Chromosome Inactivation
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Genome-Wide Association Study of Increasing Suicidal Ideation During Antidepressant Treatment in the GENDEP Project
The Pharmacogenomics Journal (2012) 12, 68–77 & 2012 Macmillan Publishers Limited. All rights reserved 1470-269X/12 www.nature.com/tpj ORIGINAL ARTICLE Genome-wide association study of increasing suicidal ideation during antidepressant treatment in the GENDEP project NPerroud1,2,3,RUher1, Suicidal thoughts during antidepressant treatment have been the focus of 1 2,3,4 several candidate gene association studies. The aim of the present genome- MYM Ng , M Guipponi , wide association study was to identify additional genetic variants involved in 5 6 JHauser, N Henigsberg , increasing suicidal ideation during escitalopram and nortriptyline treatment. WMaier7,OMors8, A total of 706 adult participants of European ancestry, treated for major M Gennarelli9, M Rietschel10, depression with escitalopram or nortriptyline over 12 weeks in the Genome- DSouery11, MZ Dernovsek12, Based Therapeutic Drugs for Depression (GENDEP) study were genotyped 13 14 with Illumina Human 610-Quad Beadchips (Illumina, San Diego, CA, USA). AS Stamp ,MLathrop , A total of 244 subjects experienced an increase in suicidal ideation AFarmer1, G Breen1,KJAitchison1, during follow-up. The genetic marker most significantly associated with CM Lewis1,IWCraig1 increasing suicidality (8.28 Â 10À7) was a single-nucleotide polymorphism and P McGuffin1 (SNP; rs11143230) located 30 kb downstream of a gene encoding guanine deaminase (GDA) on chromosome 9q21.13. Two suggestive drug-specific 1MRC Social, Genetic and Developmental Psychiatry associations within KCNIP4 (Kv channel-interacting protein 4; chromosome Centre, Institute of Psychiatry, King’s College 4p15.31) and near ELP3 (elongation protein 3 homolog; chromosome London, London, UK; 2Department of Psychiatry, 8p21.1) were found in subjects treated with escitalopram. -
Identification of the Binding Partners for Hspb2 and Cryab Reveals
Brigham Young University BYU ScholarsArchive Theses and Dissertations 2013-12-12 Identification of the Binding arP tners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non- Redundant Roles for Small Heat Shock Proteins Kelsey Murphey Langston Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Langston, Kelsey Murphey, "Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins" (2013). Theses and Dissertations. 3822. https://scholarsarchive.byu.edu/etd/3822 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Julianne H. Grose, Chair William R. McCleary Brian Poole Department of Microbiology and Molecular Biology Brigham Young University December 2013 Copyright © 2013 Kelsey Langston All Rights Reserved ABSTRACT Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactors and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston Department of Microbiology and Molecular Biology, BYU Master of Science Small Heat Shock Proteins (sHSP) are molecular chaperones that play protective roles in cell survival and have been shown to possess chaperone activity. -
The Inactive X Chromosome Is Epigenetically Unstable and Transcriptionally Labile in Breast Cancer
Supplemental Information The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer Ronan Chaligné1,2,3,8, Tatiana Popova1,4, Marco-Antonio Mendoza-Parra5, Mohamed-Ashick M. Saleem5 , David Gentien1,6, Kristen Ban1,2,3,8, Tristan Piolot1,7, Olivier Leroy1,7, Odette Mariani6, Hinrich Gronemeyer*5, Anne Vincent-Salomon*1,4,6,8, Marc-Henri Stern*1,4,6 and Edith Heard*1,2,3,8 Extended Experimental Procedures Cell Culture Human Mammary Epithelial Cells (HMEC, Invitrogen) were grown in serum-free medium (HuMEC, Invitrogen). WI- 38, ZR-75-1, SK-BR-3 and MDA-MB-436 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen) containing 10% fetal bovine serum (FBS). DNA Methylation analysis. We bisulfite-treated 2 µg of genomic DNA using Epitect bisulfite kit (Qiagen). Bisulfite converted DNA was amplified with bisulfite primers listed in Table S3. All primers incorporated a T7 promoter tag, and PCR conditions are available upon request. We analyzed PCR products by MALDI-TOF mass spectrometry after in vitro transcription and specific cleavage (EpiTYPER by Sequenom®). For each amplicon, we analyzed two independent DNA samples and several CG sites in the CpG Island. Design of primers and selection of best promoter region to assess (approx. 500 bp) were done by a combination of UCSC Genome Browser (http://genome.ucsc.edu) and MethPrimer (http://www.urogene.org). All the primers used are listed (Table S3). NB: MAGEC2 CpG analysis have been done with a combination of two CpG island identified in the gene core. Analysis of RNA allelic expression profiles (based on Human SNP Array 6.0) DNA and RNA hybridizations were normalized by Genotyping console. -
A Gene Expression Resource Generated by Genome-Wide Lacz
© 2015. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2015) 8, 1467-1478 doi:10.1242/dmm.021238 RESOURCE ARTICLE A gene expression resource generated by genome-wide lacZ profiling in the mouse Elizabeth Tuck1,**, Jeanne Estabel1,*,**, Anika Oellrich1, Anna Karin Maguire1, Hibret A. Adissu2, Luke Souter1, Emma Siragher1, Charlotte Lillistone1, Angela L. Green1, Hannah Wardle-Jones1, Damian M. Carragher1,‡, Natasha A. Karp1, Damian Smedley1, Niels C. Adams1,§, Sanger Institute Mouse Genetics Project1,‡‡, James N. Bussell1, David J. Adams1, Ramiro Ramırez-Soliś 1, Karen P. Steel1,¶, Antonella Galli1 and Jacqueline K. White1,§§ ABSTRACT composite of RNA-based expression data sets. Strong agreement was observed, indicating a high degree of specificity in our data. Knowledge of the expression profile of a gene is a critical piece of Furthermore, there were 1207 observations of expression of a information required to build an understanding of the normal and particular gene in an anatomical structure where Bgee had no essential functions of that gene and any role it may play in the data, indicating a large amount of novelty in our data set. development or progression of disease. High-throughput, large- Examples of expression data corroborating and extending scale efforts are on-going internationally to characterise reporter- genotype-phenotype associations and supporting disease gene tagged knockout mouse lines. As part of that effort, we report an candidacy are presented to demonstrate the potential of this open access adult mouse expression resource, in which the powerful resource. expression profile of 424 genes has been assessed in up to 47 different organs, tissues and sub-structures using a lacZ reporter KEY WORDS: Gene expression, lacZ reporter, Mouse, Resource gene. -
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Patterns of DNA methylation on the human X chromosome and use in analyzing X-chromosome inactivation by Allison Marie Cotton B.Sc., The University of Guelph, 2005 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in The Faculty of Graduate Studies (Medical Genetics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) January 2012 © Allison Marie Cotton, 2012 Abstract The process of X-chromosome inactivation achieves dosage compensation between mammalian males and females. In females one X chromosome is transcriptionally silenced through a variety of epigenetic modifications including DNA methylation. Most X-linked genes are subject to X-chromosome inactivation and only expressed from the active X chromosome. On the inactive X chromosome, the CpG island promoters of genes subject to X-chromosome inactivation are methylated in their promoter regions, while genes which escape from X- chromosome inactivation have unmethylated CpG island promoters on both the active and inactive X chromosomes. The first objective of this thesis was to determine if the DNA methylation of CpG island promoters could be used to accurately predict X chromosome inactivation status. The second objective was to use DNA methylation to predict X-chromosome inactivation status in a variety of tissues. A comparison of blood, muscle, kidney and neural tissues revealed tissue-specific X-chromosome inactivation, in which 12% of genes escaped from X-chromosome inactivation in some, but not all, tissues. X-linked DNA methylation analysis of placental tissues predicted four times higher escape from X-chromosome inactivation than in any other tissue. Despite the hypomethylation of repetitive elements on both the X chromosome and the autosomes, no changes were detected in the frequency or intensity of placental Cot-1 holes. -
The Role of High Density Lipoprotein Compositional and Functional Heterogeneity in Metabolic Disease
The role of high density lipoprotein compositional and functional heterogeneity in metabolic disease By Scott M. Gordon B.S. State University of New York College at Brockport October, 2012 A Dissertation Presented to the Faculty of The University of Cincinnati College of Medicine in partial fulfillment of the requirements for the Degree of Doctor of Philosophy from the Pathobiology and Molecular Medicine graduate program W. Sean Davidson Ph.D. (Chair) David Askew Ph.D. Professor and Thesis Chair Professor Department of Pathology Department of Pathology University of Cincinnati University of Cincinnati Francis McCormack M.D. Gangani Silva Ph.D. Professor Assistant Professor Department of Pathology Department of Pathology University of Cincinnati University of Cincinnati Jason Lu Ph.D. Assistant Professor Division of Bioinformatics Cincinnati Children’s Hospital i Abstract High density lipoproteins (HDL) are complexes of phospholipid, cholesterol and protein that circulate in the blood. Epidemiological studies have demonstrated a strong inverse correlation between plasma levels of HDL associated cholesterol (HDL-C) and the incidence of cardiovascular disease (CVD). Clinically, HDL-C is often measured and used in combination with low density lipoprotein cholesterol (LDL-C) to assess overall cardiovascular health. HDL have been shown to possess a wide variety of functional attributes which likely contribute to this protection including anti-inflammatory and anti- oxidative properties and the ability to remove excess cholesterol from peripheral tissues and deliver it to the liver for excretion, a process known as reverse cholesterol transport. This functional diversity might be explained by the complexity of HDL composition. Recent studies have taken advantage of advances in mass spectrometry technologies to characterize the proteome of total HDL finding that over 50 different proteins can associate with these particles. -
Research Article Characterization of the Equine Skeletal Muscle
McGivney et al. BMC Genomics 2010, 11:398 http://www.biomedcentral.com/1471-2164/11/398 RESEARCH ARTICLE Open Access CharacterizationResearch article of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training Beatrice A McGivney1, Paul A McGettigan1, John A Browne1, Alexander CO Evans1,3, Rita G Fonseca2, Brendan J Loftus3, Amanda Lohan3, David E MacHugh1,3, Barbara A Murphy1, Lisa M Katz2 and Emmeline W Hill*1 Abstract Background: Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month period of exercise training. The study cohort comprised seven Thoroughbred racehorses from a single training yard. Skeletal muscle biopsies were collected at rest from the gluteus medius at two time points: T1 - untrained, (9 ± 0.5 months old) and T2 - trained (20 ± 0.7 months old). Results: The most abundant mRNA transcripts in the muscle transcriptome were those involved in muscle contraction, aerobic respiration and mitochondrial function. A previously unreported over-representation of genes related to RNA processing, the stress response and proteolysis was observed. Following training 92 tags were differentially expressed of which 74 were annotated. Sixteen genes showed increased expression, including the mitochondrial genes ACADVL, MRPS21 and SLC25A29 encoded by the nuclear genome. Among the 58 genes with decreased expression, MSTN, a negative regulator of muscle growth, had the greatest decrease. Functional analysis of all expressed genes using FatiScan revealed an asymmetric distribution of 482 Gene Ontology (GO) groups and 18 KEGG pathways. -
Microarray Analysis Provides New Insights Into the Function of Apolipoprotein O in Hepg2 Cell Line Chen-Lu Wu, Shui-Ping Zhao* and Bi-Lian Yu*
Wu et al. Lipids in Health and Disease 2013, 12:186 http://www.lipidworld.com/content/12/1/186 RESEARCH Open Access Microarray analysis provides new insights into the function of apolipoprotein O in HepG2 cell line Chen-Lu Wu, Shui-Ping Zhao* and Bi-Lian Yu* Abstract Background: Apolipoprotein O (apoO) is a new member of the apolipoprotein family. However, data on its physiological functions are limited and inconsistent. Using a microarray expression analysis, this study explored the function of apoO in liver cells. Methods: HepG2 cells were treated either with oleic acid or tumor necrosis factor-α for 24 h. mRNA and protein expression of apoO were assessed by quantitative real-time PCR (qRT-PCR) and Western blot respectively. An efficient lentiviral siRNA vector targeting the human apoO gene was designed and constructed. The gene expression profile of HepG2 human hepatocellular carcinoma cells transfected with the apoO silencing vector was investigated using a whole-genome oligonucleotide microarray. The expression levels of some altered genes were validated using qRT-PCR. Results: ApoO expression in HepG2 cells was dramatically affected by lipid and inflammatory stimuli. A total of 282 differentially expressed genes in apoO-silenced HepG2 cells were identified by microarray analysis. These genes included those participating in fatty acid metabolism, such as ACSL4, RGS16, CROT and CYP4F11, and genes participating in the inflammatory response, such as NFKBIZ, TNFSF15, USP2, IL-17, CCL23, NOTCH2, APH-1B and N2N. The gene Uncoupling protein 2 (UCP2), which is involved in both these metabolic pathways, demonstrated significant changes in mRNA level after transfection. -
Karla Alejandra Vizcarra Zevallos Análise Da Função De Genes
Karla Alejandra Vizcarra Zevallos Análise da função de genes candidatos à manutenção da inativação do cromossomo X em humanos Dissertação apresentada ao Pro- grama de Pós‐Graduação Inter- unidades em Biotecnologia USP/ Instituto Butantan/ IPT, para obtenção do Título de Mestre em Ciências. São Paulo 2017 Karla Alejandra Vizcarra Zevallos Análise da função de genes candidatos à manutenção da inativação do cromossomo X em humanos Dissertação apresentada ao Pro- grama de Pós‐Graduação Inter- unidades em Biotecnologia do Instituto de Ciências Biomédicas USP/ Instituto Butantan/ IPT, para obtenção do Título de Mestre em Ciências. Área de concentração: Biotecnologia Orientadora: Profa. Dra. Lygia da Veiga Pereira Carramaschi Versão corrigida. A versão original eletrônica encontra-se disponível tanto na Biblioteca do ICB quanto na Biblioteca Digital de Teses e Dissertações da USP (BDTD) São Paulo 2017 UNIVERSIDADE DE SÃO PAULO Programa de Pós-Graduação Interunidades em Biotecnologia Universidade de São Paulo, Instituto Butantan, Instituto de Pesquisas Tecnológicas Candidato(a): Karla Alejandra Vizcarra Zevallos Título da Dissertação: Análise da função de genes candidatos à manutenção da inativação do cromossomo X em humanos Orientador: Profa. Dra. Lygia da Veiga Pereira Carramaschi A Comissão Julgadora dos trabalhos de Defesa da Dissertação de Mestrado, em sessão pública realizada a ........./......../.........., considerou o(a) candidato(a): ( ) Aprovado(a) ( ) Reprovado(a) Examinador(a): Assinatura: .............................................................................. -
E L If D a R B U K a Ist a N B U L Ü N Ive R Sit E Si Sa Ğ . B Il. E N St
ELIF DARBUKA İSTANBUL ÜNİVERSİTESİ SAĞ. BİL. ENST. YÜKSEK LİSANS TEZİ İSTANBUL-2018 T.C. İSTANBUL ÜNİVERSİTESİ SAĞLIK BİLİMLERİ ENSTİTÜSÜ ( YÜKSEK LİSANS TEZİ ) KOLOREKTAL KANSERLİ HASTALARDA TCEAL7 GENİNİN ARAŞTIRILMASI ELİF DARBUKA DANIŞMAN PROF. DR. ALİ NUR TURGUT ULUTİN GENETİK ANABİLİM DALI GENETİK PROGRAMI İSTANBUL-2018 ii TEZ ONAYI iii BEYAN Bu tez çalışmasının kendi çalışmam olduğunu, tezin planlanmasından yazımına kadar bütün safhalarda etik dışı davranışımın olmadığını, bu tezdeki bütün bilgileri akademik ve etik kurallar içinde elde ettiğimi, bu tez çalışmasıyla elde edilmeyen bütün bilgi ve yorumlara kaynak gösterdiğimi ve bu kaynakları da kaynaklar listesine aldığımı, yine bu tezin çalışılması ve yazımı sırasında patent ve telif haklarını ihlal edici bir davranışımın olmadığı beyan ederim. Elif DARBUKA iv İTHAF Tez çalışmamı; Aileme ithaf ediyorum… v TEŞEKKÜR Tez süresince ilgisini ve desteğini esirgemeyen tez danışmanım Prof. Dr.Turgut ULUTİN’e, Tez çalışmam ve yüksek lisans eğitimim boyunca değerli bilgilerini, katkılarını ve sabrını esirgemeyen, her konuda tecrübesine sonuna kadar güvendiğim değerli hocam Prof. Dr. Nur BUYRU’ya, Tez çalışmamın gerçekleşmesi için gerekli dokuların temin edilmesini sağlayan ve bu süreçte bana destek olan Uzm. Dr. Süleyman DEMİRYAS’a ve patolojik incelemelerde uzmanlığından faydalandığım Uzm. Dr. Nuray KEPİL’e Moleküler Genetik Laboratuvarı’na ilk adımımı attığımdan beri her konuda yardımcı olan, yol gösteren ve sabırla destek veren Doç Dr. Onur BAYKARA’ya, Dr. Seda Ekizoğlu ERATAK’a, Dr. Filiz ÖZDEMİR’e, MSc. Asuman ÇELEBİ’ye ve Dr. Didem SEVEN’e, Doç Dr. Hikmet KÖSEOĞLU’na, Laboratuvar ve yüksek lisans eğitim arkadaşlığından öte benim için dost olan, MSc. Aslı KARACAN’a, BSc. Pelin BULUT’a, BSc. Ceren ORHAN’a, MSc. -
Characterization of an Eutherian Gene Cluster Generated After Transposon Domestication Identifies Bex3 As Relevant for Advanced
Navas-Pérez et al. Genome Biology (2020) 21:267 https://doi.org/10.1186/s13059-020-02172-3 RESEARCH Open Access Characterization of an eutherian gene cluster generated after transposon domestication identifies Bex3 as relevant for advanced neurological functions Enrique Navas-Pérez1†, Cristina Vicente-García2†, Serena Mirra1,3,4,5†, Demian Burguera1,6, Noèlia Fernàndez-Castillo1,4,7, José Luis Ferrán8, Macarena López-Mayorga2, Marta Alaiz-Noya9,10, Irene Suárez-Pereira9,11, Ester Antón-Galindo1, Fausto Ulloa3,5, Carlos Herrera-Úbeda1, Pol Cuscó12,13, Rafael Falcón-Moya9, Antonio Rodríguez-Moreno9, Salvatore D’Aniello14, Bru Cormand1,4,7, Gemma Marfany1,4,7, Eduardo Soriano3,5,15, Ángel M. Carrión9, Jaime J. Carvajal2* and Jordi Garcia-Fernàndez1* * Correspondence: [email protected]; [email protected] Abstract †Enrique Navas-Pérez, Cristina Vicente-García and Serena Mirra Background: One of the most unusual sources of phylogenetically restricted genes contributed equally to this work. is the molecular domestication of transposable elements into a host genome as 2Centro Andaluz de Biología del functional genes. Although these kinds of events are sometimes at the core of key Desarrollo, CSIC-UPO-JA, Universidad Pablo de Olavide, macroevolutionary changes, their origin and organismal function are generally poorly 41013 Sevilla, Spain understood. 1Department of Genetics, Microbiology and Statistics, Faculty Results: Here, we identify several previously unreported transposable element of Biology, and Institut de domestication events in the human and mouse genomes. Among them, we find a Biomedicina (IBUB), University of remarkable molecular domestication that gave rise to a multigenic family in placental Barcelona, 08028 Barcelona, Spain Full list of author information is mammals, the Bex/Tceal gene cluster. -
Methylation of L1hs Promoters Is Lower on the Inactive X, Has A
Human Molecular Genetics, 2012, Vol. 21, No. 1 219–235 doi:10.1093/hmg/ddr456 Advance Access published on October 4, 2011 Methylation of L1Hs promoters is lower on the inactive X, has a tendency of being higher on autosomes in smaller genomes and shows inter-individual variability at some loci Heike Singer1, Maja Walier2, Nicole Nu¨ sgen1, Christian Meesters2,{, Felix Schreiner3, Joachim Woelfle3, Rolf Fimmers2, Thomas Wienker2, Vera M. Kalscheuer4, Tim Becker2,5, Rainer Schwaab1, Johannes Oldenburg1 and Osman El-Maarri1,∗ 1Institute of Experimental Hematology and Transfusion Medicine, 2Institute of Medical Biometry, Informatics and Downloaded from Epidemiology (IMBIE) and 3Pediatric Endocrinology Division, Children’s Hospital, University of Bonn, Bonn, Germany, 4Max Planck Institute for Molecular Genetics, Berlin, Germany and 5German Center for Neurodegenerative Diseases, DZNE, Bonn, Germany Received June 8, 2011; Revised and Accepted September 28, 2011 http://hmg.oxfordjournals.org/ LINE-1 repeats account for ∼17% of the human genome. Little is known about their individual methylation patterns, because their repetitive, almost identical sequences make them difficult to be individually targeted. Here, we used bisulfite conversion to study methylation at individual LINE-1 repeats. The loci studied included 39 X-linked loci and 5 autosomal loci. On the X chromosome in women, we found statistically sig- nificant less methylation at almost all L1Hs compared with men. Methylation at L1P and L1M did not correlate with the inactivation status of the host DNA, while the majority of L1Hs that were possible to be studied lie in at MPI Molec Genetics on April 4, 2013 inactivated regions. To investigate whether the male–female differences at L1Hs on the X are linked to the inactivation process itself rather than to a mere influence of gender, we analyzed six of the L1Hs loci on the X chromosome in Turners and Klinefelters which have female and male phenotype, respectively, but with reversed number of X chromosomes.