Human C-Mnc One Gene Is Located on the Region of Chromosome 8
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Bayesian GWAS and Network Analysis Revealed New Candidate Genes for Number of Teats in Pigs
J Appl Genetics DOI 10.1007/s13353-014-0240-y ANIMAL GENETICS • ORIGINAL PAPER Bayesian GWAS and network analysis revealed new candidate genes for number of teats in pigs L. L. Verardo & F. F. Silva & L. Varona & M. D. V. Resende & J. W. M. Bastiaansen & P. S. Lopes & S. E. F. Guimarães Received: 7 March 2014 /Revised: 27 May 2014 /Accepted: 23 July 2014 # Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2014 Abstract The genetic improvement of reproductive traits comparisons based on deviance posterior distribution indicat- such as the number of teats is essential to the success of the ed the superiority of Gaussian model. In general, our results pig industry. As opposite to most SNP association studies that suggest the presence of 19 significant SNPs, which mapped consider continuous phenotypes under Gaussian assumptions, 13 genes. Besides, we predicted gene interactions through this trait is characterized as a discrete variable, which could networks that are consistent with the mammals known breast potentially follow other distributions, such as the Poisson. biology (e.g., development of prolactin receptor signaling, and Therefore, in order to access the complexity of a counting cell proliferation), captured known regulation binding sites, random regression considering all SNPs simultaneously as and provided candidate genes for that trait (e.g., TINAGL1 covariate under a GWAS modeling, the Bayesian inference and ICK). tools become necessary. Currently, another point that deserves to be highlighted in GWAS is the genetic dissection of com- Keywords Counting data . Genes . Reproductive traits . SNP plex phenotypes through candidate genes network derived association from significant SNPs. -
Novel Protein-Tyrosine Kinase Gene (Hck) Preferentially Expressed in Cells of Hematopoietic Origin STEVEN F
MOLECULAR AND CELLULAR BIOLOGY, June 1987, p. 2276-2285 Vol. 7, No. 6 0270-7306/87/062276-10$02.00/0 Copyright © 1987, American Society for Microbiology Novel Protein-Tyrosine Kinase Gene (hck) Preferentially Expressed in Cells of Hematopoietic Origin STEVEN F. ZIEGLER,"12 JAMEY D. MARTH,"', DAVID B. LEWIS,4 AND ROGER M. PERLMUTTER' 2,5* Howard Hughes Medical Institute' and the Departments ofBiochemistry,2 Medicine,s Pediatrics,4 and Pharmacology,3 University of Washington School of Medicine, Seattle, Washington 98195 Received 16 December 1986/Accepted 18 March 1987 Protein-tyrosine kinases are implicated in the control of cell growth by virtue of their frequent appearance as products of retroviral oncogenes and as components of growth factor receptors. Here we report the characterization of a novel human protein-tyrosine kinase gene (hck) that is primarily expressed in hematopoietic cells, particularly granulocytes. The hck gene encodes a 505-residue polypeptide that is closely related to pp56kk, a lymphocyte-specific protein-tyrosine kinase. The exon breakpoints of the hck gene, partially defined by using murine genomic clones, demonstrate that hck is a member of the src gene family and has been subjected to strong selection pressure during mammalian evolution. High-level expression of hck transcripts in granulocytes is especially provocative since these cells are terminally differentiated and typically survive in vivo for only a few hours. Thus the hck gene, like other members of the src gene family, appears to function primarily in cells with little growth potential. Specific phosphorylation of proteins on tyrosine residues line Ml induces monocytoid differentiation (18), presumably was first detected in lysates of cells infected with acutely as a result of activation of endogenous pp60csrc (7). -
Several Galactosyltransferase Activities Are Associated with Mouse Chromosome 17
Copyright 0 1986 by the Genetics Society of America SEVERAL GALACTOSYLTRANSFERASE ACTIVITIES ARE ASSOCIATED WITH MOUSE CHROMOSOME 17 KIYOSHI FURUKAWA,**' STEPHEN ROTH* AND JANET SAWICKI? *Department of Biology, University of Pennsylvania, and +Wistar Institute of Anatomy and Biology, Philadelphia, Pennsylvania 19104 Manuscript received May 20, 1986 Accepted July 24, 1986 ABSTRACT Indirect evidence suggests that some major histocompatibility complex (MHC) proteins are glycosyltransferases. No sequence or mapping information is avail- able for transferases, although ganglioside variations in mice are linked to the H-2 complex on chromosome 17, and one galactosyltransferase activity on mouse sperm varies with T/t complex genotypes, also on chromosome 17. In the present experiments, diploid and trisomy 17 mouse embryos were assayed for four dif- ferent galactosyltransferase activities. The same preparations were assayed for isocitrate dehydrogenase (ld-1, chromosome I) and glyoxalase-1 (Glo-1, chro- mosome 17). Galactosyltransferase specific activities in trisomy 17 embryos are almost 1.5 times higher than in diploid embryos. The correlation between gal- actosyltransferase activities and chromosome 17 dosage indicates that the struc- tural or regulatory gene for these enzymes are located on chromosome 17. LYCOSYLTRANSFERASES transfer sugars from activated donors to an G exceedingly wide variety of acceptors. Several lines of evidence suggest a relationship between glycosyltransferases and the products of the major his- tocompatibility complex (MHC) family of genes (ROTH 1985). First, like MHC products, some transferases have intercellular recognition functions (ROTH, MCGUIREand ROSEMAN197 1; SHUR 1982). Second, when carefully purified, glycosyltransferases appear to exist in structurally related groups (NAGAI, MUENSCHand YOSHIDA1976; NACAI et al. 1978a, b; FURUKAWAand ROTH 1985). -
Frequent Multiplication of the Long Arm of Chromosome 8 in Hepatocellular Carcinoma1
[CANCER RESEARCH 53. 857-860. February 15. 1993] Frequent Multiplication of the Long Arm of Chromosome 8 in Hepatocellular Carcinoma1 Yoshiyuki Fujiwara, Monto Monden, Takesada Mori, Yusuke Nakamura,2 and Mitsuru Emi Department of Biochemistry ¡Y.F., Y. N.. M. E.l. Cancer Institute. 1-37-1 Kaini-lkebukuro. Tiishinia-ku. Tokyo 170. and the Second Department of Surgen' ¡Y.F.. M. M., T. M.], Osaka University MédiraiSellimi. 1-1-50 Fukushima. Fukushima, Osaka 53}, Japan ABSTRACT normal and tumor DNAs enabled visualization of subtle changes that had occurred in tumor DNAs. Frequent allelic losses at loci on several chromosomes have been de We initiated a systematic RFLP analysis of paired DNAs from tected in human hepatocellular carcinomas, but other types of chromo HCCs and their corresponding normal tissues to examine whether somal abnormalities have not been characterized well. Using eight poly multiplication of chromosomal segments may take place during de morphic DNA markers on chromosome 8, we examined 120 primary hepatocellular carcinomas for abnormalities in the copy number of these velopment of HCC. In this paper, we present results of RFLP analysis loci in tumor cells. A 2- to 6-fold increase in intensities of bands repre at loci on chromosome 8, and we demonstrate that multiplication of senting single alÃeleswas observed in 32 of the 78 tumors that were single alÃeleson part or all of the long arm of chromosome 8 has informative for one or more of the markers, indicating an increase in copy occurred in a large proportion of HCCs. number ("multiplication") of alÃeleson8q. -
A Study on Acute Myeloid Leukemias with Trisomy 8, 11, Or 13, Monosomy 7, Or Deletion 5Q
Leukemia (2005) 19, 1224–1228 & 2005 Nature Publishing Group All rights reserved 0887-6924/05 $30.00 www.nature.com/leu Genomic gains and losses influence expression levels of genes located within the affected regions: a study on acute myeloid leukemias with trisomy 8, 11, or 13, monosomy 7, or deletion 5q C Schoch1, A Kohlmann1, M Dugas1, W Kern1, W Hiddemann1, S Schnittger1 and T Haferlach1 1Laboratory for Leukemia Diagnostics, Department of Internal Medicine III, University Hospital Grosshadern, Ludwig-Maximilians-University, Munich, Germany We performed microarray analyses in AML with trisomies 8 aim of this study to investigate whether gains and losses on the (n ¼ 12), 11 (n ¼ 7), 13 (n ¼ 7), monosomy 7 (n ¼ 9), and deletion genomic level translate into altered genes expression also in 5q (n ¼ 7) as sole changes to investigate whether genomic gains and losses translate into altered expression levels of other areas of the genome in AML. genes located in the affected chromosomal regions. Controls were 104 AML with normal karyotype. In subgroups with trisomy, the median expression of genes located on gained Materials and methods chromosomes was higher, while in AML with monosomy 7 and deletion 5q the median expression of genes located in deleted Samples regions was lower. The 50 most differentially expressed genes, as compared to all other subtypes, were equally distributed Bone marrow samples of AML patients at diagnosis were over the genome in AML subgroups with trisomies. In contrast, 30 and 86% of the most differentially expressed genes analyzed: 12 cases with trisomy 8 (AML-TRI8), seven with characteristic for AML with 5q deletion and monosomy 7 are trisomy 11 (AML-TRI11), seven with trisomy 13 (AML-TRI13), located on chromosomes 5 or 7. -
8 Translocation in Burkitt Lymphoma Interrupts the VK Locus (Gene Localization/Immunoglobulin Genes/Genetics of B-Cell Neoplasia/In Situ Hybridization) BEVERLY S
Proc. Natl. Acad. Sci. USA Vol. 81, pp. 2444-2446, April 1984 Genetics The 2p breakpoint of a 2;8 translocation in Burkitt lymphoma interrupts the VK locus (gene localization/immunoglobulin genes/genetics of B-cell neoplasia/in situ hybridization) BEVERLY S. EMANUEL*, JULES R. SELDENt, R. S. K. CHAGANTIt, SURESH JHANWARt, PETER C. NOWELL, AND CARLO M. CROCEt§ *Departments of Pediatrics and of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, and tThe Wistar Institute of Anatomy and Biology, 36th Street at Spruce, Philadelphia, PA 19104; and MLaboratory of Cancer Genetics and Cytogenetics, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021 Contributed by Peter C. Nowell, January 3, 1984 ABSTRACT The majority of chromosomal rearrange- have demonstrated translocation from 8q24 to 14q32 and ments observed in Burkitt lymphomas involve a translocation deregulation of transcription of the c-myc oncogene (18, 20). between 8q and 14q, while the remaining minority carry vari- Close proximity between immunoglobulin heavy chain and ant translocations between chromosome 8 and either 2 or 22. c-myc DNA sequences on the 14q+ chromosome are a result We have studied the JI Burkitt lymphoma cell line carrying of the translocation (15-18, 20). In Burkitt lines with the 8;22 the variant 2;8 chromosome translocation using a combination rearrangement, there is evidence for translocation of X se- of high-resolution and molecular cytogenetic techniques. We quences to the 8q+ chromosome (9, 10), resulting in tran- have determined that the chromosome 2 breakpoint of the 2;8 scriptional activation of the c-myc that remains on the in- translocation in these cells is in the distal portion of 2pll.2. -
The Cytogenetics of Hematologic Neoplasms 1 5
The Cytogenetics of Hematologic Neoplasms 1 5 Aurelia Meloni-Ehrig that errors during cell division were the basis for neoplastic Introduction growth was most likely the determining factor that inspired early researchers to take a better look at the genetics of the The knowledge that cancer is a malignant form of uncon- cell itself. Thus, the need to have cell preparations good trolled growth has existed for over a century. Several biologi- enough to be able to understand the mechanism of cell cal, chemical, and physical agents have been implicated in division became of critical importance. cancer causation. However, the mechanisms responsible for About 50 years after Boveri’s chromosome theory, the this uninhibited proliferation, following the initial insult(s), fi rst manuscripts on the chromosome makeup in normal are still object of intense investigation. human cells and in genetic disorders started to appear, fol- The fi rst documented studies of cancer were performed lowed by those describing chromosome changes in neoplas- over a century ago on domestic animals. At that time, the tic cells. A milestone of this investigation occurred in 1960 lack of both theoretical and technological knowledge with the publication of the fi rst article by Nowell and impaired the formulations of conclusions about cancer, other Hungerford on the association of chronic myelogenous leu- than the visible presence of new growth, thus the term neo- kemia with a small size chromosome, known today as the plasm (from the Greek neo = new and plasma = growth). In Philadelphia (Ph) chromosome, to honor the city where it the early 1900s, the fundamental role of chromosomes in was discovered (see also Chap. -
Rapid Molecular Assays to Study Human Centromere Genomics
Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Method Rapid molecular assays to study human centromere genomics Rafael Contreras-Galindo,1 Sabrina Fischer,1,2 Anjan K. Saha,1,3,4 John D. Lundy,1 Patrick W. Cervantes,1 Mohamad Mourad,1 Claire Wang,1 Brian Qian,1 Manhong Dai,5 Fan Meng,5,6 Arul Chinnaiyan,7,8 Gilbert S. Omenn,1,9,10 Mark H. Kaplan,1 and David M. Markovitz1,4,11,12 1Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA; 2Laboratory of Molecular Virology, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay 11400; 3Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan 48109, USA; 4Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; 5Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan 48109, USA; 6Department of Psychiatry, University of Michigan, Ann Arbor, Michigan 48109, USA; 7Michigan Center for Translational Pathology and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA; 8Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA; 9Department of Human Genetics, 10Departments of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA; 11Program in Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA; 12Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan 48109, USA The centromere is the structural unit responsible for the faithful segregation of chromosomes. Although regulation of cen- tromeric function by epigenetic factors has been well-studied, the contributions of the underlying DNA sequences have been much less well defined, and existing methodologies for studying centromere genomics in biology are laborious. -
Intestinal Cell Kinase, a Protein Associated with Endocrine-Cerebro-Osteodysplasia Syndrome, Is a Key Regulator of Cilia Length and Hedgehog Signaling
Intestinal cell kinase, a protein associated with endocrine-cerebro-osteodysplasia syndrome, is a key regulator of cilia length and Hedgehog signaling Heejung Moona,1, Jieun Songa,1, Jeong-Oh Shinb, Hankyu Leea, Hong-Kyung Kimb, Jonathan T. Eggenschwillerc, Jinwoong Bokb,2, and Hyuk Wan Koa,2 aCollege of Pharmacy, Dongguk University-Seoul, Goyang, 410-820, Korea; bDepartment of Anatomy, BK21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, Korea; and cDepartment of Genetics, University of Georgia, Athens, GA 30606 Edited by Kathryn V. Anderson, Sloan-Kettering Institute, New York, NY, and approved April 29, 2014 (received for review December 12, 2013) Endocrine-cerebro-osteodysplasia (ECO) syndrome is a recessive and MAPK/MAK/(MAK-related kinase)MRK-overlapping kinase genetic disorder associated with multiple congenital defects in (MOK) (4). All RCK family kinases are composed of an N-ter- endocrine, cerebral, and skeletal systems that is caused by a mis- minal catalytic domain with a TDY motif and variable lengths of sense mutation in the mitogen-activated protein kinase-like intestinal a C-terminal domain with unknown function. In a study of the cell kinase (ICK) gene. In algae and invertebrates, ICK homologs are function of RCK family kinases, MAK was found to negatively involved in flagellar formation and ciliogenesis, respectively. How- regulate cilia length in photoreceptor cells by phosphorylating ever, it is not clear whether this role of ICK is conserved in mammals retinitis pigmentosa 1 (5). In lower organisms, physiological roles and how a lack of functional ICK results in the characteristic pheno- of RCK family kinases are relatively well studied. -
Trisomy 8 Mosaicism
Trisomy 8 Mosaicism rarechromo.org Sources Trisomy 8 Mosaicism Trisomy 8 mosaicism (T8M) is a chromosome disorder caused by and the presence of a complete extra chromosome 8 in some cells of References the body. The remaining cells have the usual number of 46 The information in chromosomes, with two copies of chromosome 8 in each cell. this guide is Occasionally T8M is called Warkany syndrome after Dr Josef drawn partly from Warkany, the American paediatrician who first identified the published medical condition and its cause in the 1960s. Full trisomy 8 – where all cells literature. The have an extra copy of chromosome 8 - is believed to be incompatible first-named with survival, so babies and children in whom an extra chromosome author and 8 is found are believed to be always mosaic (Berry 1978; Chandley publication date 1980; Jordan 1998; Karadima 1998). are given to allow you to look for the Genes and chromosomes abstracts or The human body is made up of trillions of cells. Most of the cells original articles contain a set of around 20,000 different genes; this genetic on the internet in information tells the body how to develop, grow and function. Genes PubMed are carried on structures called chromosomes, which carry the (www.ncbi.nlm. genetic material, or DNA, that makes up our genes. nih.gov/pubmed). If you wish, you Chromosomes usually come in pairs: one chromosome from each can obtain most parent. Of these 46 chromosomes, two are a pair of sex articles from chromosomes: XX (a pair of X chromosomes) in females, and XY Unique. -
A Multiplex Human Syndrome Implicates a Key Role for Intestinal Cell Kinase in Development of Central Nervous, Skeletal, and Endocrine Systems
ARTICLE A Multiplex Human Syndrome Implicates a Key Role for Intestinal Cell Kinase in Development of Central Nervous, Skeletal, and Endocrine Systems Piya Lahiry,1,2 Jian Wang,1 John F. Robinson,1 Jacob P. Turowec,2 David W. Litchfield,2 Matthew B. Lanktree,1,2 Gregory B. Gloor,2 Erik G. Puffenberger,3 Kevin A. Strauss,3 Mildred B. Martens,4 David A. Ramsay,4 C. Anthony Rupar,2,5,6 Victoria Siu,2,5,6 and Robert A. Hegele1,2,* Six infants in an Old Order Amish pedigree were observed to be affected with endocrine-cerebro-osteodysplasia (ECO). ECO is a previ- ously unidentified neonatal lethal recessive disorder with multiple anomalies involving the endocrine, cerebral, and skeletal systems. Autozygosity mapping and sequencing identified a previously unknown missense mutation, R272Q, in ICK, encoding intestinal cell kinase (ICK). Our results established that R272 is conserved across species and among ethnicities, and three-dimensional analysis of the protein structure suggests protein instability due to the R272Q mutation. We also demonstrate that the R272Q mutant fails to localize at the nucleus and has diminished kinase activity. These findings suggest that ICK plays a key role in the development of multiple organ systems. Introduction Amish population reportedly have a high degree of consan- guinity,10 this pedigree was ideal for autozygosity mapping Protein kinases belong to one of the largest and most func- of the putative molecular defect.11,12 tionally diverse gene families in eukaryotes, constituting We delineate the clinical features of ECO and report the approximately 1.7% of all human genes.1 By phosphory- first mutation, R272Q (c.1305G/A), within ICK, encod- lating substrates, kinases can direct activity, localization, ing intestinal cell kinase (ICK). -
Diagnostic Interpretation of Genetic Studies in Patients with Primary
AAAAI Work Group Report Diagnostic interpretation of genetic studies in patients with primary immunodeficiency diseases: A working group report of the Primary Immunodeficiency Diseases Committee of the American Academy of Allergy, Asthma & Immunology Ivan K. Chinn, MD,a,b Alice Y. Chan, MD, PhD,c Karin Chen, MD,d Janet Chou, MD,e,f Morna J. Dorsey, MD, MMSc,c Joud Hajjar, MD, MS,a,b Artemio M. Jongco III, MPH, MD, PhD,g,h,i Michael D. Keller, MD,j Lisa J. Kobrynski, MD, MPH,k Attila Kumanovics, MD,l Monica G. Lawrence, MD,m Jennifer W. Leiding, MD,n,o,p Patricia L. Lugar, MD,q Jordan S. Orange, MD, PhD,r,s Kiran Patel, MD,k Craig D. Platt, MD, PhD,e,f Jennifer M. Puck, MD,c Nikita Raje, MD,t,u Neil Romberg, MD,v,w Maria A. Slack, MD,x,y Kathleen E. Sullivan, MD, PhD,v,w Teresa K. Tarrant, MD,z Troy R. Torgerson, MD, PhD,aa,bb and Jolan E. Walter, MD, PhDn,o,cc Houston, Tex; San Francisco, Calif; Salt Lake City, Utah; Boston, Mass; Great Neck and Rochester, NY; Washington, DC; Atlanta, Ga; Rochester, Minn; Charlottesville, Va; St Petersburg, Fla; Durham, NC; Kansas City, Mo; Philadelphia, Pa; and Seattle, Wash AAAAI Position Statements,Work Group Reports, and Systematic Reviews are not to be considered to reflect current AAAAI standards or policy after five years from the date of publication. The statement below is not to be construed as dictating an exclusive course of action nor is it intended to replace the medical judgment of healthcare professionals.