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Functional genomics

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https://www.readbyqxmd.com/read/29786918/novel-genes-and-insights-in-complete-asthma-remission
#1
Judith M Vonk, Maartje A E Nieuwenhuis, F Nicole Dijk, Anne Boudier, Valerie Siroux, Emmanuelle Bouzigon, Nicole Probst-Hensch, Medea Imboden, Dirk Keidel, Don Sin, Yohan Bossé, Ke Hao, Maarten van den Berge, Alen Faiz, Gerard H Koppelman, Dirkje S Postma
BACKGROUND: Asthma is a chronic respiratory disease without a cure, though there exists spontaneous remission. Genome wide association(GWA) studies have pinpointed genes associated with asthma development, but did not investigate asthma remission. OBJECTIVES: We performed a GWA study to develop insights in asthma remission. METHODS: Clinical remission (ClinR) was defined by absence of asthma treatment and wheezing in the last year and asthma attacks in the last 3 years, and complete remission (ComR) similarly but additionally with normal lung function and absence of bronchial hyperresponsiveness (BHR)...
May 22, 2018: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29786815/role-of-circulating-micrornas-in-acute-appendicitis
#2
Avni Uygar Seyhan, Elif Funda Şener, Oğuzhan Bol, Serpil Taheri, Tugba Topaloglu, Esra Tufan, Reyhan Tahtasakal, Nahide Ekici Günay, Hatice Karabulut, Nurullah Günay
BACKGROUND: Acute appendicitis (AA) is a momentous, emergency, surgical pathology that has still been investigated for both etiopathogenetic unknowns and challenges in diagnosis. Presently, there is little information about the role of microRNAs (miRNAs), which have basic biological functions in the cell, can be a marker, and are associated with various pathologies, in patients with AA. The aim of this study was to investigate the expressions of some miRNAs in AA. METHODS: Overall, 41 miRNAs were screened in 48 individuals comprising 24 patients with AA and 24 healthy controls at Erciyes University Genome and Stem Cell Center (GENKOK)...
May 2018: Ulusal Travma Ve Acil Cerrahi Dergisi, Turkish Journal of Trauma & Emergency Surgery: TJTES
https://www.readbyqxmd.com/read/29786687/genome-wide-analysis-of-circular-rnas-in-bovine-cumulus-cells-treated-with-bmp15-and-gdf9
#3
Yao Fu, Hao Jiang, Jian-Bo Liu, Xu-Lei Sun, Zhe Zhang, Sheng Li, Yan Gao, Bao Yuan, Jia-Bao Zhang
Circular RNAs (circRNAs) are important members of the non-coding RNA family, and those relating to animal physiologies have been widely studied in recent years. This study aimed to explore the roles of circRNAs in the regulation of follicular development. We constructed four bovine cumulus cell cDNA libraries, including a negative control group (NC) and groups treated with BMP15, GDF9 and BMP15 + GDF9, and we sequenced the libraries on the Illumina HiSeq Xten platform. We identified 1706 circRNAs and screened for differential circRNA expression...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29786565/modelling-non-alcoholic-fatty-liver-disease-in-human-hepatocyte-like-cells
#4
Marcus J Lyall, Jessy Cartier, John P Thomson, Kate Cameron, Jose Meseguer-Ripolles, Eoghan O'Duibhir, Dagmara Szkolnicka, Baltasar Lucendo Villarin, Yu Wang, Giovanny Rodriguez Blanco, Warwick B Dunn, Richard R Meehan, David C Hay, Amanda J Drake
Non-alcoholic fatty liver disease (NAFLD) is the most common cause of liver disease in developed countries. An in vitro NAFLD model would permit mechanistic studies and enable high-throughput therapeutic screening. While hepatic cancer-derived cell lines are a convenient, renewable resource, their genomic, epigenomic and functional alterations mean their utility in NAFLD modelling is unclear. Additionally, the epigenetic mark 5-hydroxymethylcytosine (5hmC), a cell lineage identifier, is rapidly lost during cell culture, alongside expression of the Ten-eleven-translocation ( TET ) methylcytosine dioxygenase enzymes, restricting meaningful epigenetic analysis...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29786424/tuning-gene-activity-by-inducible-and-targeted-regulation-of-gene-expression-in-minimal-bacterial-cells
#5
Ana M Mariscal, Shigeyuki Kakizawa, Jonathan Y Hsu, Kazuki Tanaka, Luis González-González, Alicia Broto, Enrique Querol, Maria Lluch-Senar, Carlos Piñero-Lambea, Lijie Sun, Philip D Weyman, Kim S Wise, Chuck Merryman, Gavin Tse, Adam J Moore, Clyde A Hutchison, Hamilton O Smith, Masaru Tomita, J Craig Venter, John I Glass, Jaume Piñol, Yo Suzuki
Functional genomics studies in minimal mycoplasma cells enable unobstructed access to some of the most fundamental processes in biology. Conventional transposon bombardment and gene knockout approaches often fail to reveal functions of genes that are essential for viability, where lethality precludes phenotypic characterization. Conditional inactivation of genes is effective for characterizing functions central to cell growth and division, but tools are limited for this purpose in mycoplasmas. Here we demonstrate systems for inducible repression of gene expression based on clustered regularly interspaced short palindromic repeats-mediated interference (CRISPRi) in Mycoplasma pneumoniae and synthetic Mycoplasma mycoides, two organisms with reduced genomes actively used in systems biology studies...
May 22, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29786095/high-throughput-creation-and-functional-profiling-of-dna-sequence-variant-libraries-using-crispr-cas9-in-yeast
#6
Xiaoge Guo, Alejandro Chavez, Angela Tung, Yingleong Chan, Christian Kaas, Yi Yin, Ryan Cecchi, Santiago Lopez Garnier, Eric D Kelsic, Max Schubert, James E DiCarlo, James J Collins, George M Church
Construction and characterization of large genetic variant libraries is essential for understanding genome function, but remains challenging. Here, we introduce a Cas9-based approach for generating pools of mutants with defined genetic alterations (deletions, substitutions, and insertions) with an efficiency of 80-100% in yeast, along with methods for tracking their fitness en masse. We demonstrate the utility of our approach by characterizing the DNA helicase SGS1 with small tiling deletion mutants that span the length of the protein and a series of point mutations against highly conserved residues in the protein...
May 21, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29785963/swi-snf-and-rsc-cooperate-to-reposition-and-evict-promoter-nucleosomes-at-highly-expressed-genes-in-yeast
#7
Yashpal Rawal, Răzvan V Chereji, Hongfang Qiu, Sudha Ananthakrishnan, Chhabi K Govind, David J Clark, Alan G Hinnebusch
The nucleosome remodeling complex RSC functions throughout the yeast genome to set the positions of -1 and +1 nucleosomes and thereby determines the widths of nucleosome-depleted regions (NDRs). The related complex SWI/SNF participates in nucleosome remodeling/eviction and promoter activation at certain yeast genes, including those activated by transcription factor Gcn4, but did not appear to function broadly in establishing NDRs. By analyzing the large cohort of Gcn4-induced genes in mutants lacking the catalytic subunits of SWI/SNF or RSC, we uncovered cooperation between these remodelers in evicting nucleosomes from different locations in the promoter and repositioning the +1 nucleosome downstream to produce wider NDRs-highly depleted of nucleosomes-during transcriptional activation...
May 21, 2018: Genes & Development
https://www.readbyqxmd.com/read/29785946/-crispr-cas-systems-in-genome-engineering-of-bacteriophages
#8
Cai Jiao Liang, Fan Mei Meng, Yun Can Ai
Researches on CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) systems, that are adaptive immunity systems encoded by prokaryotes, have promoted the development of new genome-editing tools. Bacteriophages are not only the driving elements for the evolution of prokaryotes' CRISPR arrays, but also the targets of the CRISPR/Cas systems. Studies on functional genomics of bacteriophages have been lagging behind the discovery of new phage strains and the sequencing of their genomes...
May 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29785615/molecular-characterization-of-proton-beam-induced-mutations-in-soybean-using-genotyping-by-sequencing
#9
Woon Ji Kim, Jaihyunk Ryu, Juhyun Im, Sang Hun Kim, Si-Yong Kang, Jeong-Hee Lee, Sung-Hwan Jo, Bo-Keun Ha
Proton beam irradiation is a next-generation technique to develop mutant crop varieties. The mutagenic effects and molecular mechanisms of radiation are important multi-disciplinary research subjects. This study was conducted to investigate the types of mutations induced in the soybean genome by proton beam irradiation. In total, 22 plants, including 10 M2 plants treated with proton beam irradiation at 118 and 239 Gy, each, and two wild-type plants (Daepung) were sequenced by genotyping-by-sequencing (GBS)...
May 21, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29785409/-de-novo-genome-and-transcriptome-resources-of-the-adzuki-bean-borer-ostrinia-scapulalis-lepidoptera-crambidae
#10
B Gschloessl, F Dorkeld, P Audiot, A Bretaudeau, C Kerdelhué, R Streiff
We present a draft genome assembly with a de novo prediction and automated functional annotation of coding genes, and a reference transcriptome of the Adzuki bean borer, Ostrinia scapulalis , based on RNA sequencing of various tissues and developmental stages. The genome assembly spans 419 Mb, has a GC content of 37.4% and includes 26,120 predicted coding genes. The reference transcriptome holds 33,080 unigenes and contains a high proportion of a set of genes conserved in eukaryotes and arthropods, used as quality assessment of the reconstructed transcripts...
April 2018: Data in Brief
https://www.readbyqxmd.com/read/29785397/whole-genome-sequencing-of-greater-amberjack-seriola-dumerili-for-snp-identification-on-aligned-scaffolds-and-genome-structural-variation-analysis-using-parallel-resequencing
#11
Kazuo Araki, Jun-Ya Aokic, Junya Kawase, Kazuhisa Hamada, Akiyuki Ozaki, Hiroshi Fujimoto, Ikki Yamamoto, Hironori Usuki
Greater amberjack ( Seriola dumerili ) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish. We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29785339/identification-of-potential-crucial-genes-and-pathways-associated-with-vein-graft-restenosis-based-on-gene-expression-analysis-in-experimental-rabbits
#12
Qiang Liu, Xiujie Yin, Mingzhu Li, Li Wan, Liqiao Liu, Xiang Zhong, Zhuoqi Liu, Qun Wang
Occlusive artery disease (CAD) is the leading cause of death worldwide. Bypass graft surgery remains the most prevalently performed treatment for occlusive arterial disease, and veins are the most frequently used conduits for surgical revascularization. However, the clinical efficacy of bypass graft surgery is highly affected by the long-term potency rates of vein grafts, and no optimal treatments are available for the prevention of vein graft restenosis (VGR) at present. Hence, there is an urgent need to improve our understanding of the molecular mechanisms involved in mediating VGR...
2018: PeerJ
https://www.readbyqxmd.com/read/29785177/characterization-of-new-microsatellite-markers-based-on-the-transcriptome-sequencing-of-clematis-finetiana
#13
Zhigao Liu, Weili Shao, Yamei Shen, Mengcheng Ji, Wenchao Chen, Ying Ye, Yongbao Shen
Background: Clematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the "Queen of the Vines". However, the genomic information and phylogeny of Clematis based on existing molecular studies are limited. In this paper, new microsatellites (SSR) markers were identified from the transcriptome data of C...
2018: Hereditas
https://www.readbyqxmd.com/read/29785121/association-between-angiogenesis-and-cytotoxic-signatures-in-the-tumor-microenvironment-of-gastric-cancer
#14
Yi Feng, Ying Dai, Zhihua Gong, Jia-Nan Cheng, Longhui Zhang, Chengdu Sun, Xianghua Zeng, Qingzhu Jia, Bo Zhu
Background: A suppressive immune microenvironment and pathological angiogenesis are hallmarks of gastric cancer. Theoretically, immune checkpoint inhibitors (ICIs) stimulate pre-primed neoantigen-specific T cells, and antiangiogenic agents then facilitate their infiltration into the tumor niche by promoting vascular normalization. Currently, the interconnections of these two phenotypes and their relevance to the tumor microenvironment (TME) have not been fully characterized in gastric cancer...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29785087/transcriptomic-impacts-of-rumen-epithelium-induced-by-butyrate-infusion-in-dairy-cattle-in-dry-period
#15
Ransom L Baldwin, Robert W Li, Yankai Jia, Cong-Jun Li
The purpose of this study was to evaluate the effects of butyrate infusion on rumen epithelial transcriptome. Next-generation sequencing (NGS) and bioinformatics are used to accelerate our understanding of regulation in rumen epithelial transcriptome of cattle in the dry period induced by butyrate infusion at the level of the whole transcriptome. Butyrate, as an essential element of nutrients, is a histone deacetylase (HDAC) inhibitor that can alter histone acetylation and methylation, and plays a prominent role in regulating genomic activities influencing rumen nutrition utilization and function...
2018: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/29785056/genome-wide-mapping-reveals-that-deoxyuridine-is-enriched-in-the-human-centromeric-dna
#16
Xiaoting Shu, Menghao Liu, Zhike Lu, Chenxu Zhu, Haowei Meng, Sihao Huang, Xiaoxue Zhang, Chengqi Yi
Uracil in DNA can be generated by cytosine deamination or dUMP misincorporation; however, its distribution in the human genome is poorly understood. Here we present a selective labeling and pull-down technology for genome-wide uracil profiling and identify thousands of uracil peaks in three different human cell lines. Surprisingly, uracil is highly enriched at the centromere of the human genome. Using mass spectrometry, we demonstrate that human centromeric DNA contains a higher level of uracil. We also directly verify the presence of uracil within two centromeric uracil peaks on chromosomes 6 and 11...
May 21, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29785040/archetypal-transcriptional-blocks-underpin-yeast-gene-regulation-in-response-to-changes-in-growth-conditions
#17
David Talavera, Christopher J Kershaw, Joseph L Costello, Lydia M Castelli, William Rowe, Paul F G Sims, Mark P Ashe, Chris M Grant, Graham D Pavitt, Simon J Hubbard
The transcriptional responses of yeast cells to diverse stresses typically include gene activation and repression. Specific stress defense, citric acid cycle and oxidative phosphorylation genes are activated, whereas protein synthesis genes are coordinately repressed. This view was achieved from comparative transcriptomic experiments delineating sets of genes whose expression greatly changed with specific stresses. Less attention has been paid to the biological significance of 1) consistent, albeit modest, changes in RNA levels across multiple conditions, and 2) the global gene expression correlations observed when comparing numerous genome-wide studies...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29785027/targeting-g-quadruplex-dna-as-cognitive-function-therapy-for-atr-x-syndrome
#18
Norifumi Shioda, Yasushi Yabuki, Kouya Yamaguchi, Misaki Onozato, Yue Li, Kenji Kurosawa, Hideyuki Tanabe, Nobuhiko Okamoto, Takumi Era, Hiroshi Sugiyama, Takahito Wada, Kohji Fukunaga
Alpha-thalassemia X-linked intellectual disability (ATR-X) syndrome is caused by mutations in ATRX, which encodes a chromatin-remodeling protein. Genome-wide analyses in mouse and human cells indicate that ATRX tends to bind to G-rich sequences with a high potential to form G-quadruplexes. Here, we report that Atrx mutation induces aberrant upregulation of Xlr3b expression in the mouse brain, an outcome associated with neuronal pathogenesis displayed by ATR-X model mice. We show that ATRX normally binds to G-quadruplexes in CpG islands of the imprinted Xlr3b gene, regulating its expression by recruiting DNA methyltransferases...
May 21, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29785013/genetic-identification-of-brain-cell-types-underlying-schizophrenia
#19
Nathan G Skene, Julien Bryois, Trygve E Bakken, Gerome Breen, James J Crowley, Héléna A Gaspar, Paola Giusti-Rodriguez, Rebecca D Hodge, Jeremy A Miller, Ana B Muñoz-Manchado, Michael C O'Donovan, Michael J Owen, Antonio F Pardiñas, Jesper Ryge, James T R Walters, Sten Linnarsson, Ed S Lein, Patrick F Sullivan, Jens Hjerling-Leffler
With few exceptions, the marked advances in knowledge about the genetic basis of schizophrenia have not converged on findings that can be confidently used for precise experimental modeling. By applying knowledge of the cellular taxonomy of the brain from single-cell RNA sequencing, we evaluated whether the genomic loci implicated in schizophrenia map onto specific brain cell types. We found that the common-variant genomic results consistently mapped to pyramidal cells, medium spiny neurons (MSNs) and certain interneurons, but far less consistently to embryonic, progenitor or glial cells...
May 21, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29785010/genome-wide-analyses-identify-68-new-loci-associated-with-intraocular-pressure-and-improve-risk-prediction-for-primary-open-angle-glaucoma
#20
Anthony P Khawaja, Jessica N Cooke Bailey, Nicholas J Wareham, Robert A Scott, Mark Simcoe, Robert P Igo, Yeunjoo E Song, Robert Wojciechowski, Ching-Yu Cheng, Peng T Khaw, Louis R Pasquale, Jonathan L Haines, Paul J Foster, Janey L Wiggs, Chris J Hammond, Pirro G Hysi
Glaucoma is the leading cause of irreversible blindness globally 1 . Despite its gravity, the disease is frequently undiagnosed in the community 2 . Raised intraocular pressure (IOP) is the most important risk factor for primary open-angle glaucoma (POAG)3,4 . Here we present a meta-analysis of 139,555 European participants, which identified 112 genomic loci associated with IOP, 68 of which are novel. These loci suggest a strong role for angiopoietin-receptor tyrosine kinase signaling, lipid metabolism, mitochondrial function and developmental processes underlying risk for elevated IOP...
May 21, 2018: Nature Genetics
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