Identification of a Biosynthetic Gene Cluster for the Polyene Macrolactam
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DE-Kupl: Exhaustive Capture of Biological Variation in RNA-Seq Data Through K-Mer Decomposition
Audoux et al. Genome Biology (2017) 18:243 DOI 10.1186/s13059-017-1372-2 METHOD Open Access DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition Jérôme Audoux1, Nicolas Philippe2,3, Rayan Chikhi4, Mikaël Salson4, Mélina Gallopin5, Marc Gabriel5,6, Jérémy Le Coz5,EmilieDrouineau5, Thérèse Commes1,2 and Daniel Gautheret5,6* Abstract We introduce a k-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq libraries, independently of a reference genome or transcriptome. DE-kupl extracts all k-mers with differential abundance directly from the raw data files. This enables the retrieval of virtually all variation present in an RNA-seq data set. This variation is subsequently assigned to biological events or entities such as differential long non-coding RNAs, splice and polyadenylation variants, introns, repeats, editing or mutation events, and exogenous RNA. Applying DE-kupl to human RNA-seq data sets identified multiple types of novel events, reproducibly across independent RNA-seq experiments. Background diversity is genomic variation. Polymorphism and struc- Successive generations of RNA-sequencing technologies tural variations within transcribed regions produce RNAs have bolstered the notion that organisms produce a highly with single-nucleotide variations (SNVs), tandem dupli- diverse and adaptable set of RNA molecules. Modern cations or deletions, transposon integrations, unstable transcript catalogs, such as GENCODE [1], now include microsatellites, or fusion events. These events are major hundreds of thousands of transcripts, reflecting pervasive sources of transcript variation that can strongly impact transcription and widespread alternative RNA processing. RNA processing, transport, and coding potential. -
RESEARCH ARTICLES Gene Cluster Statistics with Gene Families
RESEARCH ARTICLES Gene Cluster Statistics with Gene Families Narayanan Raghupathy*1 and Dannie Durand* *Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA; and Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such ‘‘gene clusters’’ is an essential component of comparative genomic analyses. However, currently there are no practical statistical tests for gene clusters that model the influence of the number of homologs in each gene family on cluster significance. In this work, we demonstrate empirically that failure to incorporate gene family size in gene cluster statistics results in overestimation of significance, leading to incorrect conclusions. We further present novel analytical methods for estimating gene cluster significance that take gene family size into account. Our methods do not require complete genome data and are suitable for testing individual clusters found in local regions, such as contigs in an unfinished assembly. We consider pairs of regions drawn from the same genome (paralogous clusters), as well as regions drawn from two different genomes (orthologous clusters). Determining cluster significance under general models of gene family size is computationally intractable. By assuming that all gene families are of equal size, we obtain analytical expressions that allow fast approximation of cluster probabilities. We evaluate the accuracy of this approximation by comparing the resulting gene cluster probabilities with cluster probabilities obtained by simulating a realistic, power-law distributed model of gene family size, with parameters inferred from genomic data. -
Transcriptional Mechanisms of Resistance to Anti-PD-1 Therapy
Author Manuscript Published OnlineFirst on February 13, 2017; DOI: 10.1158/1078-0432.CCR-17-0270 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Transcriptional mechanisms of resistance to anti-PD-1 therapy Maria L. Ascierto1, Alvin Makohon-Moore2, 11, Evan J. Lipson1, Janis M. Taube3,4, Tracee L. McMiller5, Alan E. Berger6, Jinshui Fan6, Genevieve J. Kaunitz3, Tricia R. Cottrell4, Zachary A. Kohutek7, Alexander Favorov8,10, Vladimir Makarov7,11, Nadeem Riaz7,11, Timothy A. Chan7,11, Leslie Cope8, Ralph H. Hruban4,9, Drew M. Pardoll1, Barry S. Taylor11,12,13, David B. Solit13, Christine A Iacobuzio-Donahue2,11, and Suzanne L. Topalian5 From the 1Departments of Oncology, 3Dermatology, 4Pathology, 5Surgery, 6The Lowe Family Genomics Core, 8Oncology Bioinformatics Core, and the 9 Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287; the 10Laboratory of System Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia; and 2Pathology, 7Radiation Oncology, 11Human Oncology and Pathogenesis Program, 12Department of Epidemiology and Biostatistics, and the 13Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York NY 10065. MLA, AM-M, EJL, and JMT contributed equally to this work Running title: Transcriptional mechanisms of resistance to anti-PD-1 Key Words: melanoma, cancer genetics, immunotherapy, anti-PD-1 Financial Support: This study was supported by the Melanoma Research Alliance (to SLT and CI-D), the Bloomberg~Kimmel Institute for Cancer Immunotherapy (to JMT, DMP, and SLT), the Barney Family Foundation (to SLT), Moving for Melanoma of Delaware (to SLT), the 1 Downloaded from clincancerres.aacrjournals.org on October 2, 2021. -
MUC4/MUC16/Muc20high Signature As a Marker of Poor Prognostic for Pancreatic, Colon and Stomach Cancers
Jonckheere and Van Seuningen J Transl Med (2018) 16:259 https://doi.org/10.1186/s12967-018-1632-2 Journal of Translational Medicine RESEARCH Open Access Integrative analysis of the cancer genome atlas and cancer cell lines encyclopedia large‑scale genomic databases: MUC4/MUC16/ MUC20 signature is associated with poor survival in human carcinomas Nicolas Jonckheere* and Isabelle Van Seuningen* Abstract Background: MUC4 is a membrane-bound mucin that promotes carcinogenetic progression and is often proposed as a promising biomarker for various carcinomas. In this manuscript, we analyzed large scale genomic datasets in order to evaluate MUC4 expression, identify genes that are correlated with MUC4 and propose new signatures as a prognostic marker of epithelial cancers. Methods: Using cBioportal or SurvExpress tools, we studied MUC4 expression in large-scale genomic public datasets of human cancer (the cancer genome atlas, TCGA) and cancer cell line encyclopedia (CCLE). Results: We identifed 187 co-expressed genes for which the expression is correlated with MUC4 expression. Gene ontology analysis showed they are notably involved in cell adhesion, cell–cell junctions, glycosylation and cell signal- ing. In addition, we showed that MUC4 expression is correlated with MUC16 and MUC20, two other membrane-bound mucins. We showed that MUC4 expression is associated with a poorer overall survival in TCGA cancers with diferent localizations including pancreatic cancer, bladder cancer, colon cancer, lung adenocarcinoma, lung squamous adeno- carcinoma, skin cancer and stomach cancer. We showed that the combination of MUC4, MUC16 and MUC20 signature is associated with statistically signifcant reduced overall survival and increased hazard ratio in pancreatic, colon and stomach cancer. -
Applications of Xâ
Downloaded from genesdev.cshlp.org on June 30, 2009 - Published by Cold Spring Harbor Laboratory Press ‘IN n e-fr £ Development Targeted mutagenesis by homologous recombination in D. melanogaster Yikang S. Rong, Simon W. Titen, Heng B. Xie, et al. G e n e s D e v . 2002 16: 1568-1581 Access the most recent version at doi:10.1101/gad.986602 References This article cites 43 articles, 24 of which can be accessed free at: http://genesdev.cshlp.org/content/16/12/1568.fuN.html#ref-Nst-1 Article cited in: http://genesdev.cshlp.org/content/16/12/1568.full.html#related-urls Email alerting Receive free email alerts when new articles cite this article - sign up in the box at the service top right corner of the article or click here To subscribe to Genes & Development go to: http://genesdev.cshlp.org/subscriptions Cold Spring Harbor Laboratory Press Downloaded from genesdev.cshlp.org on June 30, 2009 - Published by Cold Spring Harbor Laboratory Press m utagenesis by recom bination in D . m elanogaster Yikang S. Rong,1,2,4 Simon W. Titen,1,2 Heng B. Xie,1,2 Mary M. Golic,1,2 Michael Bastiani,1 Pradip Bandyopadhyay,1 Baldomero M. Olivera,1 Michael Brodsky,3,5 Gerald M. Rubin,3 and Kent G. Golic1,2,6 departm ent of Biology, University of Utah, Salt Lake City, Utah 84112, USA; 2Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA; 3Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA Wc used a recently developed method to produce mutant alleles of five endogenous D r o s o p h ila genes, including the homolog of the p 5 3 tumor suppressor. -
Evolution of Orthologous Tandemly Arrayed Gene Clusters
Tremblay Savard et al. BMC Bioinformatics 2011, 12(Suppl 9):S2 http://www.biomedcentral.com/1471-2105/12/S9/S2 PROCEEDINGS Open Access Evolution of orthologous tandemly arrayed gene clusters Olivier Tremblay Savard1*, Denis Bertrand2*, Nadia El-Mabrouk1* From Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Com- parative Genomics Galway, Ireland. 8-10 October 2011 Abstract Background: Tandemly Arrayed Gene (TAG) clusters are groups of paralogous genes that are found adjacent on a chromosome. TAGs represent an important repertoire of genes in eukaryotes. In addition to tandem duplication events, TAG clusters are affected during their evolution by other mechanisms, such as inversion and deletion events, that affect the order and orientation of genes. The DILTAG algorithm developed in [1] makes it possible to infer a set of optimal evolutionary histories explaining the evolution of a single TAG cluster, from an ancestral single gene, through tandem duplications (simple or multiple, direct or inverted), deletions and inversion events. Results: We present a general methodology, which is an extension of DILTAG, for the study of the evolutionary history of a set of orthologous TAG clusters in multiple species. In addition to the speciation events reflected by the phylogenetic tree of the considered species, the evolutionary events that are taken into account are simple or multiple tandem duplications, direct or inverted, simple or multiple deletions, and inversions. We analysed the performance of our algorithm on simulated data sets and we applied it to the protocadherin gene clusters of human, chimpanzee, mouse and rat. Conclusions: Our results obtained on simulated data sets showed a good performance in inferring the total number and size distribution of duplication events. -
Nematostella Genome
Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor Nicholas H. Putnam[1], Mansi Srivastava[2], Uffe Hellsten[1], Bill Dirks[2], Jarrod Chapman[1], Asaf Salamov[1], Astrid Terry[1], Harris Shapiro[1], Erika Lindquist[1], Vladimir V. Kapitonov[3], Jerzy Jurka[3], Grigory Genikhovich[4], Igor Grigoriev[1], JGI Sequencing Team[1], Robert E. Steele[5], John Finnerty[6], Ulrich Technau[4], Mark Q. Martindale[7], Daniel S. Rokhsar[1,2] [1] Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 [2] Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley CA 94720 [3] Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043 [4] Sars International Centre for Marine Molecular Biology, University of Bergen, Thormoeøhlensgt 55; 5008, Bergen, Norway [5] Department of Biological Chemistry and the Developmental Biology Center, University of California, Irvine, CA 92697 [6] Department of Biology, Boston University, Boston, MA 02215 [7] Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI 96813 Abstract Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the Cnidaria, the oldest eumetazoan phylum. Here we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet anemone Nematostella vectensis. The anemone genome is surprisingly complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes. These results imply that the genome of the eumetazoan ancestor was similarly complex, and that fly and nematode genomes have been modified via sequence divergence, gene and intron loss, and genomic rearrangement. -
Partial Retrotransposon-Like DNA Sequence in the Genomic Clone of Aspergillus flavus, Paf28
Mycol. Res. 107 (7): 841–846 (July 2003). f The British Mycological Society 841 DOI: 10.1017/S0953756203008116 Printed in the United Kingdom. Partial retrotransposon-like DNA sequence in the genomic clone of Aspergillus flavus, pAF28 1 1 1 2 Patricia A. OKUBARA #, Brian K. TIBBOT , Alice S. TARUN , Cesaria E. MCALPIN and Sui-Sheng T. HUA1* 1 USDA, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA. 2 USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA. E-mail : [email protected] Received 18 February 2003; accepted 21 May 2003. A genomic clone of the aflatoxin-producing fungus Aspergillus flavus, designated pAF28, has been used as a probe for Southern blot fingerprinting of fungal strains. A large number of A. flavus strains isolated from corn fields and tree-nut orchards can be distinguished because the DNA fingerprint patterns are highly polymorphic. We have completed the sequencing of a 6355 bp insert in pAF28. The sequence features motifs and open reading frames characteristic of transposable elements of the gypsy class. We have named this new element AfRTL-1, for A. flavus retrotransposon-like DNA. INTRODUCTION characterized vegetative compatibility groups (Papa 1986, McAlpin & Mannarelli 1995, McAlpin et al. Aspergillus flavus is the most common aflatoxin-pro- 2002) indicates its further utility. In this study, we ducing species on corn, cotton, peanuts and tree nuts demonstrate that the genomic insert of pAF28 carries (Diener et al. 1987). Aflatoxin is a potent hepatoxin and a partial retrotransposon-like element homologous to carcinogen that poses a serious food safety hazard to the gypsy-class retrotransposon MAGGY, originally both humans and animals. -
The Evolutionary Life History of P Transposons: from Horizontal Invaders to Domesticated Neogenes
Chromosoma (2001) 110:148–158 DOI 10.1007/s004120100144 CHROMOSOMA FOCUS Wilhelm Pinsker · Elisabeth Haring Sylvia Hagemann · Wolfgang J. Miller The evolutionary life history of P transposons: from horizontal invaders to domesticated neogenes Received: 5 February 2001 / In revised form: 15 March 2001 / Accepted: 15 March 2001 / Published online: 3 May 2001 © Springer-Verlag 2001 Abstract P elements, a family of DNA transposons, are uct of their self-propagating lifestyle. One of the most known as aggressive intruders into the hitherto uninfected intensively studied examples is the P element of Dro- gene pool of Drosophila melanogaster. Invading through sophila, a family of DNA transposons that has proved horizontal transmission from an external source they useful not only as a genetic tool (e.g., transposon tag- managed to spread rapidly through natural populations ging, germline transformation vector), but also as a model within a few decades. Owing to their propensity for rapid system for investigating general features of the evolu- propagation within genomes as well as within popula- tionary behavior of mobile DNA (Kidwell 1994). P ele- tions, they are considered as the classic example of self- ments were first discovered as the causative agent of hy- ish DNA, causing havoc in a genomic environment per- brid dysgenesis in Drosophila melanogaster (Kidwell et missive for transpositional activity. Tracing the fate of P al. 1977) and were later characterized as a family of transposons on an evolutionary scale we describe differ- DNA transposons -
Xenopus Transgenic Nomenclature Guidelines
This document was last updated: October 23rd, 2014. Executive Summary: Xenopus Transgenic Nomenclature Guidelines These guidelines cover the naming of transgenic constructs developed and used in Xenopus research, and the naming of mutant and transgenic Xenopus lines . ● Only those transgenic (Tg) constructs that are supplied to other researchers, or are maintained by a lab or at a stock center, require standardized names following these guidelines. ● Xenbase will record and curate transgenes using these rules. ● Transgenic construct names are italicized following this basic formulae: Tg(enhancer or promoter:ORF/gene) ● Multiple cassette on the same plasmid are separated by a comma within the parenthesis. Tg(enhancer or promoter:ORF/gene, enhancer or promoter:ORF/gene) cassette 1 cassette 2 ● Transgenic Xenopus lines are named based on their unique combination of Tg constructs (in standard text) and indicate Xenopus species and the lab of origin: Xl.Tg(enhancer or promoter:ORF/gene, enhancer or promoter:ORF/gene)#ILAR lab code species cassette 1 cassette 2 lab code ● Xenopus research labs that generate Tg animals are identified using lab codes registered with the ILAR which maintains a searchable database for model organism laboratories. Section 1. Provides an overview for Naming Tg Constructs Section 2. Outlines specific rules for Naming Tg Constructs Section 3. Provides an overview for Naming Tg Xenopus lines and Xenopus lines with mutant alleles. Section 4. Provides guidelines for naming enhancer and gene trap constructs, and lines using these constructs. Section 5. Outlines rules for naming transposon-induced mutations and inserts. Section 6. Discusses disambiguation of wild type Xenopus strains versus transgenic and mutant Xenopus lines. -
ORGANIC CHEMICAL TOXICOLOGY of FISHES This Is Volume 33 in The
ORGANIC CHEMICAL TOXICOLOGY OF FISHES This is Volume 33 in the FISH PHYSIOLOGY series Edited by Anthony P. Farrell and Colin J. Brauner Honorary Editors: William S. Hoar and David J. Randall A complete list of books in this series appears at the end of the volume ORGANIC CHEMICAL TOXICOLOGY OF FISHES Edited by KEITH B. TIERNEY Department of Biological Sciences University of Alberta Edmonton, Alberta Canada ANTHONY P. FARRELL Department of Zoology, and Faculty of Land and Food Systems The University of British Columbia Vancouver, British Columbia Canada COLIN J. BRAUNER Department of Zoology The University of British Columbia Vancouver, British Columbia Canada AMSTERDAM BOSTON HEIDELBERG LONDON NEW YORK OXFORD PARIS SAN DIEGO SAN FRANCISCO SINGAPORE SYDNEY TOKYO Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier 32 Jamestown Road, London NW1 7BY, UK 225 Wyman Street, Waltham, MA 02451, USA 525 B Street, Suite 1800, San Diego, CA 92101-4495, USA Copyright r 2014 Elsevier Inc. All rights reserved The cover illustrates the diversity of effects an example synthetic organic water pollutant can have on fish. The chemical shown is 2,4-D, an herbicide that can be found in streams near urbanization and agriculture. The fish shown is one that can live in such streams: rainbow trout (Oncorhynchus mykiss). The effect shown on the left is the ability of 2,4-D (yellow line) to stimulate olfactory sensory neurons vs. control (black line) (measured as an electro- olfactogram; EOG). The effect shown on the right is the ability of 2,4-D to induce the expression of an egg yolk precursor protein (vitellogenin) in male fish. -
Transposable Element Insertions Shape Gene Regulation and Melanin
Krishnan et al. BMC Biology (2018) 16:78 https://doi.org/10.1186/s12915-018-0543-2 RESEARCH ARTICLE Open Access Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat Parvathy Krishnan1, Lukas Meile1, Clémence Plissonneau1,2, Xin Ma1, Fanny E. Hartmann1,3, Daniel Croll1,4, Bruce A. McDonald1 and Andrea Sánchez-Vallet1* Abstract Background: Fungal plant pathogens pose major threats to crop yield and sustainable food production if they are highly adapted to their host and the local environment. Variation in gene expression contributes to phenotypic diversity within fungal species and affects adaptation. However, very few cases of adaptive regulatory changes have been reported in fungi and the underlying mechanisms remain largely unexplored. Fungal pathogen genomes are highly plastic and harbor numerous insertions of transposable elements, which can potentially contribute to gene expression regulation. In this work, we elucidated how transposable elements contribute to variation in melanin accumulation, a quantitative trait in fungi that affects survival under stressful conditions. Results: We demonstrated that differential transcriptional regulation of the gene encoding the transcription factor Zmr1, which controls expression of the genes in the melanin biosynthetic gene cluster, is responsible for variation in melanin accumulation in the fungal plant pathogen Zymoseptoria tritici. We show that differences in melanin levels between two strains of Z. tritici are due to two levels of transcriptional regulation: (1) variation in the promoter sequence of Zmr1 and (2) an insertion of transposable elements upstream of the Zmr1 promoter. Remarkably, independent insertions of transposable elements upstream of Zmr1 occurred in 9% of Z.