Fine Mapping of a Major QTL Influencing Morphine Preference in C57BL/6 and DBA/2 Mice Using Congenic Strains
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Piggybac Mutagenesis and Exome Sequencing Identify Genetic Driver
Noorani et al. Genome Biology (2020) 21:181 https://doi.org/10.1186/s13059-020-02092-2 RESEARCH Open Access PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas Imran Noorani1,2* , Jorge de la Rosa1†, Yoon Ha Choi1,3†, Alexander Strong1, Hannes Ponstingl1, M. S. Vijayabaskar1, Jusung Lee3, Eunmin Lee3, Angela Richard-Londt4, Mathias Friedrich1,5, Federica Furlanetto5, Rocio Fuente1, Ruby Banerjee1, Fengtang Yang1, Frances Law1, Colin Watts2,6, Roland Rad5, George Vassiliou1, Jong Kyoung Kim3, Thomas Santarius2, Sebastian Brandner4 and Allan Bradley1* * Correspondence: [email protected]; [email protected] Abstract †Jorge de la Rosa and Yoonha Choi contributed equally to this work. Background: Glioma is the most common intrinsic brain tumor and also occurs in 1The Wellcome Trust Sanger the spinal cord. Activating EGFR mutations are common in IDH1 wild-type gliomas. Institute, Wellcome Trust Genome However, the cooperative partners of EGFR driving gliomagenesis remain poorly Campus, Hinxton, Cambridgeshire CB10 1SA, UK understood. Full list of author information is Results: We explore EGFR-mutant glioma evolution in conditional mutant mice by available at the end of the article whole-exome sequencing, transposon mutagenesis forward genetic screening, and transcriptomics. We show mutant EGFR is sufficient to initiate gliomagenesis in vivo, both in the brain and spinal cord. We identify significantly recurrent somatic alterations in these gliomas including mutant EGFR amplifications and Sub1, Trp53, and Tead2 loss-of-function mutations. Comprehensive functional characterization of 96 gliomas by genome-wide piggyBac insertional mutagenesis in vivo identifies 281 known and novel EGFR-cooperating driver genes, including Cdkn2a, Nf1, Spred1, and Nav3. -
Live-Cell Imaging Rnai Screen Identifies PP2A–B55α and Importin-Β1 As Key Mitotic Exit Regulators in Human Cells
LETTERS Live-cell imaging RNAi screen identifies PP2A–B55α and importin-β1 as key mitotic exit regulators in human cells Michael H. A. Schmitz1,2,3, Michael Held1,2, Veerle Janssens4, James R. A. Hutchins5, Otto Hudecz6, Elitsa Ivanova4, Jozef Goris4, Laura Trinkle-Mulcahy7, Angus I. Lamond8, Ina Poser9, Anthony A. Hyman9, Karl Mechtler5,6, Jan-Michael Peters5 and Daniel W. Gerlich1,2,10 When vertebrate cells exit mitosis various cellular structures can contribute to Cdk1 substrate dephosphorylation during vertebrate are re-organized to build functional interphase cells1. This mitotic exit, whereas Ca2+-triggered mitotic exit in cytostatic-factor- depends on Cdk1 (cyclin dependent kinase 1) inactivation arrested egg extracts depends on calcineurin12,13. Early genetic studies in and subsequent dephosphorylation of its substrates2–4. Drosophila melanogaster 14,15 and Aspergillus nidulans16 reported defects Members of the protein phosphatase 1 and 2A (PP1 and in late mitosis of PP1 and PP2A mutants. However, the assays used in PP2A) families can dephosphorylate Cdk1 substrates in these studies were not specific for mitotic exit because they scored pro- biochemical extracts during mitotic exit5,6, but how this relates metaphase arrest or anaphase chromosome bridges, which can result to postmitotic reassembly of interphase structures in intact from defects in early mitosis. cells is not known. Here, we use a live-cell imaging assay and Intracellular targeting of Ser/Thr phosphatase complexes to specific RNAi knockdown to screen a genome-wide library of protein substrates is mediated by a diverse range of regulatory and targeting phosphatases for mitotic exit functions in human cells. We subunits that associate with a small group of catalytic subunits3,4,17. -
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 ...................................................... -
Vast Human-Specific Delay in Cortical Ontogenesis Associated With
Supplementary information Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques Supplementary Methods Sample collection We used prefrontal cortex (PFC) and cerebellar cortex (CBC) samples from postmortem brains of 33 human (aged 0-98 years), 14 chimpanzee (aged 0-44 years) and 44 rhesus macaque individuals (aged 0-28 years) (Table S1). Human samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders at the University of Maryland, USA, the Netherlands Brain Bank, Amsterdam, Netherlands and the Chinese Brain Bank Center, Wuhan, China. Informed consent for use of human tissues for research was obtained in writing from all donors or their next of kin. All subjects were defined as normal by forensic pathologists at the corresponding brain bank. All subjects suffered sudden death with no prolonged agonal state. Chimpanzee samples were obtained from the Yerkes Primate Center, GA, USA, the Anthropological Institute & Museum of the University of Zürich-Irchel, Switzerland and the Biomedical Primate Research Centre, Netherlands (eight Western chimpanzees, one Central/Eastern and five of unknown origin). Rhesus macaque samples were obtained from the Suzhou Experimental Animal Center, China. All non-human primates used in this study suffered sudden deaths for reasons other than their participation in this study and without any relation to the tissue used. CBC dissections were made from the cerebellar cortex. PFC dissections were made from the frontal part of the superior frontal gyrus. All samples contained an approximately 2:1 grey matter to white matter volume ratio. RNA microarray hybridization RNA isolation, hybridization to microarrays, and data preprocessing were performed as described previously (Khaitovich et al. -
Detection of H3k4me3 Identifies Neurohiv Signatures, Genomic
viruses Article Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis Liana Basova 1, Alexander Lindsey 1, Anne Marie McGovern 1, Ronald J. Ellis 2 and Maria Cecilia Garibaldi Marcondes 1,* 1 San Diego Biomedical Research Institute, San Diego, CA 92121, USA; [email protected] (L.B.); [email protected] (A.L.); [email protected] (A.M.M.) 2 Departments of Neurosciences and Psychiatry, University of California San Diego, San Diego, CA 92103, USA; [email protected] * Correspondence: [email protected] Abstract: Human postmortem specimens are extremely valuable resources for investigating trans- lational hypotheses. Tissue repositories collect clinically assessed specimens from people with and without HIV, including age, viral load, treatments, substance use patterns and cognitive functions. One challenge is the limited number of specimens suitable for transcriptional studies, mainly due to poor RNA quality resulting from long postmortem intervals. We hypothesized that epigenomic Citation: Basova, L.; Lindsey, A.; signatures would be more stable than RNA for assessing global changes associated with outcomes McGovern, A.M.; Ellis, R.J.; of interest. We found that H3K27Ac or RNA Polymerase (Pol) were not consistently detected by Marcondes, M.C.G. Detection of H3K4me3 Identifies NeuroHIV Chromatin Immunoprecipitation (ChIP), while the enhancer H3K4me3 histone modification was Signatures, Genomic Effects of abundant and stable up to the 72 h postmortem. We tested our ability to use H3K4me3 in human Methamphetamine and Addiction prefrontal cortex from HIV+ individuals meeting criteria for methamphetamine use disorder or not Pathways in Postmortem HIV+ Brain (Meth +/−) which exhibited poor RNA quality and were not suitable for transcriptional profiling. -
Identification of Multiple Complex Rearrangements Associated With
ORIGINAL ARTICLE Identification of Multiple Complex Rearrangements Associated with Deletions in the 6q23-27 Region in Se´zary Syndrome Katarzyna Iz˙ykowska1, Mariola Zawada1, Karina Nowicka1, Piotr Grabarczyk2, Floriane C.M. Braun2, Martin Delin2,MarkusMo¨bs3, Marc Beyer3, Wolfram Sterry3, Christian A. Schmidt2 and Grzegorz K. Przybylski1,2 The 6q23-27 region, recurrently deleted in Se´zary syndrome (SS), was characterized at the molecular level in 13 SS patients and SS cell line SeAx. Using fine-tiling comparative genomic hybridization, deletions within the 6q23-27 region were detected in half of the samples (six patients and SeAx). All samples with deletions were further analyzed by ligation-mediated PCR. In addition, in one patient sample and in SeAx, paired-end next-generation sequencing was performed on the HiSeq2000 Illumina platform. Using those techniques, 23 rearrangements associated with the deletions were identified. The majority of rearrangements showed enormous complexity and diversity, including eight inversions, three transpositions, and four translocations (with chromosomes 3, 17, 10, and 12). Fifteen genes were disrupted by those rearrangements, the MYB proto-oncogene three times and the interleukin-22 receptor subunit alpha-2 gene (IL22RA2) twice. All three patients with MYB alterations showed low MYB expression, whereas seven of the remaining patients showed overexpression. Most patients overexpressing MYB also presented increased expression of MYC, HSPA8, and BCL2. Five gene fusions were identified, of which two, CCDC28A–IL22RA2 and AIG1–GOSR1, both in SeAx, were in the same orientation and were expressed at the messenger RNA level. Journal of Investigative Dermatology (2013) 133, 2617–2625; doi:10.1038/jid.2013.188; published online 23 May 2013 INTRODUCTION patients with SS. -
Discovering Candidate Imprinted Genes and Imprinting Control Regions in the Human Genome
bioRxiv preprint doi: https://doi.org/10.1101/678151; this version posted June 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Discovering candidate imprinted genes and Imprinting Control Regions in the human genome Minou Bina Purdue University, Department of Chemistry 560 Oval Dr., West Lafayette, IN 47907 USA Contact: [email protected] ABSTRACT Genomic imprinting is a process thereby a subset of genes is expressed in a parent-of-origin specific manner. This evolutionary novelty is restricted to mammals and controlled by genomic DNA segments known as Imprinting Control Regions (ICRs). The known imprinted genes function in many important developmental and postnatal processes including organogenesis, neurogenesis, and fertility. Furthermore, defects in imprinted genes could cause severe diseases and abnormalities. Because of the importance of the ICRs to the regulation of parent-of-origin specific gene expression, I developed a genome-wide strategy for their localization. This strategy located clusters of the ZFBS-Morph overlaps along the entire human genome. Previously, I showed that in the mouse genome, clusters of 2 or more of these overlaps correctly located ~ 90% of the fully characterized ICRs and germline Differentially Methylated Regions (gDMRs). The ZFBS-Morph overlaps are composite-DNA-elements comprised of the ZFP57 binding site (ZFBS) overlapping a subset of the MLL1 morphemes. My strategy consists of creating plots to display the density of ZFBS-Morph overlaps along genomic DNA. Peaks in these plots pinpointed several of the known ICRs/gDMRs within relatively long genomic DNA sections and even along entire chromosomal DNA. -
Discovering Candidate Imprinted Genes and Imprinting Control Regions in the Human Genome Minou Bina
Bina BMC Genomics (2020) 21:378 https://doi.org/10.1186/s12864-020-6688-8 RESEARCH ARTICLE Open Access Discovering candidate imprinted genes and imprinting control regions in the human genome Minou Bina Abstract Background: Genomic imprinting is a process thereby a subset of genes is expressed in a parent-of-origin specific manner. This evolutionary novelty is restricted to mammals and controlled by genomic DNA segments known as Imprinting Control Regions (ICRs) and germline Differentially Methylated Regions (gDMRs). Previously, I showed that in the mouse genome, the fully characterized ICRs/gDMRs often includes clusters of 2 or more of a set of composite-DNA-elements known as ZFBS-morph overlaps. Results: Because of the importance of the ICRs to regulating parent-of-origin specific gene expression, I developed a genome-wide strategy for predicting their positions in the human genome. My strategy consists of creating plots to display the density of ZFBS-morph overlaps along the entire chromosomal DNA sequences. In initial evaluations, I found that peaks in these plots pinpointed several of the known ICRs/gDMRs along the DNA in chromosomal bands. I deduced that in density-plots, robust peaks corresponded to actual or candidate ICRs in the DNA. By locating the genes in the vicinity of candidate ICRs, I could discover potential imprinting genes. Additionally, my assessments revealed a connection between several of the potential imprinted genes and human developmental anomalies. Examples include Leber congenital amaurosis 11, Coffin-Siris syndrome, progressive myoclonic epilepsy- 10, microcephalic osteodysplastic primordial dwarfism type II, and microphthalmia, cleft lip and palate, and agenesis of the corpus callosum. -
Early Vertebrate Whole Genome Duplications Were Predated by a Period of Intense Genome Rearrangement
Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement Andrew L. Hufton1, Detlef Groth1,2, Martin Vingron1, Hans Lehrach1, Albert J. Poustka1, Georgia Panopoulou1* 1. Max Planck for Molecular Genetics, Ihnestr. 73, 12169 Berlin, Germany. 2. Potsdam University, Bioinformatics Group, c/o Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany * Corresponding author: Max-Planck Institut für Molekulare Genetik, Ihnestrasse 73, D- 14195 Berlin Germany. email: [email protected], Tel: +49-30-84131235, Fax: +49- 30-84131128 Running title: Early vertebrate genome duplications and rearrangements Keywords: synteny, amphioxus, genome duplications, rearrangement rate, genome instability Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Hufton et al. Abstract Researchers, supported by data from polyploid plants, have suggested that whole genome duplication (WGD) may induce genomic instability and rearrangement, an idea which could have important implications for vertebrate evolution. Benefiting from the newly released amphioxus genome sequence (Branchiostoma floridae), an invertebrate which researchers have hoped is representative of the ancestral chordate genome, we have used gene proximity conservation to estimate rates of genome rearrangement throughout vertebrates and some of their invertebrate ancestors. We find that, while amphioxus remains the best single source of invertebrate information about the early chordate genome, its genome structure is not particularly well conserved and it cannot be considered a fossilization of the vertebrate pre- duplication genome. In agreement with previous reports, we identify two WGD events in early vertebrates and another in teleost fish. -
Metastasis of Uveal Melanoma with Monosomy-3 Is Associated with a Less Glycogenetic Gene Expression Profile and the Dysregulation of Glycogen Storage
cancers Article Metastasis of Uveal Melanoma with Monosomy-3 Is Associated with a Less Glycogenetic Gene Expression Profile and the Dysregulation of Glycogen Storage Siranush Vardanyan 1 , Anton Brosig 1, Hartmut Merz 2, Mahdy Ranjbar 1, 1 1, 1, , Vinodh Kakkassery , Salvatore Grisanti y and Aysegül Tura * y 1 Department of Ophthalmology, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; [email protected] (S.V.); [email protected] (A.B.); [email protected] (M.R.); [email protected] (V.K.); [email protected] (S.G.) 2 Reference Center for Lymph Node Pathology and Haematopathology, 23562 Lübeck, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-451-500-43912 Contributed equally to this work and should be regarded as equivalent senior authors. y Received: 4 July 2020; Accepted: 27 July 2020; Published: 29 July 2020 Abstract: The prolonged storage of glucose as glycogen can promote the quiescence of tumor cells, whereas the accumulation of an aberrant form of glycogen without the primer protein glycogenin can induce the metabolic switch towards a glycolytic phenotype. Here, we analyzed the expression of n = 67 genes involved in glycogen metabolism on the uveal melanoma (UM) cohort of the Cancer Genome Atlas (TCGA) study and validated the differentially expressed genes in an independent cohort. We also evaluated the glycogen levels with regard to the prognostic factors via a differential periodic acid-Schiff (PAS) staining. UMs with monosomy-3 exhibited a less glycogenetic and more insulin-resistant gene expression profile, together with the reduction of glycogen levels, which were associated with the metastases. -
Cell-Type Specific Translational Profiling in Huntington's Disease
Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2011 Cell-Type Specific rT anslational Profiling in Huntington's Disease Mouse Models Robert J. Fenster Follow this and additional works at: http://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons Recommended Citation Fenster, Robert J., "Cell-Type Specific rT anslational Profiling in Huntington's Disease Mouse Models" (2011). Student Theses and Dissertations. Paper 148. This Thesis is brought to you for free and open access by Digital Commons @ RU. It has been accepted for inclusion in Student Theses and Dissertations by an authorized administrator of Digital Commons @ RU. For more information, please contact [email protected]. CELL-TYPE SPECIFIC TRANSLATIONAL PROFILING IN HUNTINGTON’S DISEASE MOUSE MODELS A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Robert Jonathan Fenster June 2011 © Copyright by Robert Jonathan Fenster 2011 CELL-TYPE SPECIFIC TRANSLATIONAL PROFILING IN HUNTINGTON’S DISEASE MOUSE MODELS Robert Jonathan Fenster, Ph.D. The Rockefeller University 2011 Medium spiny neurons (MSNs) are among the most vulnerable cell populations in Huntington’s Disease (HD). Within this population, striatopallidal MSNs are more vulnerable than striatonigral MSNs, which may explain the typical progression in HD of chorea to hypokinesis. The biological basis for this differential vulnerability is unknown, although differences in transcriptional dysfunction caused by mutant huntingtin (mhtt) have been proposed as a possible mechanism. In order to determine the differences in gene expression caused by mhtt in these two populations, we selectively isolated translated mRNAs from striatopallidal and striatonigral MSNs in the R6-2 and YAC128 HD mouse models at pre- and post-symptomatic time points using the BACTRAP technique (Heiman et al, 2008). -
1 Enhanced Lymph Vessel Density, Remodelling And
Page 1 of 57 Diabetes ENHANCED LYMPH VESSEL DENSITY, REMODELLING AND INFLAMMATION IS REFLECTED BY GENE EXPRESSION SIGNATURES IN DERMAL LYMPHATIC ENDOTHELIAL CELLS IN TYPE 2 DIABETES Monika Haemmerle1, Thomas Keller1, Gerda Egger1, Helga Schachner1, Carl Walter Steiner2, Dejan Stokic3, Christoph Neumayer4, Markus K. Brown1, Dontscho Kerjaschki1, Brigitte Hantusch1 1 Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria 2 Department of Internal Medicine, Division of Rheumatology, Medical University of Vienna, Vienna, Austria 3 Section for Science of Complex Systems, Medical University of Vienna, Austria 4 Department of General Surgery, Medical University of Vienna, Vienna, Austria Corresponding author: Brigitte Hantusch, PhD Clinical Institute of Pathology Medical University of Vienna Waehringer Guertel 18-20 A-1090 Vienna, Austria E-mail: [email protected] Tel.: 0043 1 40400 6389 Fax: 0043 1 40400 5193 Running title: Dermal Lymphatic Vessels in Type 2 Diabetes Word count: 3998 Number of tables: 1 Number of figures: 7 1 Diabetes Publish Ahead of Print, published online February 19, 2013 Diabetes Page 2 of 57 ABSTRACT Type 2 diabetes is associated with microvascular damage that causes frequent infections in the skin and chronic ulcers due to impaired wound healing. To trace pathological changes, we performed a comprehensive analysis of lymphatic vessels in human skin of type 2 diabetic versus non-diabetic patients. The dermis revealed enhanced lymphatic vessel density, and transcriptional profiling of ex vivo isolated lymphatic endothelial cells (LECs) identified 180 genes differentially expressed between type 2 diabetic (dLECs) and non-diabetic (ndLECs) LECs. Bioinformatic analysis of deregulated genes uncovered sets functionally related to inflammation, lymphatic vessel remodelling, lymphangiogenesis and lipid and small molecule transport.