Chapter 12 Gene Expression and Regulation
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Dna Methylation Post Transcriptional Modification
Dna Methylation Post Transcriptional Modification Blistery Benny backbiting her tug-of-war so protectively that Scot barrel very weekends. Solanaceous and unpossessing Eric pubes her creatorships abrogating while Raymundo bereave some limitations demonstrably. Clair compresses his catchings getter epexegetically or epidemically after Bernie vitriols and piffling unchangeably, hypognathous and nourishing. To explore quantitative and dynamic properties of transcriptional regulation by. MeSH Cochrane Library. In revere last check of man series but left house with various gene expression profile of the effect of. Moreover interpretation of transcriptional changes during COVID-19 has been. In transcriptional modification by post transcriptional repression and posted by selective breeding industry: patterns of dna methylation during gc cells and the study of dna. DNA methylation regulates transcriptional homeostasis of. Be local in two ways Post Translational Modifications of amino acid residues of histone. International journal of cyclic gmp in a chromatin dynamics: unexpected results in alternative splicing of reusing and diagnosis of dmrs has been identified using whole process. Dam in dna methylation to violent outbursts that have originated anywhere in england and post transcriptional gene is regulated at the content in dna methylation post transcriptional modification of. A seven sample which customers post being the dtc company for analysis. Fei zhao y, methylation dynamics and modifications on lysine is an essential that. Tag-based our Generation Sequencing. DNA methylation and histone modifications as epigenetic. Thc content of. Lysine methylation has been involved in both transcriptional activation H3K4. For instance aberrance of DNA methylation andor demethylation has been. Chromosome conformation capture from 3C to 5C and will ChIP-based modification. -
Translational Regulation During Oogenesis and Early Development: the Cap-Poly(A) Tail Relationship
C. R. Biologies 328 (2005) 863–881 http://france.elsevier.com/direct/CRASS3/ Review / Revue Translational regulation during oogenesis and early development: The cap-poly(A) tail relationship Federica Piccioni a, Vincenzo Zappavigna b, Arturo C. Verrotti a,c,∗ a CEINGE–Biotecnologie Avanzate, Via Comunale Margherita 482, 80145 Napoli, Italy b Dipartimento di Biologia Animale, Università di Modena e Reggio Emilia, Via G. Campi 213d, 41100 Modena, Italy c Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli “Federico II”, Via S. Pansini 5, 80131 Napoli, Italy Received 27 February 2005; accepted after revision 10 May 2005 Available online 8 June 2005 Presented by Stuart Edelstein Abstract Metazoans rely on the regulated translation of select maternal mRNAs to control oocyte maturation and the initial stages of embryogenesis. These transcripts usually remain silent until their translation is temporally and spatially required during early development. Different translational regulatory mechanisms, varying from cytoplasmic polyadenylation to localization of maternal mRNAs, have evolved to assure coordinated initiation of development. A common feature of these mechanisms is that they share a few key trans-acting factors. Increasing evidence suggest that ubiquitous conserved mRNA-binding factors, including the eukaryotic translation initiation factor 4E (eIF4E) and the cytoplasmic polyadenylation element binding protein (CPEB), interact with cell-specific molecules to accomplish the correct level of translational activity necessary for normal development. Here we review how capping and polyadenylation of mRNAs modulate interaction with multiple regulatory factors, thus controlling translation during oogenesis and early development. To cite this article: F. Piccioni et al., C. R. Biologies 328 (2005). 2005 Académie des sciences. -
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. -
Evolution of Genomic Expression
C H A P T E R 5 Evolution of Genomic Expression Bernardo Lemos, Christian R. Landry, Pierre Fontanillas, Susan P. Renn, Rob Kulathinal, Kyle M. Brown, and Daniel L. Hartl Introduction Genomic regulation is key to cellular differentiation, tissue morphogenesis, and development. Increasing evidence indicates that evolutionary diversity of phenotypes—from cellular to organismic—may also be, in large part, the result of variation in the regulation of genomic expression. In this chapter we explore the complexity of gene regulation from the perspective of single genes and whole genomes. The first part describes the major factors affecting gene expression levels, from rates of gene transcrip- tion—as mediated by promoter–enhancer interactions and chromatin mod- ifications—to rates of mRNA degradation. This description underscores the multiple levels at which genomic expression can be regulated as well as the complexity and variety of mechanisms used. We then briefly describe the major experimental and computational biology techniques for analyzing gene expression variation and its underlying causes. The final section reviews our understanding of the role of regulatory variation in evolution, including the molecular evolution and population genetics of noncoding DNA, as well as the inheritance and phenotypic evolution of levels of mRNA abundance. The Complex Regulation of Genomic Expression The regulation of gene expression is a complex and dynamic process. It is not a simple matter to turn a gene on and off, let alone precisely regulate its level of expression. Regulation can be accomplished through various mech- anisms at nearly every step of the process of gene expression. Furthermore, each mechanism may require a variety of elements, including DNA sequences, RNA molecules, and proteins, acting in combination to deter- 2 Chapter Five Evolution of Genomic Expression 3 mine the final amount, timing, and location of functional gene product. -
How Influenza Virus Uses Host Cell Pathways During Uncoating
cells Review How Influenza Virus Uses Host Cell Pathways during Uncoating Etori Aguiar Moreira 1 , Yohei Yamauchi 2 and Patrick Matthias 1,3,* 1 Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; [email protected] 2 Faculty of Life Sciences, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; [email protected] 3 Faculty of Sciences, University of Basel, 4031 Basel, Switzerland * Correspondence: [email protected] Abstract: Influenza is a zoonotic respiratory disease of major public health interest due to its pan- demic potential, and a threat to animals and the human population. The influenza A virus genome consists of eight single-stranded RNA segments sequestered within a protein capsid and a lipid bilayer envelope. During host cell entry, cellular cues contribute to viral conformational changes that promote critical events such as fusion with late endosomes, capsid uncoating and viral genome release into the cytosol. In this focused review, we concisely describe the virus infection cycle and highlight the recent findings of host cell pathways and cytosolic proteins that assist influenza uncoating during host cell entry. Keywords: influenza; capsid uncoating; HDAC6; ubiquitin; EPS8; TNPO1; pandemic; M1; virus– host interaction Citation: Moreira, E.A.; Yamauchi, Y.; Matthias, P. How Influenza Virus Uses Host Cell Pathways during 1. Introduction Uncoating. Cells 2021, 10, 1722. Viruses are microscopic parasites that, unable to self-replicate, subvert a host cell https://doi.org/10.3390/ for their replication and propagation. Despite their apparent simplicity, they can cause cells10071722 severe diseases and even pose pandemic threats [1–3]. -
Assessment of Mtor-Dependent Translational Regulation Of
Assessment of mTOR-Dependent Translational Regulation of Interferon Stimulated Genes Mark Livingstone, Kristina Sikström, Philippe Robert, Gilles Uzé, Ola Larsson, Sandra Pellegrini To cite this version: Mark Livingstone, Kristina Sikström, Philippe Robert, Gilles Uzé, Ola Larsson, et al.. Assessment of mTOR-Dependent Translational Regulation of Interferon Stimulated Genes. PLoS ONE, Public Library of Science, 2015, 10 (7), pp.e0133482. 10.1371/journal.pone.0133482. pasteur-02136942 HAL Id: pasteur-02136942 https://hal-pasteur.archives-ouvertes.fr/pasteur-02136942 Submitted on 22 May 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE Assessment of mTOR-Dependent Translational Regulation of Interferon Stimulated Genes Mark Livingstone1¤, Kristina Sikström2, Philippe A. Robert1, Gilles Uzé3, Ola Larsson2*, Sandra Pellegrini1* 1 Cytokine Signaling Unit, Institut Pasteur, CNRS URA1961, Paris, France, 2 Department of Oncology- Pathology, Karolinska Institutet, Stockholm, Sweden, 3 CNRS UMR5235, University of Montpellier II, Montpellier, France ¤ Current Address: tebu-bio SAS, 39 rue de Houdan—BP 15, 78612 Le Perray-en-Yvelines Cedex, France * [email protected] (SP); [email protected] (OL) Abstract Type-I interferon (IFN)-induced activation of the mammalian target of rapamycin (mTOR) OPEN ACCESS signaling pathway has been implicated in translational control of mRNAs encoding inter- Citation: Livingstone M, Sikström K, Robert PA, Uzé feron-stimulated genes (ISGs). -
INTRODUCTION Sirna and Rnai
J Korean Med Sci 2003; 18: 309-18 Copyright The Korean Academy ISSN 1011-8934 of Medical Sciences RNA interference (RNAi) is the sequence-specific gene silencing induced by dou- ble-stranded RNA (dsRNA). Being a highly specific and efficient knockdown tech- nique, RNAi not only provides a powerful tool for functional genomics but also holds Institute of Molecular Biology and Genetics and School of Biological Science, Seoul National a promise for gene therapy. The key player in RNAi is small RNA (~22-nt) termed University, Seoul, Korea siRNA. Small RNAs are involved not only in RNAi but also in basic cellular pro- cesses, such as developmental control and heterochromatin formation. The inter- Received : 19 May 2003 esting biology as well as the remarkable technical value has been drawing wide- Accepted : 23 May 2003 spread attention to this exciting new field. V. Narry Kim, D.Phil. Institute of Molecular Biology and Genetics and School of Biological Science, Seoul National University, San 56-1, Shillim-dong, Gwanak-gu, Seoul 151-742, Korea Key Words : RNA Interference (RNAi); RNA, Small interfering (siRNA); MicroRNAs (miRNA); Small Tel : +82.2-887-8734, Fax : +82.2-875-0907 hairpin RNA (shRNA); mRNA degradation; Translation; Functional genomics; Gene therapy E-mail : [email protected] INTRODUCTION established yet, testing 3-4 candidates are usually sufficient to find effective molecules. Technical expertise accumulated The RNA interference (RNAi) pathway was originally re- in the field of antisense oligonucleotide and ribozyme is now cognized in Caenorhabditis elegans as a response to double- being quickly applied to RNAi, rapidly improving RNAi stranded RNA (dsRNA) leading to sequence-specific gene techniques. -
Molecular Biology and Applied Genetics
MOLECULAR BIOLOGY AND APPLIED GENETICS FOR Medical Laboratory Technology Students Upgraded Lecture Note Series Mohammed Awole Adem Jimma University MOLECULAR BIOLOGY AND APPLIED GENETICS For Medical Laboratory Technician Students Lecture Note Series Mohammed Awole Adem Upgraded - 2006 In collaboration with The Carter Center (EPHTI) and The Federal Democratic Republic of Ethiopia Ministry of Education and Ministry of Health Jimma University PREFACE The problem faced today in the learning and teaching of Applied Genetics and Molecular Biology for laboratory technologists in universities, colleges andhealth institutions primarily from the unavailability of textbooks that focus on the needs of Ethiopian students. This lecture note has been prepared with the primary aim of alleviating the problems encountered in the teaching of Medical Applied Genetics and Molecular Biology course and in minimizing discrepancies prevailing among the different teaching and training health institutions. It can also be used in teaching any introductory course on medical Applied Genetics and Molecular Biology and as a reference material. This lecture note is specifically designed for medical laboratory technologists, and includes only those areas of molecular cell biology and Applied Genetics relevant to degree-level understanding of modern laboratory technology. Since genetics is prerequisite course to molecular biology, the lecture note starts with Genetics i followed by Molecular Biology. It provides students with molecular background to enable them to understand and critically analyze recent advances in laboratory sciences. Finally, it contains a glossary, which summarizes important terminologies used in the text. Each chapter begins by specific learning objectives and at the end of each chapter review questions are also included. -
Actin Gene Requires Myod1, Carg-Box Binding Factor, and Spl
Downloaded from genesdev.cshlp.org on October 3, 2021 - Published by Cold Spring Harbor Laboratory Press Muscle-specific expression of the cardiac -actin gene requires MyoD1, CArG-box binding factor, and Spl Vittorio Sartorelli, Keith A. Webster, 1 and Larry Kedes 2 Program in Molecular Biology and Genetics, Institute for Genetic Medicine, and Departments of Biochemistry and Medicine, University of Southern California School of Medicine, Los Angeles, California 90033 USA Expression of the human cardiac ~-actin gene (HCA) depends on the interactions of multiple transcriptional regulators with promoter elements. We report here that the tissue-specific expression of this promoter is determined by the simultaneous interaction of at least three specific protein-DNA complexes. The myogenic determinant gene MyoD1 activated the transcription of transfected HCA-CAT promoter constructs in nonmuscle cells, including CV-1 and HeLa cells. Gel mobility-shift and footprinting assays revealed that MyoD1 specifically interacted with a single consensus core sequence, CANNTG, at -50. Previously characterized sites interact with a protein identical with or related to the serum response factor (SRF) at - 100 and Spl at -70. All three elements must be intact to support transcription in muscle cells: site-specific mutation within any one of these three elements eliminated transcriptional expression by the promoter. Furthermore, expression of the promoter in embryonic Drosophila melanogaster cells that lack MyoD1 and Spl is strictly dependent on all three sites remaining intact and on the presence of exogenously supplied Spl and MyoD1. These experiments suggest that the presence of three sequence-specific binding proteins, including MyoD1, and their intact target DNA sequences are minimal requirements for muscle-specific expression of the HCA gene. -
An Efficient Protocol for Linker Scanning Mutagenesis: Analysis of the Translational Regulation of an Escherichia Coli RNA Polymerase Subunit Gene Derek M
1997 Oxford University Press Nucleic Acids Research, 1997, Vol. 25, No. 21 4209–4218 An efficient protocol for linker scanning mutagenesis: analysis of the translational regulation of an Escherichia coli RNA polymerase subunit gene Derek M. Dykxhoorn, Rebecca St. Pierre, Oded Van Ham and Thomas Linn* Department of Microbiology and Immunology, Faculty of Medicine, University of Western Ontario, London, Ontario N6A 5C1, Canada Received August 18, 1997; Accepted September 12, 1997 ABSTRACT of the synthetic linker. Though effective, this approach involves a number of time consuming steps. Many deletions have to be A protocol has been developed that is capable of generated and sequenced before appropriate 5′ and 3′ combinations saturating regions hundreds of basepairs in length can be identified, followed by a separate ligation for each 5′/3′ pair with linker scanning mutations. The efficacy of this to produce the final linker scanning mutation. method stems from the design of the linker scanning We have developed a more efficient protocol for linker scanning mutagenesis (LSM) cassette which is composed of a mutagenesis that is capable of generating a library consisting of selectable marker flanked by two oligonucleotides, hundreds of mutations. This protocol makes use of a linker scanning each of which contains a recognition site for a different mutagenesis (LSM) cassette which is composed of two synthetic restriction endonuclease. The cleavage site for one oligonucleotides surrounding the selectable tetracycline resistance endonuclease is within its recognition site, while the gene. The oligonucleotide on one side of the tetracycline resistance second endonuclease cleaves in the target DNA gene has the recognition site for SmaI, while the other beyond the end of the cassette. -
Opposing Roles of Endosomal Innate Immunity Proteins IFITM3 and TLR7 in Human Metapneumovirus Infection
bioRxiv preprint doi: https://doi.org/10.1101/290957; this version posted March 28, 2018. 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. Opposing roles of endosomal innate immunity proteins IFITM3 and TLR7 in human metapneumovirus infection Temet M. McMichael1,3, Yu Zhang2,a, Adam D. Kenney1,3, Lizhi Zhang1,3, Mijia Lu2,3, Mahesh Chemudupati1,3, Jianrong Li2,3, and Jacob S. Yount1,3 1Department of Microbial Infection and Immunity, 2Department of Veterinary Biosciences, and 3Infectious Diseases Institute, The Ohio State University, Columbus, OH aCurrent affiliation: University of Pittsburgh, Pittsburgh, PA Correspondence: J. Yount, PhD, Department of Microbial Infection and Immunity, the Ohio State University, 460 W 12th Ave, Biomedical Research Tower 790, Columbus, OH 43210 ([email protected]). ABSTRACT Human metapneumovirus (hMPV) utilizes a bifurcated cellular entry strategy, fusing either with the plasma membrane or, after endocytosis, with the endosome membrane. Whether cellular factors restrict or enhance either entry pathway is largely unknown. We found that the interferon-induced transmembrane protein 3 (IFITM3) inhibits hMPV infection to an extent similar to endocytosis-inhibiting drugs, and an IFITM3 variant that accumulates at the plasma membrane in addition to its endosome localization provided increased virus restriction. Mechanistically, IFITM3 blocks hMPV F protein-mediated membrane fusion, and inhibition of infection was reversed by the membrane destabilizing drug amphotericin B. Conversely, we unexpectedly found that infection by some hMPV strains is enhanced by Toll-like receptor 7 (TLR7), an endosomal protein, suggesting that cellular entry via endocytosis may be particularly advantageous for hMPV despite eventual restriction of this pathway upon induction of IFITM3. -
IGA 8/E Chapter 8
8 RNA: Transcription and Processing WORKING WITH THE FIGURES 1. In Figure 8-3, why are the arrows for genes 1 and 2 pointing in opposite directions? Answer: The arrows for genes 1 and 2 indicate the direction of transcription, which is always 5 to 3. The two genes are transcribed from opposite DNA strands, which are antiparallel, so the genes must be transcribed in opposite directions to maintain the 5 to 3 direction of transcription. 2. In Figure 8-5, draw the “one gene” at much higher resolution with the following components: DNA, RNA polymerase(s), RNA(s). Answer: At the higher resolution, the feathery structures become RNA transcripts, with the longer transcripts occurring nearer the termination of the gene. The RNA in this drawing has been straightened out to illustrate the progressively longer transcripts. 3. In Figure 8-6, describe where the gene promoter is located. Chapter Eight 271 Answer: The promoter is located to the left (upstream) of the 3 end of the template strand. From this sequence it cannot be determined how far the promoter would be from the 5 end of the mRNA. 4. In Figure 8-9b, write a sequence that could form the hairpin loop structure. Answer: Any sequence that contains inverted complementary regions separated by a noncomplementary one would form a hairpin. One sequence would be: ACGCAAGCUUACCGAUUAUUGUAAGCUUGAAG The two bold-faced sequences would pair and form a hairpin. The intervening non-bold sequence would be the loop. 5. How do you know that the events in Figure 8-13 are occurring in the nucleus? Answer: The figure shows a double-stranded DNA molecule from which RNA is being transcribed.