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Genome annotation

DarrenM Hutt, Salvatore Loguercio, Alexandre Rosa Campos, William E Balch
The advent of precision medicine for genetic diseases has been hampered by the large number of variants that cause familial and somatic disease, a complexity that is further confounded by the impact of genetic modifiers. To begin to understand differences in onset, progression and therapeutic response that exist among disease-causing variants, we present the proteomic variant approach (ProVarA), a proteomic method that integrates mass spectrometry with genomic tools to dissect the etiology of disease. To illustrate its value, we examined the impact of variation in cystic fibrosis (CF), where 2025 disease-associated mutations in the CF transmembrane conductance regulator (CFTR) gene have been annotated and where individual genotypes exhibit phenotypic heterogeneity and response to therapeutic intervention...
June 17, 2018: Journal of Molecular Biology
Samuel M D Seaver, Claudia Lerma-Ortiz, Neal Conrad, Arman Mikaili, Avinash Sreedasyam, Andrew D Hanson, Christopher S Henry
Genome-scale metabolic reconstructions help understand and engineer metabolism. Next-Gen sequencing technologies are delivering genomes and transcriptomes for an ever-widening range of plants. While such omic data can, in principle, be used to compare metabolic networks in different species, organs, and environmental conditions, these comparisons require a standardized framework for metabolic network reconstruction from transcript data. We previously introduced the PlantSEED as a framework covering primary metabolism for ten species...
June 20, 2018: Plant Journal: for Cell and Molecular Biology
Wei Lu, Yongcan Xu, Jiewei Xu, Zhong Wang, Guochao Ye
Recently, a growing number of evidence has revealed that long noncoding RNAs (lncRNAs) act as key regulators in various cellular biologic processes, and dysregulation of lncRNAs involves in tumorigenesis and cancer progression. However, the expression pattern, clinical relevance, and biologic function of most lncRNAs in human thyroid cancer remain unclear. To identify more thyroid-cancer-associated lncRNAs, we analyzed the expression profile of lncRNAs in thyroid cancer tissues and adjacent normal or non-tumor tissues using RNA sequencing data and gene microarray data from The Cancer Genome Atlas and Gene Expression Omnibus...
June 20, 2018: Cancer Medicine
Tsvetelina Yungareva, Zoltan Urshev
In lactobacilli the aggregation phenotype is linked to their ability to colonize the intestinal and urogenital tracts and to counteract pathogenic bacteria. In all available complete genome sequences of Lactobacillus delbrueckii ssp. bulgaricus there are at least two genes putatively related to aggregation, one of which is annotated as aggregation-promoting factor (apf). Here we report the results from the in silico analysis of this gene and its product. The apf gene was present in the genome of all 70 tested L...
June 19, 2018: World Journal of Microbiology & Biotechnology
Matthias Heinig
Genetic variants at hundreds of loci associated with cardiovascular phenotypes have been identified by genome wide association studies. Most of these variants are located in intronic or intergenic regions rendering the functional and mechanistic follow up difficult. These non-protein-coding regions harbor regulatory sequences. Thus the study of genetic variants associated with transcription-so called expression quantitative trait loci-has emerged as a promising approach to identify regulatory sequence variants...
2018: Frontiers in Cardiovascular Medicine
A He, Y Ning, Y Wen, Y Cai, K Xu, Y Cai, J Han, L Liu, Y Du, X Liang, P Li, Q Fan, J Hao, X Wang, X Guo, T Ma, F Zhang
Aim: Osteoarthritis (OA) is caused by complex interactions between genetic and environmental factors. Epigenetic mechanisms control the expression of genes and are likely to regulate the OA transcriptome. We performed integrative genomic analyses to define methylation-gene expression relationships in osteoarthritic cartilage. Patients and Methods: Genome-wide DNA methylation profiling of articular cartilage from five patients with OA of the knee and five healthy controls was conducted using the Illumina Infinium HumanMethylation450 BeadChip (Illumina, San Diego, California)...
May 2018: Bone & Joint Research
Wei Liu, Zhidan Xiao, Chao Fan, Nonghui Jiang, Xiangchun Meng, Xu Xiang
Litchi ( Litchi chinensis ) is an important subtropical fruit tree with high commercial value. However, the short and centralized fruit maturation period of litchi cultivars represents a bottleneck for litchi production. Therefore, the development of novel cultivars with extremely early fruit maturation period is critical. Previously, we showed that the genotypes of extremely early-maturing (EEM), early-maturing (EM), and middle-to-late-maturing (MLM) cultivars at a specific locus SNP51 (substitution type C/T) were consistent with their respective genetic background at the whole-genome level; a homozygous C/C genotype at SNP51 systematically differentiated EEM cultivars from others...
2018: Frontiers in Plant Science
Koen Hoogendoorn, Lena Barra, Cees Waalwijk, Jeroen S Dickschat, Theo A J van der Lee, Marnix H Medema
Plant pathogenic fungi in the Fusarium genus cause severe damage to crops, resulting in great financial losses and health hazards. Specialized metabolites synthesized by these fungi are known to play key roles in the infection process, and to provide survival advantages inside and outside the host. However, systematic studies of the evolution of specialized metabolite-coding potential across Fusarium have been scarce. Here, we apply a combination of bioinformatic approaches to identify biosynthetic gene clusters (BGCs) across publicly available genomes from Fusarium , to group them into annotated families and to study gain/loss events of BGC families throughout the history of the genus...
2018: Frontiers in Microbiology
Jolanta Groszyk, Yuliya Yanushevska, Andrzej Zielezinski, Anna Nadolska-Orczyk, Wojciech M Karlowski, Waclaw Orczyk
GLYCOGEN SYNTHASE KINASE3/Shaggy-like kinases (GSKs) represent a highly conserved group of proteins found in all eukaryotes. In plants they are encoded by multigene families and integrate signaling of brassinosteroids, auxin and abscisic acid in wide range of physiological and developmental processes with a strong impact on plant responses to environmental and biotic factors. Based on comprehensively studied structures of 10 Arabidopsis thaliana GSK genes and encoded proteins we report identification and phylogenetic reconstruction of 7 transcriptionally active GSK genes in barley...
2018: PloS One
G-M Li, C-L Zhang, R-P Rui, B Sun, W Guo
OBJECTIVE: This paper aims at screening the common differential genes of coronary atherosclerotic heart disease (CAD) and ischemic cardiomyopathy (ICM), and to conduct pathway analysis and protein-protein interaction (PPI) network analysis for the differential genes. MATERIALS AND METHODS: The CAD and ICM datasets were collected from the Gene Expression Omnibus (GEO) database for human tumors to extract data components of peripheral blood RNA of patients and normal people in GSE71226 and GSE9128 chips; "limma" package of "R" software was used to screen the differential genes, and "pheatmap" package was applied to construct heat maps for the differential genes; Cytoscape, Database for Annotation, Visualization and Integration Discovery (DAVID) and String platforms were utilized for PPI network analysis, Genome Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis on the selected differential genes...
June 2018: European Review for Medical and Pharmacological Sciences
Fei Gao, Xue Wang, Xuming Li, Mingyue Xu, Huayun Li, Merhaba Abla, Huigai Sun, Shanjun Wei, Jinchao Feng, Yijun Zhou
Background: Ammopiptanthus nanus is a rare broad-leaved shrub in the desert and arid regions of Central Asia. This plant species exhibits extremely high tolerance to drought and freezing and has been used in abiotic tolerance research in plants. As a relic of the Tertiary period, A. nanus is of great significance to plant biogeographic research in the ancient Mediterranean region. Here we report a draft genome assembly using the PacBio platform and gene annotation for A. nanus. Findings: A total of 64...
June 18, 2018: GigaScience
Claudia Langenberg, Luca A Lotta
Genome-wide association studies have implicated around 250 genomic regions in predisposition to type 2 diabetes, with evidence for causal variants and genes emerging for several of these regions. Understanding of the underlying mechanisms, including the interplay between β-cell failure, insulin sensitivity, appetite regulation, and adipose storage has been facilitated by the integration of multidimensional data for diabetes-related intermediate phenotypes, detailed genomic annotations, functional experiments, and now multiomic molecular features...
June 16, 2018: Lancet
Christophe Plomion, Jean-Marc Aury, Joëlle Amselem, Thibault Leroy, Florent Murat, Sébastien Duplessis, Sébastien Faye, Nicolas Francillonne, Karine Labadie, Grégoire Le Provost, Isabelle Lesur, Jérôme Bartholomé, Patricia Faivre-Rampant, Annegret Kohler, Jean-Charles Leplé, Nathalie Chantret, Jun Chen, Anne Diévart, Tina Alaeitabar, Valérie Barbe, Caroline Belser, Hélène Bergès, Catherine Bodénès, Marie-Béatrice Bogeat-Triboulot, Marie-Lara Bouffaud, Benjamin Brachi, Emilie Chancerel, David Cohen, Arnaud Couloux, Corinne Da Silva, Carole Dossat, François Ehrenmann, Christine Gaspin, Jacqueline Grima-Pettenati, Erwan Guichoux, Arnaud Hecker, Sylvie Herrmann, Philippe Hugueney, Irène Hummel, Christophe Klopp, Céline Lalanne, Martin Lascoux, Eric Lasserre, Arnaud Lemainque, Marie-Laure Desprez-Loustau, Isabelle Luyten, Mohammed-Amin Madoui, Sophie Mangenot, Clémence Marchal, Florian Maumus, Jonathan Mercier, Célia Michotey, Olivier Panaud, Nathalie Picault, Nicolas Rouhier, Olivier Rué, Camille Rustenholz, Franck Salin, Marçal Soler, Mika Tarkka, Amandine Velt, Amy E Zanne, Francis Martin, Patrick Wincker, Hadi Quesneville, Antoine Kremer, Jérôme Salse
Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes 1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times 2 . With 450 species spread throughout Asia, Europe and America 3 , oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans...
June 18, 2018: Nature Plants
Mengyu Shen, Yuhui Yang, Wei Shen, Lujia Cen, Jeffrey S McLean, Wenyuan Shi, Shuai Le, Xuesong He
The human oral cavity is home to a large number of bacteria and bacteriophages (phages). However, the biology of oral phages as members of the human microbiome is not well understood. Recently, we isolated an Actinomyces odontolyticus subsp. Actinosynbacte r strain XH001 from human oral cavity, and genomic analysis revealed the presence of an intact prophage, named xhp1. Here we demonstrated that xhp1 is a linear plasmid-like prophage, which is a newly identified phage of A. odontolyticus Prophage xhp1 genome is 35 kb linear double-stranded DNA with 10 bp single-stranded cohesive ends at 3' of both ends...
June 18, 2018: Applied and Environmental Microbiology
Ning Ma, Joe Zhang, Ilanit Itzhaki, Sophia L Zhang, Haodong Chen, Francois Haddad, Tomoya Kitani, Kitchener D Wilson, Lei Tian, Rajani Shrestha, Haodi Wu, Chi Keung Lam, Nazish Sayed, Joseph C Wu
Background -The progression toward low-cost and rapid next-generation sequencing has uncovered a multitude of variants of uncertain significance (VUS) in both patients and asymptomatic "healthy" individuals. A VUS is a rare or novel variant for which disease pathogenicity has not been conclusively demonstrated or excluded, and thus cannot be definitively annotated. VUS, therefore, pose critical clinical interpretation and risk-assessment challenges, and new methods are urgently needed to better characterize their pathogenicity...
June 18, 2018: Circulation
Rui Zhang, Tong-Tong Zhang, Gao-Qiang Zhai, Xian-Yu Guo, Yuan Qin, Ting-Qing Gan, Yu Zhang, Gang Chen, Wei-Jia Mo, Zhen-Bo Feng
BACKGROUND: This study was carried out to discover the underlying role that HOXA11 plays in lung squamous cancer (LUSC) and uncover the potential corresponding molecular mechanisms and functions of HOXA11-related genes. METHODS: Twenty-three clinical paired LUSC and non-LUSC samples were utilized to examine the level of HOXA11 using quantitative real-time polymerase chain reaction (qRT-PCR). The clinical significance of HOXA11 was systematically analyzed based on 475 LUSC and 18 non-cancerous adjacent tissues from The Cancer Genome Atlas (TCGA) database...
June 18, 2018: World Journal of Surgical Oncology
Peter D Karp, Daniel Weaver, Mario Latendresse
BACKGROUND: Reaction gap filling is a computational technique for proposing the addition of reactions to genome-scale metabolic models to permit those models to run correctly. Gap filling completes what are otherwise incomplete models that lack fully connected metabolic networks. The models are incomplete because they are derived from annotated genomes in which not all enzymes have been identified. Here we compare the results of applying an automated likelihood-based gap filler within the Pathway Tools software with the results of manually gap filling the same metabolic model...
June 19, 2018: BMC Systems Biology
Elizabeth M Kennedy, George N Goehring, Michael H Nichols, Chloe Robins, Divya Mehta, Torsten Klengel, Eleazar Eskin, Alicia K Smith, Karen N Conneely
BACKGROUND: Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome. RESULTS: We used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells...
June 19, 2018: BMC Genomics
Tariq Ismail, Nighat Fatima, Syed Aun Muhammad, Syed Saoud Zaidi, Nisar Rehman, Izhar Hussain, Najam Us Sahr Tariq, Imran Amirzada, Abdul Mannan
Candida albicans (Candida albicans) is one of the major sources of nosocomial infections in humans which may prove fatal in 30% of cases. The hospital acquired infection is very difficult to treat affectively due to the presence of drug resistant pathogenic strains, therefore there is a need to find alternative drug targets to cure this infection. In silico and computational level frame work was used to prioritize and establish antifungal drug targets of Candida albicans. The identification of putative drug targets was based on acquiring 5090 completely annotated genes of Candida albicans from available databases which were categorized into essential and non-essential genes...
2018: Acta Biochimica Polonica
Charlotte Capitanchik, Charles Dixon, Selene K Swanson, Laurence Florens, Alastair R W Kerr, Eric C Schirmer
Nuclear envelopathies/laminopathies yield tissue-specific pathologies, yet arise from mutation of ubiquitously-expressed genes. One possible explanation of this tissue specificity is that tissue-specific partners become disrupted from larger complexes, but a little investigated alternate hypothesis is that the mutated proteins themselves have tissue-specific splice variants. Here, we analyze RNA-Seq datasets to identify muscle-specific splice variants of nuclear envelope genes that could be relevant to the study of laminopathies, particularly muscular dystrophies, that are not currently annotated in sequence databases...
June 18, 2018: Nucleus
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