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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. -
Phenotypic and Molecular Analysis of Mes-3, a Maternal-Effect Gene Required for Proliferation and Viability of the Germ Line in C
Copyright 0 1995 by the Genetics Society of America Phenotypic and Molecular Analysis of mes-3, a Maternal-Effect Gene Required for Proliferation and Viability of the Germ Line in C. eleguns Janet E. Paulsen,' Elizabeth E. Capowski2 and Susan Strome Department of Biology, Indiana University, Bloomington, Indiana 47405 Manuscript received July 24, 1995 Accepted for publication September 14, 1995 ABSTRACT mes-3 is one of four maternaleffect sterile genes that encode maternal components required for normal postembryonic development of the germ line in Caenorhabditis elegans. mes-3 mutant mothers produce sterile progeny, which contain few germ cells andno gametes. This terminal phenotype reflects two problems: reduced proliferation of the germ line and germ cell death. Both the appearanceof the dying germ cells and the results of genetic tests indicate that germ cells in mes-3 animals undergo a necrotic-like death, not programmedcell death. The few germ cells that appear healthyin mes-3 worms do not differentiateinto gametes, even after eliminationof the signaling pathway that normally maintains the undifferentiated population of germ cells. Thus, mes-3 encodes a maternally supplied product that is required both for proliferation of the germ line and for maintenance of viable germ cells that are competent to differentiate into gametes. Cloning and molecular characterizationof mes-3 revealed that it is the upstream gene in an operon. The genes in the operon display parallel expression patterns; transcripts are present throughout development and are not restricted to germ-line tissue. Both mes-3 and the downstream gene in the operon encode novel proteins. HE germ line enables metazoan organisms to pro- germ cell, P4, at the 16-24cell stage. -
Genetic and Maternal Effect Influences on Viability of Common Frog
Heredity (2003) 91, 117–124 & 2003 Nature Publishing Group All rights reserved 0018-067X/03 $25.00 www.nature.com/hdy Genetic and maternal effect influences on viability of common frog tadpoles under different environmental conditions S Pakkasmaa1, J Merila¨2 and RB O’Hara2,3 1Department of Population Biology, Evolutionary Biology Centre, Uppsala University, Norbyva¨gen 18D, SE-75236 Uppsala, Sweden; 2Ecological Genetics Research Unit, Department of Ecology and Systematics, PO Box 65, FIN-00014 University of Helsinki, Finland; 3Rolf Nevanlinna Institute, PO Box 4, FIN-00014 University of Helsinki, Finland The influence of environmental stress on the expression of all traits were significant, independent of pH treatments and genetic and maternal effects on the viability traits has seldom typically of magnitude similar to the additive genetic effects. been assessed in wild vertebrates. We have estimated Maternal effects were large for all traits, especially for genetic and maternal effects on the viability (viz probability of viability itself, and their expression was partly dependent survival, probability of being deformed, and body size and on the environment. In the case of body size, the maternal shape) of common frog, Rana temporaria, tadpoles under effects were mediated largely through egg size. In general, stressful (low pH) and nonstressful (neutral pH) environ- the results give little evidence for the conjecture that mental conditions. A Bayesian analysis using generalized environmental stress created by low pH would impact linear mixed models was applied to data from a factorial strongly on the genetic architecture of fitness-related traits laboratory experiment. The expression of additive genetic in frogs, and hamper adaptation to stress caused by variance was independent of pH treatments, and all traits acidification. -
Maternal Variants in NLRP and Other Maternal Effect Proteins Are
Epigenetics J Med Genet: first published as 10.1136/jmedgenet-2017-105190 on 24 March 2018. Downloaded from ORIGINAL ARTICLE Maternal variants in NLRP and other maternal effect proteins are associated with multilocus imprinting disturbance in offspring Matthias Begemann,1 Faisal I Rezwan,2 Jasmin Beygo,3 Louise E Docherty,4 Julia Kolarova,5 Christopher Schroeder,3 Karin Buiting,3 Kamal Chokkalingam,6 Franziska Degenhardt,7 Emma L Wakeling,8 Stephanie Kleinle,9 Daniela González Fassrainer,9 Barbara Oehl-Jaschkowitz,10 Claire L S Turner,11 Michal Patalan,12 Maria Gizewska,12 Gerhard Binder,13 Can Thi Bich Ngoc,14 Vu Chi Dung,14 Sarju G Mehta,15 Gareth Baynam,16,17 Julian P Hamilton-Shield,18 Sara Aljareh,2 Oluwakemi Lokulo-Sodipe,2,19 Rachel Horton,2,19 Reiner Siebert,5 Miriam Elbracht,1 Isabel Karen Temple,2,19 Thomas Eggermann,1 Deborah J G Mackay2 ► Additional material is ABSTRact overgrowth, macroglossia, exomphalos, hemihy- published online only. To view Background Genomic imprinting results from pertrophy and predisposition to Wilms tumour), please visit the journal online (http:// dx. doi. org/ 10. 1136/ the resistance of germline epigenetic marks to the growth restriction disorders Silver-Russell jmedgenet- 2017- 105190). reprogramming in the early embryo for a small syndrome (SRS; restricted growth, asymmetry and number of mammalian genes. Genetic, epigenetic or poor feeding) and Temple syndrome (TS; growth For numbered affiliations see environmental insults that prevent imprints from evading restriction, poor feeding, early puberty and obesity) end of article. reprogramming may result in imprinting disorders, which and transient neonatal diabetes mellitus (TNDM; impact growth, development, behaviour and metabolism. -
Chapter 12 Gene Expression and Regulation
PYF12 3/21/05 8:04 PM Page 191 Chapter 12 Gene expression and regulation Bacterial genomes usually contain several thousand different genes. Some of the gene products are required by the cell under all growth conditions and are called house- keeping genes. These include the genes that encode such proteins as DNA poly- merase, RNA polymerase, and DNA gyrase. Many other gene products are required under specific growth conditions. These include enzymes that synthesize amino acids, break down specific sugars, or respond to a specific environmental condition such as DNA damage. Housekeeping genes must be expressed at some level all of the time. Frequently, as the cell grows faster, more of the housekeeping gene products are needed. Even under very slow growth, some of each housekeeping gene product is made. The gene prod- ucts required for specific growth conditions are not needed all of the time. These genes are frequently expressed at extremely low levels, or not expressed at all when they are not needed and yet made when they are needed. This chapter will examine gene regulation or how bacteria regulate the expression of their genes so that the genes that are being expressed meet the needs of the cell for a specific growth condition. Gene regulation can occur at three possible places in the production of an active gene product. First, the transcription of the gene can be regulated. This is known as transcriptional regulation. When the gene is transcribed and how much it is transcribed influences the amount of gene product that is made. Second, if the gene encodes a protein, it can be regulated at the translational level. -
Gene Expression: Layers of Gene Regulation
RESEARCH HIGHLIGHTS GENE EXPRESSION methylation. Spearman’s rank cor- relation between methylation levels Layers of gene regulation (within 50 kb on either side of the transcription start site) and alterna- A new study investigates genetic and expression and DNA methylation lev- tive splicing levels show that, for epigenetic influences on genome els often overlap functional elements. many of the genes tested, there is a regulation and alternative splicing, Across cell types, expression quantita- significant association. Of note, many and highlights the tissue specificity of tive trait loci (eQTLs) are enriched in of the associations between DNA some of these interactions. DNase I-hypersensitive sites, whereas methylation and alternative splicing In a previous study, the researchers methylation QTLs (mQTLs) are are cell type-specific, illustrating examined the relationship between enriched in enhancers and insulators. another layer of cellular variability. genetic variation, DNA methyation Their statistical analyses show that, A complex relationship between and gene expression using samples generally, genetic variation has a more DNA methylation and gene expres- from the GenCord cohort that were consistent effect on gene expres- sion is beginning to emerge. This derived from umbilical cords of 204 sion across cell types, although the study further defines the roles of newborn children. They genotyped strength of the effect can be variable. genomic and epigenomic variation 2.5 million single-nucleotide poly- However, the effects of epigenetic in determining cellular phenotypes, morphisms (SNPs), assayed the meth- variation on gene expression are more and the mechanisms by which these ylation levels of 482,421 CpG sites tissue-specific. Methylation sites effects might occur. -
Spatiotemporal Network Motif Reveals the Biological Traits of Developmental Gene Regulatory Networks in Drosophila Melanogaster
UC Irvine UC Irvine Previously Published Works Title Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster Permalink https://escholarship.org/uc/item/55k7w157 Journal BMC Systems Biology, 6(1) ISSN 1752-0509 Authors Kim, Man-Sun Kim, Jeong-Rae Kim, Dongsan et al. Publication Date 2012-05-01 DOI http://dx.doi.org/10.1186/1752-0509-6-31 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Kim et al. BMC Systems Biology 2012, 6:31 http://www.biomedcentral.com/1752-0509/6/31 RESEARCH ARTICLE Open Access Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster Man-Sun Kim1, Jeong-Rae Kim1,2, Dongsan Kim1, Arthur D Lander3 and Kwang-Hyun Cho1* Abstract Background: Network motifs provided a “conceptual tool” for understanding the functional principles of biological networks, but such motifs have primarily been used to consider static network structures. Static networks, however, cannot be used to reveal time- and region-specific traits of biological systems. To overcome this limitation, we proposed the concept of a “spatiotemporal network motif,” a spatiotemporal sequence of network motifs of sub-networks which are active only at specific time points and body parts. Results: On the basis of this concept, we analyzed the developmental gene regulatory network of the Drosophila melanogaster embryo. We identified spatiotemporal network motifs and investigated their distribution pattern in time and space. As a result, we found how key developmental processes are temporally and spatially regulated by the gene network. In particular, we found that nested feedback loops appeared frequently throughout the entire developmental process. -
How Are Protein Products Made from a Gene?
How are protein products made from a gene? Copyright 2016 by the Rector and Visitors of the University of Virginia How are protein products made from a gene? Step 1: Deoxyribonucleic acid (DNA) is stored within the compartment of the cell called the nucleus. Nucleus DNA is a sequence made up of building blocks called nucleotides (more information can be found DNA in “What is some basic information about DNA?”). RNA When a gene is expressed, the DNA opens up and is transcribed into RNA; this step is called transcription. Cytoplasm Copyright 2016 by the Rector and Visitors of the University of Virginia How are protein products made from a gene? Step 2: Nucleus Ribonucleic acid (RNA) is created from transcribing DNA. DNA The RNA is exported from the nucleus into RNA the large compartment of the cell called the cytoplasm. A structure called the ribosome will read the RNA sequence; this step is called translation. protein ribosome In this step, an amino acid sequence will be Cytoplasm generated. There are 20 amino acids used to make proteins (more details about DNA, RNA and amino acids can be found in “What is some basic information about DNA?”, “What is transcription?” and “What is translation?”). Copyright 2016 by the Rector and Visitors of the University of Virginia How are protein products made from a gene? Nucleus Step 3: Once the amino acid sequence is DNA generated, the molecule will fold into a three-dimensional (3-D) RNA structure. The protein may go through other processing, but essentially is ready protein to perform its function. -
Maternal-Offspring Conflict Leads to the Evolution of Dominant Zygotic Sex
Heredity (2002) 88, 102–111 2002 Nature Publishing Group All rights reserved 0018-067X/02 $25.00 www.nature.com/hdy Maternal-offspring conflict leads to the evolution of dominant zygotic sex determination JH Werren1, MJ Hatcher2 and HCJ Godfray3 1Department of Biology, University of Rochester, Rochester NY 14627, USA; 2School of Biology , University of Leeds, Leeds LS2 9JT, UK; 3NERC Centre for Population Biology, Imperial College at Silwood Park, Ascot, SL5 7PY, UK Sex determination in many species involves interactions males more negatively effect fitness within the family, a male among maternally expressed genes (eg, mRNA’s and pro- heterogametic (XY male) sex determining system evolves, teins placed into the egg) and zygotically expressed genes. whereas when females more negatively effect fitness in the Recent studies have proposed that conflicting selective family, a female heterogametic (ZW female) system evolves. pressures can occur between maternally and zygotically Individuals with the dominant sex allele are one sex, and the expressed sex determining loci and that these may play a opposite sex is determined by maternally-expressed genes role in shaping the evolution of sex determining systems. in individuals without the dominant sex allele. Results there- Here we show that such genetic conflict occurs under very fore suggest that maternal-zygotic conflict could play a role general circumstances. Whenever sex ratio among progeny in the early evolution of chromosomal sex determining sys- in a family affects the fitness of either progeny in that family tems. Predictions are made concerning the patterns of or maternal fitness, then maternal-zygotic genetic conflict expression of maternal and zygotic sex determining genes occurs. -
Epigenetics and the Biological Definition of Gene × Environment
Child Development, January/February 2010, Volume 81, Number 1, Pages 41–79 Epigenetics and the Biological Definition of Gene · Environment Interactions Michael J. Meaney McGill University Variations in phenotype reflect the influence of environmental conditions during development on cellular functions, including that of the genome. The recent integration of epigenetics into developmental psychobiol- ogy illustrates the processes by which environmental conditions in early life structurally alter DNA, provid- ing a physical basis for the influence of the perinatal environmental signals on phenotype over the life of the individual. This review focuses on the enduring effects of naturally occurring variations in maternal care on gene expression and phenotype to provide an example of environmentally driven plasticity at the level of the DNA, revealing the interdependence of gene and environmental in the regulation of phenotype. The nature–nurture debate is essentially a question prevention and intervention programs. In the social of the determinants of individual differences in the sciences, and particularly psychology, there has expression of specific traits among members of the generally been an understandable bias in favor of same species. The origin of the terms nature and explanations derived from the ‘‘nurture’’ perspec- nurture has been credited to Richard Mulcaster, a tive, which emphasizes the capacity for environ- British teacher who imagined these influences as mentally induced plasticity in brain structure and collaborative forces that shape child development function. Nevertheless, over recent decades there (West & King, 1987). History has conspired to per- has been a gradual, if at times reluctant acceptance vert Mulcaster’s intent, casting genetic and environ- that genomic variations contribute to individual dif- mental influences as independent agents in the ferences in brain development and function. -
Viable Maternal-Effect Mutations That Affect the Development
Copyright 0 1995 by the Genetics Society of America Viable Maternal-Effect Mutations ThatAffect the Development of the Nematode Caenorhabditis eZegam Siegfried Hekimi, Paula Boutis and Bernard Lakowski Department of Biology, McGill University, Montreal, Quibec, Canada H3A IBI Manuscript received June 27, 1995 Accepted for publication September 12, 1995 ABSTRACT We carried out a genetic screen for viable maternal-effect mutants to identify genes with a critical function relatively early in development. This type of mutation would not have been identified readily in previous screens for viable mutants and therefore could define previously unidentified genes. We screened 30,000 genomes and identified 41 mutations falling into 24 complementation groups. We genetically mapped these 24 loci; only two of them appear to correspond to previously identified genes. We present a partial phenotypic characterizationof the mutants anda quantitative analysis of the degree to which they can be maternally or zygotically rescued. ENETIC screens inthe nematode Caenorhabditis matically found in previous screens for viable mutants, G elegans have identified numerous genes required as in those screens in general only the first generation for normal development.Most of these genes have been of homozygotes was examined. identified through screens for viable mutants with ab- Indeed, relatively few maternal-effect viable muta- normal morphology or behavior (e.g., BRENNER1974; tions have been characterized to date. However, some HODGKINand BRENNER1977; HODGKIN1980, 1983; particularly interesting genesdisplay this type ofherita- CHALFIEand SULSTON1981; RIDDLE et al. 1981; TRENT bility, among them, genesin the dosage compensation et al. 1983; FERGUSONand HORVITZ1985; PARKand and sex-determination pathways, such as sdc-1 (VILLE- HORVITZ1986; DESAIet al. -
How Genes Work
Help Me Understand Genetics How Genes Work Reprinted from MedlinePlus Genetics U.S. National Library of Medicine National Institutes of Health Department of Health & Human Services Table of Contents 1 What are proteins and what do they do? 1 2 How do genes direct the production of proteins? 5 3 Can genes be turned on and off in cells? 7 4 What is epigenetics? 8 5 How do cells divide? 10 6 How do genes control the growth and division of cells? 12 7 How do geneticists indicate the location of a gene? 16 Reprinted from MedlinePlus Genetics (https://medlineplus.gov/genetics/) i How Genes Work 1 What are proteins and what do they do? Proteins are large, complex molecules that play many critical roles in the body. They do most of the work in cells and are required for the structure, function, and regulation of thebody’s tissues and organs. Proteins are made up of hundreds or thousands of smaller units called amino acids, which are attached to one another in long chains. There are 20 different types of amino acids that can be combined to make a protein. The sequence of amino acids determineseach protein’s unique 3-dimensional structure and its specific function. Aminoacids are coded by combinations of three DNA building blocks (nucleotides), determined by the sequence of genes. Proteins can be described according to their large range of functions in the body, listed inalphabetical order: Antibody. Antibodies bind to specific foreign particles, such as viruses and bacteria, to help protect the body. Example: Immunoglobulin G (IgG) (Figure 1) Enzyme.