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Gene Mapping

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https://www.readbyqxmd.com/read/29161273/enrichment-of-colorectal-cancer-associations-in-functional-regions-insight-for-using-epigenomics-data-in-the-analysis-of-whole-genome-sequence-imputed-gwas-data
#1
Stephanie A Bien, Paul L Auer, Tabitha A Harrison, Conghui Qu, Charles M Connolly, Peyton G Greenside, Sai Chen, Sonja I Berndt, Stéphane Bézieau, Hyun M Kang, Jeroen Huyghe, Hermann Brenner, Graham Casey, Andrew T Chan, John L Hopper, Barbara L Banbury, Jenny Chang-Claude, Stephen J Chanock, Robert W Haile, Michael Hoffmeister, Christian Fuchsberger, Mark A Jenkins, Suzanne M Leal, Mathieu Lemire, Polly A Newcomb, Steven Gallinger, John D Potter, Robert E Schoen, Martha L Slattery, Joshua D Smith, Loic Le Marchand, Emily White, Brent W Zanke, Goncalo R Abeçasis, Christopher S Carlson, Ulrike Peters, Deborah A Nickerson, Anshul Kundaje, Li Hsu
BACKGROUND: The evaluation of less frequent genetic variants and their effect on complex disease pose new challenges for genomic research. To investigate whether epigenetic data can be used to inform aggregate rare-variant association methods (RVAM), we assessed whether variants more significantly associated with colorectal cancer (CRC) were preferentially located in non-coding regulatory regions, and whether enrichment was specific to colorectal tissues. METHODS: Active regulatory elements (ARE) were mapped using data from 127 tissues and cell-types from NIH Roadmap Epigenomics and Encyclopedia of DNA Elements (ENCODE) projects...
2017: PloS One
https://www.readbyqxmd.com/read/29160564/functional-differences-in-transport-properties-of-natural-hkt1-1-variants-influence-shoot-na-exclusion-in-grapevine-rootstocks
#2
Sam W Henderson, Jake D Dunlevy, Yue Wu, Deidre H Blackmore, Rob R Walker, Everard J Edwards, Matthew Gilliham, Amanda R Walker
Under salinity, Vitis spp. rootstocks can mediate salt (NaCl) exclusion from grafted V. vinifera scions enabling higher grapevine yields and production of superior wines with lower salt content. Until now, the genetic and mechanistic elements controlling sodium (Na(+) ) exclusion in grapevine were unknown. Using a cross between two Vitis interspecific hybrid rootstocks, we mapped a dominant quantitative trait locus (QTL) associated with leaf Na(+) exclusion (NaE) under salinity stress. The NaE locus encodes six high-affinity potassium transporters (HKT)...
November 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/29159890/whole-exome-sequencing-reveals-a-mutation-in-armc9-as-a-cause-of-mental-retardation-ptosis-and-polydactyly
#3
Anjana Kar, Shubha R Phadke, Aneek Das Bhowmik, Ashwin Dalal
Intellectual disability (ID) refers to deficits in mental abilities, social behavior, and motor skills to perform activities of daily living as compared to peers. Numerous genetic and environmental factors may be responsible for ID. We report on elucidation of molecular basis for syndromic ID associated with ptosis, polydactyly, and MRI features suggestive of Joubert syndrome using homozygosity mapping followed by exome sequencing. The analysis revealed a novel synonymous variation p.T293T (c.879G>A) which leads to a splicing defect in ARMC9 gene...
November 21, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29158636/chromosome-segment-detection-for-seed-size-and-shape-traits-using-an-improved-population-of-wild-soybean-chromosome-segment-substitution-lines
#4
Hongyan Yang, Wubin Wang, Qingyuan He, Shihua Xiang, Dong Tian, Tuanjie Zhao, Junyi Gai
Size and shape of soybean seeds are closely related to seed yield and market value. Annual wild soybeans have the potential to improve cultivated soybeans, but their inferior seed characteristics should be excluded. To detect quantitative trait loci (QTLs)/segments of seed size and shape traits in annual wild soybean, its chromosome segment substitution lines (CSSLs) derived from NN1138-2 (recurrent parent, Glycine max) and N24852 (donor parent, Glycine soja) and then modified 2 iterations (coded SojaCSSLP3) were improved further to contain more lines (diagonal segments) and less heterozygous and missing portions...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29158631/mapping-quantitative-trait-loci-for-heat-tolerance-at-the-booting-stage-using-chromosomal-segment-substitution-lines-in-rice
#5
Shan Zhu, Renliang Huang, Hnin Pwint Wai, Hongliang Xiong, Xianhua Shen, Haohua He, Song Yan
High temperature stress is a major obstacle in rice productivity. Considerable progress has been made on studying heat tolerance (HT) at different stages. However, the genetic basis of HT at the booting stage is poorly understood. In this study, we analyzed the morphological features of a heat-sensitive japonica cultivar Sasanishiki under natural high temperature stress at the booting stage. The anthers became smaller and the number, and fertility, of pollen grains were decreased significantly. As a result, there was a dramatic reduction in spikelet fertility...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29158626/genome-scanning-for-identification-and-mapping-of-receptor-like-kinase-rlk-gene-superfamily-in-solanum-tuberosum
#6
Sara Dezhsetan
Receptor-like kinases (RLKs) are a key class of genes that contribute to diverse phenomena from plant development to defense responses. The availability of completed potato genome sequences provide an excellent opportunity to identify and characterize RLK gene superfamily in this lineage. We identified 747 non-redundant RLK genes in the potato genome that were classified into 52 subfamilies, of which 58% members organized into tandem repeats. Nine of potato RLK subfamilies organized into tandem repeats. Also, six subfamilies exhibited lineage-specific expansion compared to Arabidopsis...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29158546/the-aegilops-tauschii-genome-reveals-multiple-impacts-of-transposons
#7
Guangyao Zhao, Cheng Zou, Kui Li, Kai Wang, Tianbao Li, Lifeng Gao, Xiaoxia Zhang, Hongjin Wang, Zujun Yang, Xu Liu, Wenkai Jiang, Long Mao, Xiuying Kong, Yuannian Jiao, Jizeng Jia
Wheat is an important global crop with an extremely large and complex genome that contains more transposable elements (TEs) than any other known crop species. Here, we generated a chromosome-scale, high-quality reference genome of Aegilops tauschii, the donor of the wheat D genome, in which 92.5% sequences have been anchored to chromosomes. Using this assembly, we accurately characterized genic loci, gene expression, pseudogenes, methylation, recombination ratios, microRNAs and especially TEs on chromosomes...
November 20, 2017: Nature Plants
https://www.readbyqxmd.com/read/29158339/genome-wide-mapping-of-decay-factor-mrna-interactions-in-yeast-identifies-nutrient-responsive-transcripts-as-targets-of-the-deadenylase-ccr4
#8
Jason E Miller, Liye Zhang, Haoyang Jiang, Yunfei Li, B Franklin Pugh, Joseph C Reese
The Ccr4-Not complex is a major regulator of stress responses that controls gene expression at multiple levels, from transcription to mRNA decay. Ccr4, a core subunit of the complex, is the main cytoplasmic deadenylase in Saccharomyces cerevisiae, however its mRNA targets have not been mapped on a genome-wide scale. Here we describe a genome-wide approach, RNA immunoprecipitation-high throughput sequencing (RIP-seq), to identify the RNAs bound to Ccr4, and two proteins that associate with it, Dhh1 and Puf5...
November 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29158335/a-deconvolution-protocol-for-chip-seq-reveals-analogous-enhancer-structures-on-the-mouse-and-human-ribosomal-rna-genes
#9
Jean-Clement Mars, Marianne Sabourin-Felix, Michel G Tremblay, Tom Moss
The combination of Chromatin Immunoprecipitation and Massively Parallel Sequencing, or ChIP-Seq, has greatly advanced our genome-wide understanding of chromatin and enhancer structures. However, its resolution at any given genetic locus is limited by several factors. In applying ChIP-Seq to the study of the ribosomal RNA genes, we found that a major limitation to resolution was imposed by the underlying variability in sequence coverage that very often dominates the protein-DNA interaction profiles. Here we describe a simple numerical deconvolution approach that in large part corrects for this variability and significantly improves both the resolution and quantitation of protein-DNA interaction maps deduced from ChIP-Seq data...
November 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29158257/structural-dissection-of-an-interaction-between-transcription-initiation-and-termination-factors-implicated-in-promoter-terminator-crosstalk
#10
Matthew Bratkowski, Ilona Christy Unarta, Lizhe Zhu, Murtada Shubbar, Xuhui Huang, Xin Liu
Functional crosstalk between the promoter and terminator of a gene has long been noted. Promoters and terminators are juxtaposed to form gene loops in several organisms and gene looping is thought to be involved in transcriptional regulation. The general transcription factor II B (TFIIB) and the C-terminal domain phosphatase Ssu72, essential factors of the transcription pre-initiation complex and the mRNA processing and polyadenylation complex, respectively, are important for gene loop formation. TFIIB and Ssu72 interact both genetically and physically, but the molecular basis of this interaction is not known...
November 20, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29157197/selection-for-female-traits-of-high-fertility-affects-male-reproductive-performance-and-alters-the-testicular-transcriptional-profile
#11
Marten Michaelis, Alexander Sobczak, Dirk Koczan, Martina Langhammer, Norbert Reinsch, Jennifer Schoen, Joachim M Weitzel
BACKGROUND: Many genes important for reproductive performance are shared by both sexes. However, fecundity indices are primarily based on female parameters such as litter size. We examined a fertility mouse line (FL2), which has a considerably increased number of offspring and a total litter weight of 180% compared to a randomly bred control line (Ctrl) after more than 170 generations of breeding. In the present study, we investigated whether there might be a parallel evolution in males after more than 40 years of breeding in this outbred mouse model...
November 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29157087/thanatos-an-integrative-data-resource-of-proteins-and-post-translational-modifications-in-the-regulation-of-autophagy
#12
Wankun Deng, Lili Ma, Ying Zhang, Jiaqi Zhou, Yongbo Wang, Zexian Liu, Yu Xue
Macroautophagy/autophagy is a highly conserved process for degrading cytoplasmic contents, determines cell survival or death, and regulates the cellular homeostasis. Besides ATG proteins, numerous regulators together with various post-translational modifications (PTMs) are also involved in autophagy. In this work, we collected 4,237 experimentally identified proteins regulated in autophagy and cell death pathways from the literature. Then we computationally identified potential orthologs of known proteins, and developed a comprehensive database of The Autophagy, Necrosis, ApopTosis OrchestratorS (THANATOS, http://thanatos...
November 20, 2017: Autophagy
https://www.readbyqxmd.com/read/29156785/in-silico-and-in-vitro-identification-of-inhibitory-activities-of-sorafenib-on-histone-deacetylases-in-hepatocellular-carcinoma-cells
#13
Tsang-Pai Liu, Yi-Han Hong, Pei-Ming Yang
Although sorafenib has been approved for treating hepatocellular carcinoma (HCC), clinical results are not satisfactory. Polypharmacology (one drug with multiple molecular targets) is viewed as an attractive strategy for identifying novel mechanisms of a drug and then rationally designing more-effective next-generation therapeutic agents. In this study, a polypharmacological study of sorafenib was performed by mining the next-generation Connectivity Map (CMap) database, CLUE (https://clue.io/). We found that sorafenib may act as a histone deacetylase (HDAC) inhibitor based on similar gene expression profiles...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156009/discovering-cancer-vulnerabilities-using-high-throughput-micro-rna-screening
#14
Iva Nikolic, Benjamin Elsworth, Eoin Dodson, Sunny Z Wu, Cathryn M Gould, Pieter Mestdagh, Glenn M Marshall, Lisa G Horvath, Kaylene J Simpson, Alexander Swarbrick
Micro-RNAs (miRNAs) are potent regulators of gene expression and cellular phenotype. Each miRNA has the potential to target hundreds of transcripts within the cell thus controlling fundamental cellular processes such as survival and proliferation. Here, we exploit this important feature of miRNA networks to discover vulnerabilities in cancer phenotype, and map miRNA-target relationships across different cancer types. More specifically, we report the results of a functional genomics screen of 1280 miRNA mimics and inhibitors in eight cancer cell lines, and its presentation in a sophisticated interactive data portal...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29156005/abiofilm-a-resource-of-anti-biofilm-agents-and-their-potential-implications-in-targeting-antibiotic-drug-resistance
#15
Akanksha Rajput, Anamika Thakur, Shivangi Sharma, Manoj Kumar
Biofilms play an important role in the antibiotic drug resistance, which is threatening public health globally. Almost, all microbes mimic multicellular lifestyle to form biofilm by undergoing phenotypic changes to adapt adverse environmental conditions. Many anti-biofilm agents have been experimentally validated to disrupt the biofilms during last three decades. To organize this data, we developed the 'aBiofilm' resource (http://bioinfo.imtech.res.in/manojk/abiofilm/) that harbors a database, a predictor, and the data visualization modules...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155794/an-array-based-comparative-genomic-hybridization-platform-for-efficient-detection-of-copy-number-variations-in-fast-neutron-induced-medicago-truncatula-mutants
#16
Yuhui Chen, Xianfu Wang, Shunfei Lu, Hongcheng Wang, Shibo Li, Rujin Chen
Mutants are invaluable genetic resources for gene function studies. To generate mutant collections, three types of mutagens can be utilized, including biological such as T-DNA or transposon, chemical such as ethyl methanesulfonate (EMS), or physical such as ionization radiation. The type of mutation observed varies depending on the mutagen used. For ionization radiation induced mutants, mutations include deletion, duplication, or rearrangement. While T-DNA or transposon-based mutagenesis is limited to species that are susceptible to transformation, chemical or physical mutagenesis can be applied to a broad range of species...
November 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155775/mapping-genome-wide-accessible-chromatin-in-primary-human-t-lymphocytes-by-atac-seq
#17
Ivana Grbesa, Miriam Tannenbaum, Avital Sarusi-Portuguez, Michal Schwartz, Ofir Hakim
Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method used for the identification of open (accessible) regions of chromatin. These regions represent regulatory DNA elements (e.g., promoters, enhancers, locus control regions, insulators) to which transcription factors bind. Mapping the accessible chromatin landscape is a powerful approach for uncovering active regulatory elements across the genome. This information serves as an unbiased approach for discovering the network of relevant transcription factors and mechanisms of chromatin structure that govern gene expression programs...
November 13, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155150/enhancement-of-cutaneous-immunity-during-ageing-by-blocking-p38-mapkinase-induced-inflammation
#18
Milica Vukmanovic-Stejic, Emma S Chambers, Mayte Suarez- Farinas, Daisy Sandhu, Judilyn Fuentes-Duculan, Neil Patel, Elaine Agius, Katie E Lacy, Carolin T Turner, Anis Larbi, Veronique Birault, Mahdad Noursadeghi, Neil A Mabbott, Malcolm H A Rustin, James Krueger, Arne N Akbar
BACKGROUND: Immunity declines with age that leads to re-activation of varicella zoster virus (VZV). In humans, age associated immune changes are usually measured in blood leukocytes however this may not reflect alterations in tissue-specific immunity. OBJECTIVES: We used a VZV antigen challenge system in the skin to investigate changes in tissue specific mechanisms involved in the decreased response to this virus during ageing. METHODS: We assessed cutaneous immunity by the extent of erythema and induration after intradermal VZV antigen injection...
November 16, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29155030/transcriptome-analysis-and-discovery-of-genes-involved-in-immune-pathways-from-coelomocytes-of-onchidium-struma-after-bacterial-challenge
#19
Mingming Zhang, Guo Qiao, Qiang Li, De-Hai Xu, Zhitao Qi, Aiming Wang, Mengyao Xu, Jintian Huang
Onchidium struma widely distributes in subtidal and low-tidal zones, which is considered to be an economical species with rich nutrition, a valuable biomonitor for heavy metal pollution and a representative species for evolution from ocean to land. However, there is limited genetic information available for O. struma development. This study compared transcriptomic profiles of coelomocytes from normal and bacteria infected O. struma by Illumina-based paired-end sequencing to explore the molecular immune mechanism of O...
November 15, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29154832/carboxylesterase-genes-in-pyrethroid-resistant-house-flies-musca-domestica
#20
Xuechun Feng, Ming Li, Nannan Liu
Carboxylesterases are one of the major enzyme families involved in the detoxification of pyrethroids. Up-regulation of carboxylesterase genes is thought to be a major component of insecticide resistant mechanisms in insects. Based on the house fly transcriptome and genome database, a total of 39 carboxylesterase genes of different functional clades have been identified in house flies. In this study, eleven of these genes were found to be significantly overexpressed in the resistant ALHF house fly strain compared with susceptible aabys and wild-type CS strains...
November 14, 2017: Insect Biochemistry and Molecular Biology
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