experiments established at high and low elevation sites to assess the differences in growth and survival among populations and between the two common garden sites. The studied traits showed significant variation between the two test sites and among populations, suggesting adaptive divergence. To ...
Source: Frontiers in Genetics - February 11, 2020 Category: Genetics & Stem Cells Source Type: research

Emerging Roles of Heat-Induced circRNAs Related to Lactogenesis in Lactating Sows
In this study we establish a valuable resource for circRNA biology in sow lactation. Analysis of a circRNA-miRNA-mRNA network further uncovered a novel layer of post-transcriptional regulation that could be used to improve sow milk production. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 11, 2020 Category: Genetics & Stem Cells Source Type: research

Corrigendum: Identification of Breast Cancer Subtype Specific MicroRNAs Using Survival Analysis to Find Their Role in Transcriptomic Regulation
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 11, 2020 Category: Genetics & Stem Cells Source Type: research

Endoplasmic Reticulum Stress Activation in Alport Syndrome Varies Between Genotype and Cell Type
In this study, we explored the relationship between the COL4A5 genotype and cell type in ERS activation. We obtained skin fibroblasts from Alport syndrome patients with different COL4A5 mutation categories [i.e., a missense mutation (c.4298G> T, p.Gly1433Val) in exon 47, a splicing mutation (c.1949–1G> A) in intron 25 and an insertion (c.573_c.574insG, p. Pro193Alafs*23) in exon 10], and then reprogrammed these fibroblasts into induced pluripotent stem cells (iPSCs). Interestingly, no significant dysregulation of ERS pathway markers was observed for the three COL4A5 mutant iPSCs; however, significant activation...
Source: Frontiers in Genetics - February 10, 2020 Category: Genetics & Stem Cells Source Type: research

The Genetics of Differential Gene Expression Related to Fruit Traits in Strawberry (Fragaria ×ananassa)
Octoploid strawberry (Fragaria ×ananassa) is a major specialty crop under intense annual selection for traits relating to plant vigor and fruit quality. Most functional validation experiments rely on transgenic or transient gene expression assays in the mature receptacle. These findings are not typically translatable to breeding without identifying a natural genetic source of transcript level variation, and developing reliable markers for selection in octoploids. Expression QTL (eQTL) analysis is a genetic/transcriptomic association approach for identifying sequence variants predicting differential expression. This e...
Source: Frontiers in Genetics - February 8, 2020 Category: Genetics & Stem Cells Source Type: research

Analysis of Alternative Splicing and Alternative Polyadenylation in Populus alba var. pyramidalis by Single-Molecular Long-Read Sequencing
In this study, using single-molecular real-time (SMRT) and next-generation high-throughput sequencing (NGS) platform, we sequenced transcripts from leaf, root, xylem, and phloem of P. alba var. pyramidalis, to obtain the full-length mRNA transcripts and annotate the complete structure. In total, 86,327 mapped full-length non-chimeric (FLNC) reads were identified, with 705 previously unannotated loci and 3,410 long noncoding RNAs (lncRNAs) and 174 fusion genes found. Alternative spicing (AS) events were detected in 7,536 genes, of which 4,652 genes had multiple AS events. A total of 10,213 alternative polyadenylation (APA) ...
Source: Frontiers in Genetics - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Current Understanding of Host Genetics of Otitis Media
The pathogenesis of otitis media (OM), an inflammatory disease of the middle ear (ME), involves interplay between many different factors, including the pathogenicity of infectious pathogens, host immunological status, environmental factors, and genetic predisposition, which is known to be a key determinant of OM susceptibility. Animal models and human genetics studies have identified many genes and gene variants associated with OM susceptibility: genes that encode components of multiple signaling pathways involved in host immunity and inflammatory responses of the ME mucosa; genes involved in cellular function, such as muc...
Source: Frontiers in Genetics - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Alveolar Macrophage Chromatin Is Modified to Orchestrate Host Response to Mycobacterium bovis Infection
Bovine tuberculosis is caused by infection with Mycobacterium bovis, which can also cause disease in a range of other mammals, including humans. Alveolar macrophages are the key immune effector cells that first encounter M. bovis and how the macrophage epigenome responds to mycobacterial pathogens is currently not well understood. Here, we have used chromatin immunoprecipitation sequencing (ChIP-seq), RNA-seq and miRNA-seq to examine the effect of M. bovis infection on the bovine alveolar macrophage (bAM) epigenome. We show that H3K4me3 is more prevalent, at a genome-wide level, in chromatin from M. bovis-infected bAM comp...
Source: Frontiers in Genetics - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Analysis of the Clinicopathologic Characteristics of Lung Adenocarcinoma With CTNNB1 Mutation
ConclusionsFemale patients and nonsmokers are likely to harbor CTNNB1 mutation and primary lung adenocarcinoma with mutated CTNNB1 has a poor prognosis. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Transcriptome Changes of Mycobacterium marinum in the Process of Resuscitation From Hypoxia-Induced Dormancy
In this study, we examined the transcriptional changes of Mycobacterium marinum (M. marinum), a pathogenic mycobacterial species closely related to M. tb, at different stages of resuscitation from hypoxia-induced dormancy. RNA-seq analyses were performed on M. marinum cultures recovered at multiple time points after resuscitation. Differentially expressed genes (DEGs) at each time period were identified and analyzed. Co-expression networks of transcription factors and DEGs in each period were constructed. In addition, we performed a weighted gene co-expression network analysis (WGCNA) on all genes and obtained 12 distinct ...
Source: Frontiers in Genetics - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Novel and Known Gene-Smoking Interactions With cIMT Identified as Potential Drivers for Atherosclerosis Risk in West-African Populations of the AWI-Gen Study
DiscussionThis is the first gene-smoking interaction study for cIMT, as a risk factor for atherosclerosis, in sub-Saharan African populations. In addition to replicating previously known signals for RCBTB1, we identified two novel genomic regions (TBC1D8, near BCHE) involved in this gene-environment interaction. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Erratum: Construction of a Suite of Computable Biological Network Models Focused on Mucociliary Clearance in the Respiratory Tract
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Normalization Methods on Single-Cell RNA-seq Data: An Empirical Survey
Data normalization is vital to single-cell sequencing, addressing limitations presented by low input material and various forms of bias or noise present in the sequencing process. Several such normalization methods exist, some of which rely on spike-in genes, molecules added in known quantities to serve as a basis for a normalization model. Depending on available information and the type of data, some methods may express certain advantages over others. We compare the effectiveness of seven available normalization methods designed specifically for single-cell sequencing using two real data sets containing spike-in genes and...
Source: Frontiers in Genetics - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Inferring Regulatory Networks From Mixed Observational Data Using Directed Acyclic Graphs
We present a new mixed DAG (mDAG) algorithm to infer the regulatory pathway from mixed observational data containing both continuous variables (e.g. expression of genes) and categorical variables (e.g. categorical phenotypes or single nucleotide polymorphisms). Our method can identify upstream causal factors and downstream effectors closely linked to a variable and generate hypotheses for causal direction of regulatory pathways. We propose a new permutation method to test the conditional independence of variables of mixed types, which is the key for mDAG. We also utilize an L1 regularization in mDAG to ensure it can recove...
Source: Frontiers in Genetics - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Phylogenetic Tree Inference: A Top-Down Approach to Track Tumor Evolution
In this study, we present a novel and easy-to-use method, PTI (Phylogenetic Tree Inference), which use an iterative top-down approach to infer the phylogenetic tree structure of multiple tumor biopsies from same patient using just the presence or absence of somatic mutations without their allele frequencies. Therefore PTI can be used in a wide range of cases even when allele frequency data is not available. Comparison with existing state-of-the-art methods, such as LICHeE, Treeomics, and BAMSE, shows that PTI achieves similar or slightly better performance within a short run time. Moreover, this method is generally applica...
Source: Frontiers in Genetics - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Identification of Biological Pathways Contributing to Marbling in Skeletal Muscle to Improve Beef Cattle Breeding
Red meat is an important dietary source that provides part of the nutritional requirements. Intramuscular fat, known as marbling, is located throughout skeletal muscle. Marbling is a trait of major economic relevance that positively influences sensory quality aspects. The aim of the present study was to identify and better understand biological pathways defining marbling in beef cattle. Pathway analysis was performed in PathVisio with publicly available transcriptomic data from semitendinosus muscle of well-marbled and lean-marbled beef. Moreover, for Bos taurus we created a gene identifier mapping database with bridgeDb a...
Source: Frontiers in Genetics - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Sparse Convolutional Neural Networks for Genome-Wide Prediction
In conclusion, the CNNGWP provides a promising approach for GWP, but the magnitude of improvement depends on the genetic architecture and the heritability. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 6, 2020 Category: Genetics & Stem Cells Source Type: research

Corrigendum: Digitaldlsorter: Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 6, 2020 Category: Genetics & Stem Cells Source Type: research

H3K9 Demethylation-Induced R-Loop Accumulation Is Linked to Disorganized Nucleoli
The nucleolar structure and integrity are important for a range of cellular functions of the nucleoli. It has been shown that cells lacking histone H3 Lysine 9 (H3K9) methylation form fragmented nucleoli. However, the molecular mechanism involved remains poorly understood. Here, we present evidence suggesting that loss of H3K9 dimethylation (H3K9me2) triggers R-loop accumulation at the rDNA locus, which further leads to the multilobed nucleoli. We reveal that suppression of H3K9 methyltransferase G9a by the inhibitor BIX 01294 causes R-loop accumulation at the rDNA region as well as inducing formation of multiple nucleoli....
Source: Frontiers in Genetics - February 6, 2020 Category: Genetics & Stem Cells Source Type: research

Functional Innovation in the Evolution of the Calcium-Dependent System of the Eukaryotic Endoplasmic Reticulum
We present evidence that the key EF-hand Ca2+-binding components had their origins in a likely bacterial symbiont other than the mitochondrial progenitor, whereas the protein phosphatase subunit of the ancestral calcineurin complex was likely inherited from the asgard archaeal progenitor of the stem eukaryote. This further points to the potential origin of the eukaryotes in a Ca2+-rich biomineralized environment such as stromatolites. We further show that throughout eukaryotic evolution there were several acquisitions from bacteria of key components of the Ca2+-stores system, even though no prokaryotic lineage possesses a ...
Source: Frontiers in Genetics - February 6, 2020 Category: Genetics & Stem Cells Source Type: research

Histone Acetylation as a Regenerative Target in the Dentine-Pulp Complex
If dental caries (or tooth decay) progresses without intervention, the infection will advance through the dentine leading to severe pulpal inflammation (irreversible pulpitis) and pulp death. The current management of irreversible pulpits is generally root-canal-treatment (RCT), a destructive, expensive, and often unnecessary procedure, as removal of the injurious stimulus alone creates an environment in which pulp regeneration may be possible. Current dental-restorative-materials stimulate repair non-specifically and have practical limitations; as a result, opportunities exist for the development of novel therapeutic stra...
Source: Frontiers in Genetics - February 6, 2020 Category: Genetics & Stem Cells Source Type: research

The Genetics and Epigenetics of 22q11.2 Deletion Syndrome
Chromosome 22q11.2 deletion syndrome (22q11.2del) is a complex, multi-organ disorder noted for its varying severity and penetrance among those affected. The clinical problems comprise congenital malformations; cardiac problems including outflow tract defects, hypoplasia of the thymus, hypoparathyroidism, and/or dysmorphic facial features. Additional clinical issues that can appear over time are autoimmunity, renal insufficiency, developmental delay, malignancy and neurological manifestations such as schizophrenia. The majority of individuals with 22q11.2del have a 3 Mb deletion of DNA on chromosome 22, leading to a haploin...
Source: Frontiers in Genetics - February 6, 2020 Category: Genetics & Stem Cells Source Type: research

Erratum: Identification of Breast Cancer Stem Cell Related Genes Using Functional Cellular Assays Combined With Single-Cell RNA Sequencing in MDA-MB-231 Cells
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 5, 2020 Category: Genetics & Stem Cells Source Type: research

CHG: A Systematically Integrated Database of Cancer Hallmark Genes
ConclusionsIn summary, CHG, which was constructed based on a hallmark feature set, provides a new perspective for analyzing the diversity and development of cancers. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - February 5, 2020 Category: Genetics & Stem Cells Source Type: research