The Golgi Glycoprotein MGAT4D Is an Intrinsic Protector Of
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Integrative Genomic and Epigenomic Analyses Identified IRAK1 As a Novel Target for Chronic Inflammation-Driven Prostate Tumorigenesis
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.16.447920; this version posted June 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Integrative genomic and epigenomic analyses identified IRAK1 as a novel target for chronic inflammation-driven prostate tumorigenesis Saheed Oluwasina Oseni1,*, Olayinka Adebayo2, Adeyinka Adebayo3, Alexander Kwakye4, Mirjana Pavlovic5, Waseem Asghar5, James Hartmann1, Gregg B. Fields6, and James Kumi-Diaka1 Affiliations 1 Department of Biological Sciences, Florida Atlantic University, Florida, USA 2 Morehouse School of Medicine, Atlanta, Georgia, USA 3 Georgia Institute of Technology, Atlanta, Georgia, USA 4 College of Medicine, Florida Atlantic University, Florida, USA 5 Department of Computer and Electrical Engineering, Florida Atlantic University, Florida, USA 6 Department of Chemistry & Biochemistry and I-HEALTH, Florida Atlantic University, Florida, USA Corresponding Author: [email protected] (S.O.O) Running Title: Chronic inflammation signaling in prostate tumorigenesis bioRxiv preprint doi: https://doi.org/10.1101/2021.06.16.447920; this version posted June 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The impacts of many inflammatory genes in prostate tumorigenesis remain understudied despite the increasing evidence that associates chronic inflammation with prostate cancer (PCa) initiation, progression, and therapy resistance. -
A Multistep Bioinformatic Approach Detects Putative Regulatory
BMC Bioinformatics BioMed Central Research article Open Access A multistep bioinformatic approach detects putative regulatory elements in gene promoters Stefania Bortoluzzi1, Alessandro Coppe1, Andrea Bisognin1, Cinzia Pizzi2 and Gian Antonio Danieli*1 Address: 1Department of Biology, University of Padova – Via Bassi 58/B, 35131, Padova, Italy and 2Department of Information Engineering, University of Padova – Via Gradenigo 6/B, 35131, Padova, Italy Email: Stefania Bortoluzzi - [email protected]; Alessandro Coppe - [email protected]; Andrea Bisognin - [email protected]; Cinzia Pizzi - [email protected]; Gian Antonio Danieli* - [email protected] * Corresponding author Published: 18 May 2005 Received: 12 November 2004 Accepted: 18 May 2005 BMC Bioinformatics 2005, 6:121 doi:10.1186/1471-2105-6-121 This article is available from: http://www.biomedcentral.com/1471-2105/6/121 © 2005 Bortoluzzi et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Searching for approximate patterns in large promoter sequences frequently produces an exceedingly high numbers of results. Our aim was to exploit biological knowledge for definition of a sheltered search space and of appropriate search parameters, in order to develop a method for identification of a tractable number of sequence motifs. Results: Novel software (COOP) was developed for extraction of sequence motifs, based on clustering of exact or approximate patterns according to the frequency of their overlapping occurrences. -
Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ...................................................... -
Essential Role of Microphthalmia Transcription Factor for DNA Replication, Mitosis and Genomic Stability in Melanoma
Oncogene (2011) 30, 2319–2332 & 2011 Macmillan Publishers Limited All rights reserved 0950-9232/11 www.nature.com/onc ORIGINAL ARTICLE Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma T Strub1,4, S Giuliano2,4,TYe1, C Bonet2, C Keime1, D Kobi1, S Le Gras1, M Cormont3, R Ballotti2, C Bertolotto2 and I Davidson1 1Institut de Ge´ne´tique et de Biologie Mole´culaire et Cellulaire, CNRS, INSERM, Universite´ de Strasbourg, Illkirch, France; 2INSERM U895 Team 1 and Department of Dermatology, CHU Nice, France and 3INSERM U895 Team 7, Nice, France Malignant melanoma is an aggressive cancer known use of internal promoters (Steingrimsson, 2008). The for its notorious resistance to most current therapies. MITF-M isoform (hereafter designated simply as The basic helix-loop-helix microphthalmia transcription MITF) is the major form produced specifically in the factor (MITF) is the master regulator determining the melanocyte lineage from an intronic promoter (Goding, identity and properties of the melanocyte lineage, and is 2000b). MITF is essential for the survival of melano- regarded as a lineage-specific ‘oncogene’ that has a blasts and postnatal melanocytes (McGill et al., 2002; critical role in the pathogenesis of melanoma. MITF Hou and Pavan, 2008), in which it also controls the promotes melanoma cell proliferation, whereas sustained expression of genes required for the melanin synthesis supression of MITF expression leads to senescence. (Bertolotto et al., 1998). By combining chromatin immunoprecipitation coupled to In addition to regulating multiple aspects of normal high throughput sequencing (ChIP-seq) and RNA sequen- melanocyte function, MITF also has a critical role in cing analyses, we show that MITF directly regulates a melanoma, in which it is required for survival, and set of genes required for DNA replication, repair and controls the proliferation, invasive and metastatic mitosis. -
Gene Expression Patterns Induced by HPV-16 L1 Virus-Like Particles in Leukocytes from Vaccine Recipients
Gene Expression Patterns Induced by HPV-16 L1 Virus-Like Particles in Leukocytes from Vaccine Recipients This information is current as Alfonso J. García-Piñeres, Allan Hildesheim, Lori Dodd, of October 3, 2021. Troy J. Kemp, Jun Yang, Brandie Fullmer, Clayton Harro, Douglas R. Lowy, Richard A. Lempicki and Ligia A. Pinto J Immunol 2009; 182:1706-1729; ; doi: 10.4049/jimmunol.182.3.1706 http://www.jimmunol.org/content/182/3/1706 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2009/01/15/182.3.1706.DC1 Material http://www.jimmunol.org/ References This article cites 53 articles, 16 of which you can access for free at: http://www.jimmunol.org/content/182/3/1706.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on October 3, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2009 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Gene Expression Patterns Induced by HPV-16 L1 Virus-Like Particles in Leukocytes from Vaccine Recipients1 Alfonso J. -
The Golgi Glycoprotein MGAT4D Is an Intrinsic Protector of Testicular
www.nature.com/scientificreports OPEN The Golgi Glycoprotein MGAT4D is an Intrinsic Protector of Testicular Germ Cells From Mild Heat Stress Ayodele Akintayo 1,5, Meng Liang 1,3,5, Boris Bartholdy 1, Frank Batista 1, Jennifer Aguilan 2, Jillian Prendergast 1,4, Afsana Sabrin 1, Subha Sundaram 1 & Pamela Stanley 1* Male germ cells are sensitive to heat stress and testes must be maintained outside the body for optimal fertility. However, no germ cell intrinsic mechanism that protects from heat has been reported. Here, we identify the germ cell specifc Golgi glycoprotein MGAT4D as a protector of male germ cells from heat stress. Mgat4d is highly expressed in spermatocytes and spermatids. Unexpectedly, when the Mgat4d gene was inactivated globally or conditionally in spermatogonia, or mis-expressed in spermatogonia, spermatocytes or spermatids, neither spermatogenesis nor fertility were afected. On the other hand, when males were subjected to mild heat stress of the testis (43 °C for 25 min), germ cells with inactivated Mgat4d were markedly more sensitive to the efects of heat stress, and transgenic mice expressing Mgat4d were partially protected from heat stress. Germ cells lacking Mgat4d generally mounted a similar heat shock response to control germ cells, but could not maintain that response. Several pathways activated by heat stress in wild type were induced to a lesser extent in Mgat4d[−/−] heat-stressed germ cells (NFκB response, TNF and TGFβ signaling, Hif1α and Myc genes). Thus, the Golgi glycoprotein MGAT4D is a novel, intrinsic protector of male germ cells from heat stress. MGAT4D is designated family member D of the MGAT4 gene family by the Human Genome Nomenclature Committee based on sequence similarity to other members, including MGAT4A and MGAT4B. -
A Genome-Wide CRISPR/Cas Phenotypic Screen for Modulators Of
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.27.223420; this version posted July 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 A genome-wide CRISPR/Cas phenotypic screen for 2 modulators of DUX4 cytotoxicity reveals screen 3 complications 4 5 Ator Ashoti1*, Francesco Limone2,5*, Melissa van Kranenburg1, Anna 6 Alemany1, Mirna Baak1, Judith Vivié1,3, Federica Piccioni8, Menno 7 Creyghton1,6, Kevin Eggan2,5**, Niels Geijsen1,4** 8 9 1Hubrecht Institute, Developmental Biology and Stem Cell Research, 10 Utrecht, Netherlands 11 2Department of Stem Cell and Regenerative Biology, Harvard University 12 Cambridge, MA, USA 13 5Stanley Center for Psychiatric Research, Broad Institute of MIT and 14 Harvard, Cambridge, MA, USA 15 3Single Cell Discoveries, Utrecht, Netherlands 16 4Leiden University Medical Center, Leiden, The Netherlands 17 6Erasmus University Medical Centre, Rotterdam, The Netherlands 18 8Broad institute, Cambridge, MA, USA 19 20 * Equal contribution 21 **Correspondence: [email protected], [email protected] 22 23 Acknowledgements 24 This study was supported by Stichting FSHD and the SingelSwim Utrecht. The authors 25 like to thank Nune Schelling, Peng Shang, Stefan van der Elst, en Reinier van der 26 Linden for excellent technical assistance. 27 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.27.223420; this version posted July 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Glycosyltransferase Genes That Cause Monogenic Congenital
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Archive Ouverte en Sciences de l'Information et de la Communication Glycosyltransferase genes that cause monogenic congenital disorders of glycosylation are distinct from glycosyltransferase genes associated with complex diseases Hiren Joshi, Lars Hansen, Yoshiki Narimatsu, Hudson Freeze, Bernard Henrissat, Eric Bennett, Hans Wandall, Henrik Clausen, Katrine Schjoldager To cite this version: Hiren Joshi, Lars Hansen, Yoshiki Narimatsu, Hudson Freeze, Bernard Henrissat, et al.. Glycosyl- transferase genes that cause monogenic congenital disorders of glycosylation are distinct from glyco- syltransferase genes associated with complex diseases. Glycobiology, Oxford University Press (OUP), 2018, 28 (5), pp.284-294. 10.1093/glycob/cwy015. hal-02094575 HAL Id: hal-02094575 https://hal-amu.archives-ouvertes.fr/hal-02094575 Submitted on 10 Apr 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License -
Building a Statistical Model for Predicting Cancer Genes
Dartmouth College Dartmouth Digital Commons Open Dartmouth: Published works by Dartmouth faculty Faculty Work 11-15-2012 Building a Statistical Model for Predicting Cancer Genes Ivan P. Gorlov The University of Texas MD Anderson Cancer Center Christopher J. Logothetis The University of Texas MD Anderson Cancer Center Shenying Fang The University of Texas MD Anderson Cancer Center Olga Y. Gorlova The University of Texas MD Anderson Cancer Center Christopher Amos Dartmouth College Follow this and additional works at: https://digitalcommons.dartmouth.edu/facoa Part of the Oncology Commons Dartmouth Digital Commons Citation Gorlov, Ivan P.; Logothetis, Christopher J.; Fang, Shenying; Gorlova, Olga Y.; and Amos, Christopher, "Building a Statistical Model for Predicting Cancer Genes" (2012). Open Dartmouth: Published works by Dartmouth faculty. 2572. https://digitalcommons.dartmouth.edu/facoa/2572 This Article is brought to you for free and open access by the Faculty Work at Dartmouth Digital Commons. It has been accepted for inclusion in Open Dartmouth: Published works by Dartmouth faculty by an authorized administrator of Dartmouth Digital Commons. For more information, please contact [email protected]. Building a Statistical Model for Predicting Cancer Genes Ivan P. Gorlov1*, Christopher J. Logothetis1, Shenying Fang2, Olga Y. Gorlova3, Christopher Amos4 1 Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America, 2 Department of Cancer Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America, 3 Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America, 4 Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire, United States of America Abstract More than 400 cancer genes have been identified in the human genome. -
Unraveling the Molecular Mechanism Underlying ALS-Linked Astrocyte
Unraveling the molecular mechanism underlying ALS- linked astrocyte toxicity for motor neurons Burcin Ikiz Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2013 © 2013 Burcin Ikiz All rights reserved Abstract Unraveling the molecular mechanism underlying ALS-linked astrocyte toxicity for motor neurons Burcin Ikiz Mutations in superoxide dismutase-1 (SOD1) cause a familial form of amyotrophic lateral sclerosis (ALS), a fatal paralytic disorder. Transgenic mutant SOD1 rodents capture the hallmarks of this disease, which is characterized by a progressive loss of motor neurons. Studies in chimeric and conditional transgenic mutant SOD1 mice indicate that non-neuronal cells, such as astrocytes, play an important role in motor neuron degeneration. Consistent with this non-cell autonomous scenario are the demonstrations that wild-type primary and embryonic stem cell- derived motor neurons selectively degenerate when cultured in the presence of either mutant SOD1-expressing astrocytes or medium conditioned with such mutant astrocytes. The work in this thesis rests on the use of an unbiased genomic strategy that combines RNA-Seq and “reverse gene engineering” algorithms in an attempt to decipher the molecular underpinnings of motor neuron degeneration caused by mutant astrocytes. To allow such analyses, first, mutant SOD1- induced toxicity on purified embryonic stem cell-derived motor neurons was validated and characterized. This was followed by the validation of signaling pathways identified by bioinformatics in purified embryonic stem cell-derived motor neurons, using both pharmacological and genetic techniques, leading to the discovery that nuclear factor kappa B (NF-κB) is instrumental in the demise of motor neurons exposed to mutant astrocytes in vitro. -
Table 10: H. Sapiens Recon 1 Network Confidence Scores and Citations
Table 10: H. sapiens Recon 1 network confidence scores and citations. Alphabetized list of reactions and their corresponding confidence scores, literature citations, and curator notes. Confidence scores (ranging from 0 to 3) are defined in the text. Reaction Abbreviation Score Authors Article or Book Title Journal Year PubMed ID Curation Notes This reaction takes place in kidney Human 25-hydroxyvitamin D 24-hydroxylase based on Vitamins, G.F.M. Ball,2004, Blackwell publishing, Labuda M, Lemieux N, Tihy cytochrome P450 subunit maps to a different 24,25VITD2Hm 3 J Bone Miner Res 1993 8266831 1st ed (book) pg.196 F, Prinster C, Glorieux FH. chromosomal location than that of pseudovitamin D- 1-4 ng/ml blood deficient rickets. is produced if neither ca2+ nor pi i needed (regulated by these compounds concentration) IT This reaction takes place in kidney Kusudo T, Sakaki T, Abe D, based on Vitamins, G.F.M. Ball,2004, Blackwell publishing, Fujishima T, Kittaka A, Metabolism of A-ring diastereomers of 1alpha,25- Biochem Biophys Res 24,25VITD2Hm 3 2004 15358094 1st ed (book) pg.196 Takayama H, Hatakeyama S, dihydroxyvitamin D3 by CYP24A1. Commun 1-4 ng/ml blood Ohta M, Inouye K. is produced if neither ca2+ nor pi i needed (regulated by these compounds concentration) IT This reaction takes place in kidney St-Arnaud R, Messerlian S, The 25-hydroxyvitamin D 1-alpha-hydroxylase gene based on Vitamins, G.F.M. Ball,2004, Blackwell publishing, 25VITD3Hm 3 Moir JM, Omdahl JL, Glorieux maps to the pseudovitamin D-deficiency rickets J Bone Miner Res 1997 9333115 1st ed (book) pg.196 FH. -
A Potential Role for Intragenic Mirnas on Their Hosts' Interactome
Hinske et al. BMC Genomics 2010, 11:533 http://www.biomedcentral.com/1471-2164/11/533 RESEARCH ARTICLE Open Access A potential role for intragenic miRNAs on their hosts’ interactome Ludwig Christian G Hinske1,2*, Pedro AF Galante3, Winston P Kuo4,5, Lucila Ohno-Machado2 Abstract Background: miRNAs are small, non-coding RNA molecules that mainly act as negative regulators of target gene messages. Due to their regulatory functions, they have lately been implicated in several diseases, including malignancies. Roughly half of known miRNA genes are located within previously annotated protein-coding regions ("intragenic miRNAs”). Although a role of intragenic miRNAs as negative feedback regulators has been speculated, to the best of our knowledge there have been no conclusive large-scale studies investigating the relationship between intragenic miRNAs and host genes and their pathways. Results: miRNA-containing host genes were three times longer, contained more introns and had longer 5’ introns compared to a randomly sampled gene cohort. These results are consistent with the observation that more than 60% of intronic miRNAs are found within the first five 5’ introns. Host gene 3’-untranslated regions (3’-UTRs) were 40% longer and contained significantly more adenylate/uridylate-rich elements (AREs) compared to a randomly sampled gene cohort. Coincidentally, recent literature suggests that several components of the miRNA biogenesis pathway are required for the rapid decay of mRNAs containing AREs. A high-confidence set of predicted mRNA targets of intragenic miRNAs also shared many of these features with the host genes. Approximately 20% of intragenic miRNAs were predicted to target their host mRNA transcript.