Glossary of Common Terms in Genetics
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Gene Mapping Techniques
Developmental Neurobiology, edited by Philippe Evrard and Alexandre Minkowski. Nestle Nutrition Workshop Series, Vol. 12. Nestec Ltd., Vevey/Raven Press, Ltd., New York © 1989. Gene Mapping Techniques Jean-Louis Guenet Institut Pasteur, 75724 Paris Cedex 15, France Very accurate gene mapping is essential in both man and laboratory mammals (1- 3). Several techniques have been used over the last 50 years to localize mammalian genes on the chromosomes of a given species. This chapter reviews these tech- niques, with special emphasis on the most recent ones that represent a true break- through in formal genetics. CLASSICAL GENE MAPPING TECHNIQUES AND THEIR LIMITATIONS When two genes are linked they have a tendency to cosegregate during successive generations. The closer the linkage, the more absolute is the cosegregation. This is the fundamental principle of gene mapping, which has been successfully applied to all species, including plants, over many years. In mammals such as humans and mice, the continued discovery of marker genes scattered throughout the genome has facilitated the mapping of new genes so that we now possess for these two species, particularly the mouse, linkage maps that are far more detailed than those existing for other mammals. In the mouse, special matings can be set up, with appropriate stocks, to test for possible autosomal linkage after two successive reproductive rounds: In general, cross-back crosses are used, cross-intercrosses being reserved for studies in which the viability or the fertility of the homozygous mutant under study is impaired. In humans investigations concerning linkage are based on pedigree analysis. In other words, for both species it is essential to define as a starting point a situa- tion where two genes are heterozygous and either in repulsion A + / + B or in cou- pling AB/ + +, then to look for changes in this configuration after a reproductive cycle (forms in coupling giving rise to forms in repulsion and vice versa), and fi- nally to count the percentage or frequency of these recombination events. -
DNA Insertion Mutations Can Be Predicted by a Periodic Probability
Research article DNA insertion mutations can be predicted by a periodic probability function Tatsuaki Tsuruyama1 1Department of Pathology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan Running title: Probability prediction of mutation Correspondence to: Tatsuaki Tsuruyama Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan Tel.: +81-75-751-3488; Fax: +81-75-761-9591 E-mail: [email protected] 1 Abstract It is generally difficult to predict the positions of mutations in genomic DNA at the nucleotide level. Retroviral DNA insertion is one mode of mutation, resulting in host infections that are difficult to treat. This mutation process involves the integration of retroviral DNA into the host-infected cellular genomic DNA following the interaction between host DNA and a pre-integration complex consisting of retroviral DNA and integrase. Here, we report that retroviral insertion sites around a hotspot within the Zfp521 and N-myc genes can be predicted by a periodic function that is deduced using the diffraction lattice model. In conclusion, the mutagenesis process is described by a biophysical model for DNA–DNA interactions. Keywords: Insertion, mutagenesis, palindromic sequence, retroviral DNA 2 Text Introduction Extensive research has examined retroviral insertions to further our understanding of DNA mutations. Retrovirus-related diseases, including leukemia/lymphoma and AIDS, develop after retroviral genome insertion into the genomic DNA of the infected host cell. Retroviral DNA insertion is one of the modes of insertional mutation. After reverse-transcription of the retroviral genomic RNA into DNA, the retroviral DNA forms a pre-insertion complex (PIC) with the integrase enzyme, which catalyzes the insertion reaction. -
DNA Sequence Insertion and Evolutionary Variation in Gene Regulation (Mobile Elements/Long Terminal Repeats/Alu Sequences/Factor-Binding Sites) Roy J
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 9374-9377, September 1996 Colloquium Paper This paper was presented at a colloquium entitled "Biology of Developmental Transcription Control, " organized by Eric H. Davidson, Roy J. Britten, and Gary Felsenfeld, held October 26-28, 1995, at the National Academy of Sciences in Irvine, CA. DNA sequence insertion and evolutionary variation in gene regulation (mobile elements/long terminal repeats/Alu sequences/factor-binding sites) RoY J. BRITrEN Division of Biology, California Institute of Technology, 101 Dahlia Avenue, Corona del Mar, CA 92625 ABSTRACT Current evidence on the long-term evolution- 3 and 4). Sequence change, obscuring the original structure, ary effect of insertion of sequence elements into gene regions has occurred in the long history, and the underlying rate of is reviewed, restricted to cases where a sequence derived from base substitution that is responsible is known (5). a past insertion participates in the regulation of expression of The requirements for a convincing example are: (i) that a useful gene. Ten such examples in eukaryotes demonstrate there be a trace of a known class of elements present in gene that segments of repetitive DNA or mobile elements have been region; (ii) that there is evidence that it has been there long inserted in the past in gene regions, have been preserved, enough to not just be a transient mutation; (iii) that some sometimes modified by selection, and now affect control of sequence residue of the mobile element or repeat participates transcription ofthe adjacent gene. Included are only examples in regulation of expression of the gene; (iv) that the gene have in which transcription control was modified by the insert. -
DNA Microarrays (Gene Chips) and Cancer
DNA Microarrays (Gene Chips) and Cancer Cancer Education Project University of Rochester DNA Microarrays (Gene Chips) and Cancer http://www.biosci.utexas.edu/graduate/plantbio/images/spot/microarray.jpg http://www.affymetrix.com Part 1 Gene Expression and Cancer Nucleus Proteins DNA RNA Cell membrane All your cells have the same DNA Sperm Embryo Egg Fertilized Egg - Zygote How do cells that have the same DNA (genes) end up having different structures and functions? DNA in the nucleus Genes Different genes are turned on in different cells. DIFFERENTIAL GENE EXPRESSION GENE EXPRESSION (Genes are “on”) Transcription Translation DNA mRNA protein cell structure (Gene) and function Converts the DNA (gene) code into cell structure and function Differential Gene Expression Different genes Different genes are turned on in different cells make different mRNA’s Differential Gene Expression Different genes are turned Different genes Different mRNA’s on in different cells make different mRNA’s make different Proteins An example of differential gene expression White blood cell Stem Cell Platelet Red blood cell Bone marrow stem cells differentiate into specialized blood cells because different genes are expressed during development. Normal Differential Gene Expression Genes mRNA mRNA Expression of different genes results in the cell developing into a red blood cell or a white blood cell Cancer and Differential Gene Expression mRNA Genes But some times….. Mutations can lead to CANCER CELL some genes being Abnormal gene expression more or less may result -
Dna the Code of Life Worksheet
Dna The Code Of Life Worksheet blinds.Forrest Jowled titter well Giffy as misrepresentsrecapitulatory Hughvery nomadically rubberized herwhile isodomum Leonerd exhumedremains leftist forbiddenly. and sketchable. Everett clem invincibly if arithmetical Dawson reinterrogated or Rewriting the Code of Life holding for Genetics and Society. C A process look a genetic code found in DNA is copied and converted into value chain of. They may negatively impact of dna worksheet answers when published by other. Cracking the Code of saw The Biotechnology Institute. DNA lesson plans mRNA tRNA labs mutation activities protein synthesis worksheets and biotechnology experiments for open school property school biology. DNA the code for life FutureLearn. Cracked the genetic code to DNA cloning twins and Dolly the sheep. Dna are being turned into consideration the code life? DNA The Master Molecule of Life CDN. This window or use when he has been copied to a substantial role in a qualified healthcare professional journals as dna the pace that the class before scientists have learned. Explore the Human Genome Project within us Learn about DNA and genomics role in medicine and excellent at the Smithsonian National Museum of Natural. DNA The Double Helix. Most enzymes create a dna the code of life worksheet is getting the. Worksheet that describes the structure of DNA students color the model according to instructions Includes a. Biology Materials Handout MA-H2 Microarray Virtual Lab Activity Worksheet. This user has, worksheet the dna code of life, which proteins are carried on. Notes that scientists have worked 10 years to disappoint the manner human genome explains that DNA is a chemical message that began more data four billion years ago. -
DNA Repair and Synthetic Lethality
Int J Oral Sci (2011) 3:176-179. www.ijos.org.cn REVIEW DNA repair and synthetic lethality Gong-she Guo1, Feng-mei Zhang1, Rui-jie Gao2, Robert Delsite4, Zhi-hui Feng1,3*, Simon N. Powell4* 1School of Public Health, Shandong University, Jinan 250012, China; 2Second People’s Hospital of Weifang, Weifang 261041, China; 3Department of Radiation Oncology, Washington University in St Louis, St Louis MO 63108, USA; 4Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York NY 10065, USA Tumors often have DNA repair defects, suggesting additional inhibition of other DNA repair pathways in tumors may lead to synthetic lethality. Accumulating data demonstrate that DNA repair-defective tumors, in particular homologous recombination (HR), are highly sensitive to DNA-damaging agents. Thus, HR-defective tumors exhibit potential vulnerability to the synthetic lethality approach, which may lead to new therapeutic strategies. It is well known that poly (adenosine diphosphate (ADP)-ribose) polymerase (PARP) inhibitors show the synthetically lethal effect in tumors defective in BRCA1 or BRCA2 genes encoded proteins that are required for efficient HR. In this review, we summarize the strategies of targeting DNA repair pathways and other DNA metabolic functions to cause synthetic lethality in HR-defective tumor cells. Keywords: DNA repair; homologous recombination; synthetic lethality; BRCA; Rad52 International Journal of Oral Science (2011) 3: 176-179. doi: 10.4248/IJOS11064 Introduction polymerase (PARP) inhibitors are specifically toxic to homologous recombination (HR)-defective cells [3-4]. Synthetic lethality is defined as a genetic combination Playing a key role in maintaining genetic stability, HR is of mutations in two or more genes that leads to cell a major repair pathway for double-strand breaks (DSBs) death, whereas a mutation in any one of the genes does utilizing undamaged homologous DNA sequence [5-6]. -
Insertion Element (IS1 Insertion Sequence/Chloramphenicol Resistance Transposon Tn9/Integrative Recombination) L
Proc. Nati. Acad. Sci. USA Vol. 75, No. 3, pp. 1490-1494, March 1978 Genetics Chromosomal integration of phage X by means of a DNA insertion element (IS1 insertion sequence/chloramphenicol resistance transposon Tn9/integrative recombination) L. A. MACHATTIE AND J. A. SHAPIRO Department of Microbiology, University of Chicago, Chicago, Illinois 60637 Communicated by Albert Dorfman, January 10, 1978 ABSTRACT Phage Xcamll2, which contains the chlor- carries a deletion of the gal-attB-bio region of the Escherichia amphenicol resistance transposon Tn9 and has a deletion of attP coil chromosome. MGBO is a gal+bio+ transductant of and the int gene, will lysogenize Escherichia coli K-12. Pro- phage integration occurs at different chromosomal sites, in- MADO. MS6 is a galE indicator for detection of XgalE + T- cluding lacYand maiB, but not at attB. All Xcamll2 prophages transducing particles and S1653 is a gal deletion strain for de- are excised from the chromosome after induction but with tection of Xgal + particles (3). Strain 200PS is a thi lacY strain various efficiencies for different locations. Heteroduplex from the Pasteur collection. Strain QL carries a complete lac analysis of XplacZ transducing phages isolated from a lacY:: deletion, strain X9003 carries the nonpolar M15 lacZ deletion, Xcamll2 prophage reveals an insertion sequence 1 (IS1) element and either will serve as indicator for XplacZ phage in a blue at theloint of viral and chromosomal DNA. Two lines of evi- dencekdicate that Xcamll2 encodes an excision activity that plaque assay (8). recognizes the ISI element: (i) prophage derepression increases Media. Our basic minimal medium and complete TYE the frequency of excision from IacYto yield lac+ revertants, and medium have been described (9). -
Genetic Mapping and Manipulation: Chapter 2-Two-Point Mapping with Genetic Markers* §
Genetic mapping and manipulation: Chapter 2-Two-point mapping with genetic markers* § David Fay , Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071-3944 USA Table of Contents 1. The basics ..............................................................................................................................1 2. Calculating map distances ......................................................................................................... 3 3. Other considerations ................................................................................................................. 5 4. References ..............................................................................................................................6 1. The basics The basics. Two-point mapping, wherein a mutation in the gene of interest is mapped against a marker mutation, is primarily used to assign mutations to individual chromosomes. It can also give at least a rough indication of distance between the mutation and the markers used. On the surface, the concept of two-point mapping to determine chromosomal linkage is relatively straightforward. It can, however, be the source of some confusion when it comes to processing the actual data based on phenotypic frequencies to accurately determine genetic distances. It is also worth noting that most researchers don't bother much with exhaustive two-point mapping anymore. Once we've assigned our mutation to a linkage group, it's generally off to the races with three-point and SNP mapping -
GENOME GENERATION Glossary
GENOME GENERATION Glossary Chromosome An organism’s DNA is packaged into chromosomes. Humans have 23 pairs of chromosomesincluding one pair of sex chromosomes. Women have two X chromosomes and men have one X and one Y chromosome. Dominant (see also recessive) Genes come in pairs. A dominant form of a gene is the “stronger” version that will be expressed. Therefore if someone has one dominant and one recessive form of a gene, only the characteristics of the dominant form will appear. DNA DNA is the long molecule that contains the genetic instructions for nearly all living things. Two strands of DNA are twisted together into a double helix. The DNA code is made up of four chemical letters (A, C, G and T) which are commonly referred to as bases or nucleotides. Gene A gene is a section of DNA that is the code for a specific biological component, usually a protein. Each gene may have several alternative forms. Each of us has two copies of most of our genes, one copy inherited from each parent. Most of our traits are the result of the combined effects of a number of different genes. Very few traits are the result of just one gene. Genetic sequence The precise order of letters (bases) in a section of DNA. Genome A genome is the complete DNA instructions for an organism. The human genome contains 3 billion DNA letters and approximately 23,000 genes. Genomics Genomics is the study of genomes. This includes not only the DNA sequence itself, but also an understanding of the function and regulation of genes both individually and in combination. -
A Gain-Of-Function P53-Mutant Oncogene Promotes Cell Fate Plasticity and Myeloid Leukemia Through the Pluripotency Factor FOXH1
Published OnlineFirst May 8, 2019; DOI: 10.1158/2159-8290.CD-18-1391 RESEARCH ARTICLE A Gain-of-Function p53-Mutant Oncogene Promotes Cell Fate Plasticity and Myeloid Leukemia through the Pluripotency Factor FOXH1 Evangelia Loizou1,2, Ana Banito1, Geulah Livshits1, Yu-Jui Ho1, Richard P. Koche3, Francisco J. Sánchez-Rivera1, Allison Mayle1, Chi-Chao Chen1, Savvas Kinalis4, Frederik O. Bagger4,5, Edward R. Kastenhuber1,6, Benjamin H. Durham7, and Scott W. Lowe1,8 Downloaded from cancerdiscovery.aacrjournals.org on September 27, 2021. © 2019 American Association for Cancer Research. Published OnlineFirst May 8, 2019; DOI: 10.1158/2159-8290.CD-18-1391 ABSTRACT Mutations in the TP53 tumor suppressor gene are common in many cancer types, including the acute myeloid leukemia (AML) subtype known as complex karyotype AML (CK-AML). Here, we identify a gain-of-function (GOF) Trp53 mutation that accelerates CK-AML initiation beyond p53 loss and, surprisingly, is required for disease maintenance. The Trp53 R172H muta- tion (TP53 R175H in humans) exhibits a neomorphic function by promoting aberrant self-renewal in leu- kemic cells, a phenotype that is present in hematopoietic stem and progenitor cells (HSPC) even prior to their transformation. We identify FOXH1 as a critical mediator of mutant p53 function that binds to and regulates stem cell–associated genes and transcriptional programs. Our results identify a context where mutant p53 acts as a bona fi de oncogene that contributes to the pathogenesis of CK-AML and suggests a common biological theme for TP53 GOF in cancer. SIGNIFICANCE: Our study demonstrates how a GOF p53 mutant can hijack an embryonic transcrip- tion factor to promote aberrant self-renewal. -
An Introduction to Recurrent Nucleotide Interactions in RNA Blake A
Overview An introduction to recurrent nucleotide interactions in RNA Blake A. Sweeney,1 Poorna Roy2 and Neocles B. Leontis2∗ RNA secondary structure diagrams familiar to molecular biologists summarize at a glance the folding of RNA chains to form Watson–Crick paired double helices. However, they can be misleading: First of all, they imply that the nucleotides in loops and linker segments, which can amount to 35% to 50% of a structured RNA, do not significantly interact with other nucleotides. Secondly, they give the impression that RNA molecules are loosely organized in three-dimensional (3D) space. In fact, structured RNAs are compactly folded as a result of numerous long-range, sequence-specific interactions, many of which involve loop or linker nucleotides. Here, we provide an introduction for students and researchers of RNA on the types, prevalence, and sequence variations of inter-nucleotide interactions that structure and stabilize RNA 3D motifs and architectures, using Escherichia coli (E. coli) 16S ribosomal RNA as a concrete example. The picture that emerges is that almost all nucleotides in structured RNA molecules, including those in nominally single-stranded loop or linker regions, form specific interactions that stabilize functional structures or mediate interactions with other molecules. The small number of noninteracting, ‘looped-out’ nucleotides make it possible for the RNA chain to form sharp turns. Base-pairing is the most specific interaction in RNA as it involves edge-to-edge hydrogen bonding (H-bonding) of the bases. Non-Watson–Crick base pairs are a significant fraction (30% or more) of base pairs in structured RNAs. © 2014 John Wiley & Sons, Ltd. -
Zinc Fingers and a Green Thumb: Manipulating Gene Expression in Plants Segal, Stege and Barbas 165
163 Zinc fingers and a green thumb: manipulating gene expression in plants David J Segaly, Justin T Stegez and Carlos F Barbas IIIç Artificial transcription factors can be rapidly constructed A variety of techniques have been developed to manip- from predefined zinc-finger modules to regulate virtually any ulate gene expression in plants. Increased expression of gene. Stable, heritable up- and downregulation of endogenous genes is most commonly achieved through endogenous genes has been demonstrated in transgenic transgene overexpression [1]. The introduction of tissue- plants. These advances promise new approaches for creating specific and inducible promoters has improved the utility functional knockouts and conditional overexpression, and of this approach, and efficient and robust plant transforma- for other gene discovery and manipulation applications in tion techniques have made the construction of transgenes plants. a relatively routine task. However, variable expression and co-suppression of transgenes often complicate this process. Addresses Furthermore, transgenes cannot accommodate alternative ÃThe Skaggs Institute for Chemical Biology and the Department of splicing, which may be important for the appropriate Molecular Biology, The Scripps Research Institute, La Jolla, function of some transgenes [2]. California 92037, USA yDepartment of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, USA Reducing or eliminating the expression of a gene in plants zDiversa Corporation, San Diego, California 92121, USA is not as simple as overexpressing a gene. Gene disruption §The Scripps Research Institute, BCC-550, North Torrey Pines Road, by homologous recombination, tDNA insertions and che- La Jolla, California 92037, USA mical mutagenesis has been used successfully, but these e-mail: [email protected] Correspondence: Carlos F Barbas III approaches are inefficient and time-consuming technolo- gies.