A Decade of 3C Technologies: Insights Into Nuclear Organization
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Nuclear DNA Content, Chromatin Organization and Chromosome Banding in Brown and Yellow Seeds of Dasypyrum Villosum (L.) P
Heredity 72 (1994) 365—373 Received 7 September 1993 Genetical Society of Great Britain Nuclear DNA content, chromatin organization and chromosome banding in brown and yellow seeds of Dasypyrum villosum (L.) P. Candargy R. CREMONINI*, N. COLONNAI-, A. STEFANIt, I. GALASSO4 & D. PIGNONE4 Dipartimento di Scienze Botaniche, Università di Pisa, Via L. Ghini 5, 56126 Pisa, tScuo/a Super/ore Studi Universitari e Perfezionamento 'S. Anna Via Carducci 40, 56127 Pisa, and Istituto del Germoplasma, CNR, Via Amendola 165, 70123 Ban, Italy Bandingpatterns of metaphase chromosomes and nuclear DNA content in root meristematic cells of yellow and brown seeds of Dasypyrum villosum were determined. Microdensitometric evaluation of nuclear absorptions at different thresholds of optical density after Feulgen reaction indicated the organization of the chromatin in interphase nuclei, and allowed an evaluation of the amount of heterochromatin. These results were compared with those obtained after the application of banding techniques. Keywords:chromatinorganization, chromosome banding, Dasypyrum villosum, fluorochromes, kernels. evident morphological differences; both of them are Introduction able to produce ears with yellow and brown caryopses Manyspecies closely related to Triticum are known to (Stefani & Onnis, 1983). have agronomic characters that make them interesting A different behaviour of seed germination and for wheat improvement, and many studies have been viability during ripening and ageing (Meletti & Onnis, carried out on the possibility of introducing alien genes 1961; Stefani & Onnis, 1983; De Gara et al., 1991) into cultivated wheats (Knott, 1987). and a different duration of the mitotic cycle (Innocenti The genus Dasypyrum includes two Mediterranean & Bitonti, 1983) have been reported for the two types wild species: an annual outcrossing diploid, Dasypyrum of caryopses. -
Mutation Detection & Analysis
PRO55 G-Biosciences ♦ 1-800-628-7730 ♦ 1-314-991-6034 ♦ [email protected] A Geno Technology, Inc. (USA) brand name Mutation Detection & Analysis Teacher’s Guidebook (Cat. # BE-314) think proteins! think G-Biosciences www.GBiosciences.com MATERIALS INCLUDED WITH THE KIT ................................................................................ 3 CHECKLIST .......................................................................................................................... 3 SPECIAL HANDLING INSTRUCTIONS ................................................................................... 3 ADDITIONAL EQUIPMENT REQUIRED ................................................................................ 3 TIME REQUIRED ................................................................................................................. 3 OBJECTIVES ........................................................................................................................ 4 BACKGROUND ................................................................................................................... 4 POLYMERASE CHAIN REACTION .................................................................................... 5 RESTRICTION ENZYMES ................................................................................................. 8 TEACHER’S PRE EXPERIMENT SET UP .............................................................................. 11 PREPARE PCR AND RESTRICTION DIGESTION REAGENTS ............................................ 11 -
Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture
Genes 2015, 6, 790-811; doi:10.3390/genes6030790 OPEN ACCESS genes ISSN 2073-4425 www.mdpi.com/journal/genes Review Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture Navneet K. Matharu 1,* and Sajad H. Ahanger 2,* 1 Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA 2 Department of Ophthalmology, Lab for Retinal Cell Biology, University of Zurich, Wagistrasse 14, Zurich 8952, Switzerland * Authors to whom correspondence should be addressed; E-Mails: [email protected] (N.K.M.); [email protected] (S.H.A.). Academic Editor: Jessica Tyler Received: 8 June 2015 / Accepted: 20 August 2015 / Published: 1 September 2015 Abstract: The spatial organization of metazoan genomes has a direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. It is imperative to understand the mechanisms that shape the 3D organization of the eukaryotic genomes. Chromatin insulators have emerged as one of the central components of the genome organization tool-kit across species. Recent advancements in chromatin conformation capture technologies have provided important insights into the architectural role of insulators in genomic structuring. Insulators are involved in 3D genome organization at multiple spatial scales and are important for dynamic reorganization of chromatin structure during reprogramming and differentiation. In this review, we will discuss the classical view and our renewed understanding of insulators as global genome organizers. We will also discuss the plasticity of chromatin structure and its re-organization during pluripotency and differentiation and in situations of cellular stress. -
Repetitive Elements in Humans
International Journal of Molecular Sciences Review Repetitive Elements in Humans Thomas Liehr Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany; [email protected] Abstract: Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called ‘genetic background’, being able to at least potentially influence disease susceptibilities. Here, the known ‘bad boys’ among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well. Keywords: variable numbers of tandem repeats (VNTRs); microsatellites; minisatellites; small-scale repetitive elements (SSREs); chromosomal heteromorphisms (CHs); higher-order repeat (HOR); retroviral DNA 1. Introduction Citation: Liehr, T. Repetitive In humans, like in other higher species, the genome of one individual never looks 100% Elements in Humans. Int. J. Mol. Sci. alike to another one [1], even among those of the same gender or between monozygotic 2021, 22, 2072. -
Structures of Restriction Endonuclease Hindiii in Complex with Its Cognate DNA and Divalent Cations
Title Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations Author(s) Watanabe, Nobuhisa; Takasaki, Yozo; Sato, Chika; Ando, Shoji; Tanaka, Isao Acta Crystallographica. Section D, Biological Crystallography, 65(12), 1326-1333 Citation https://doi.org/10.1107/S0907444909041134 Issue Date 2009-12 Doc URL http://hdl.handle.net/2115/39986 Type article File Information watanabe_ActaCristD65.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP electronic reprint Acta Crystallographica Section D Biological Crystallography ISSN 0907-4449 Editors: E. N. Baker and Z. Dauter Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations Nobuhisa Watanabe, Yozo Takasaki, Chika Sato, Shoji Ando and Isao Tanaka Acta Cryst. (2009). D65, 1326–1333 Copyright c International Union of Crystallography Author(s) of this paper may load this reprint on their own web site or institutional repository provided that this cover page is retained. Republication of this article or its storage in electronic databases other than as specified above is not permitted without prior permission in writing from the IUCr. For further information see http://journals.iucr.org/services/authorrights.html Acta Crystallographica Section D: Biological Crystallography welcomes the submission of papers covering any aspect of structural biology, with a particular emphasis on the struc- tures of biological macromolecules and the methods used to determine them. Reports on new protein structures are particularly encouraged, as are structure–function papers that could include crystallographic binding studies, or structural analysis of mutants or other modified forms of a known protein structure. The key criterion is that such papers should present new insights into biology, chemistry or structure. -
Effects on Transcription and Nuclear Organization
30 Oct 2001 7:3 AR AR144-08.tex AR144-08.SGM ARv2(2001/05/10) P1: GJC Annu. Rev. Genet. 2001. 35:193–208 Copyright c 2001 by Annual Reviews. All rights reserved CHROMATIN INSULATORS AND BOUNDARIES: Effects on Transcription and Nuclear Organization Tatiana I. Gerasimova and Victor G. Corces Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218; e-mail: [email protected]; [email protected] Key Words DNA, chromatin, insulators, transcription, nucleus ■ Abstract Chromatin boundaries and insulators are transcriptional regulatory el- ements that modulate interactions between enhancers and promoters and protect genes from silencing effects by the adjacent chromatin. Originally discovered in Drosophila, insulators have now been found in a variety of organisms, ranging from yeast to hu- mans. They have been found interspersed with regulatory sequences in complex genes and at the boundaries between active and inactive chromatin. Insulators might mod- ulate transcription by organizing the chromatin fiber within the nucleus through the establishment of higher-order domains of chromatin structure. CONTENTS INTRODUCTION .....................................................193 SPECIFIC EXAMPLES OF INSULATOR ELEMENTS .......................194 Insulator Elements in Drosophila .......................................195 The Chicken -Globin Locus and Other Vertebrate Boundary Elements ........................................198 Yeast Boundary Elements .............................................199 MECHANISMS OF INSULATOR FUNCTION .............................200 OTHER FACTORS INVOLVED IN INSULATOR FUNCTION .................203 INTRODUCTION Insulators or chromatin boundaries are DNA sequences defined operationally by two characteristics: They interfere with enhancer-promoter interactions when present between them, and they buffer transgenes from chromosomal position effects (diagrammed in Figures 1 and 2) (30). These two properties must be mani- festations of the normal role these sequences play in the control of gene expression. -
A Short History of the Restriction Enzymes Wil A
Published online 18 October 2013 Nucleic Acids Research, 2014, Vol. 42, No. 1 3–19 doi:10.1093/nar/gkt990 NAR Breakthrough Article SURVEY AND SUMMARY Highlights of the DNA cutters: a short history of the restriction enzymes Wil A. M. Loenen1,*, David T. F. Dryden2,*, Elisabeth A. Raleigh3,*, Geoffrey G. Wilson3,* and Noreen E. Murrayy 1Leiden University Medical Center, Leiden, the Netherlands, 2EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and 3New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA Received August 14, 2013; Revised September 24, 2013; Accepted October 2, 2013 ABSTRACT Type II REases represent the largest group of characterized enzymes owing to their usefulness as tools for recombinant In the early 1950’s, ‘host-controlled variation in DNA technology, and they have been studied extensively. bacterial viruses’ was reported as a non-hereditary Over 300 Type II REases, with >200 different sequence- phenomenon: one cycle of viral growth on certain specificities, are commercially available. Far fewer Type I, bacterial hosts affected the ability of progeny virus III and IV enzymes have been characterized, but putative to grow on other hosts by either restricting or examples are being identified daily through bioinformatic enlarging their host range. Unlike mutation, this analysis of sequenced genomes (Table 1). change was reversible, and one cycle of growth in Here we present a non-specialists perspective on import- the previous host returned the virus to its original ant events in the discovery and understanding of REases. form. These simple observations heralded the dis- Studies of these enzymes have generated a wealth of covery of the endonuclease and methyltransferase information regarding DNA–protein interactions and catalysis, protein family relationships, control of restric- activities of what are now termed Type I, II, III and tion activity and plasticity of protein domains, as well IV DNA restriction-modification systems. -
Dynamics and Interplay of Nuclear Architecture, Genome Organization, and Gene Expression
Downloaded from genesdev.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Dynamics and interplay of nuclear architecture, genome organization, and gene expression Robert Schneider and Rudolf Grosschedl1 Max Planck Institute of Immunobiology, 79108 Freiburg, Germany The organization of the genome in the nucleus of a eu- The nucleus is organized in specific compartments karyotic cell is fairly complex and dynamic. Various fea- that include proteinaceous nuclear bodies, eukaryotic tures of the nuclear architecture, including compart- and heterochromatic chromatin domains, compartmen- mentalization of molecular machines and the spatial talized multiprotein complexes, and nuclear pores that arrangement of genomic sequences, help to carry out and allow for nucleocytoplasmic transport. The dynamic, regulate nuclear processes, such as DNA replication, temporal, and spatial organization of the eukaryotic cell DNA repair, gene transcription, RNA processing, and nucleus emerges as a central determinant of genome mRNA transport. Compartmentalized multiprotein function, and it is important to understand the relation- complexes undergo extensive modifications or exchange ship between nuclear architecture, genome organization, of protein subunits, allowing for an exquisite dynamics and gene expression. Recently, high-resolution tech- of structural components and functional processes of the niques have permitted new insights into the nuclear ar- nucleus. The architecture of the interphase nucleus is chitecture and its relationship to gene expression. linked to the spatial arrangement of genes and gene clus- In this review, we focus on the dynamic organization ters, the structure of chromatin, and the accessibility of of the genome into chromosome territories and chroma- regulatory DNA elements. In this review, we discuss re- tin domains. -
Promiscuous Restriction Is a Cellular Defense Strategy That Confers Fitness
Promiscuous restriction is a cellular defense strategy PNAS PLUS that confers fitness advantage to bacteria Kommireddy Vasua, Easa Nagamalleswaria, and Valakunja Nagarajaa,b,1 aDepartment of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; and bJawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India Edited by Werner Arber, der Universitat Basel, Basel, Switzerland, and approved March 20, 2012 (received for review November 22, 2011) Most bacterial genomes harbor restriction–modification systems, ognition and cofactor utilization, whereas the cognate MTase is encoding a REase and its cognate MTase. On attack by a foreign very site-specific (14). In addition to its recognition sequence, DNA, the REase recognizes it as nonself and subjects it to restric- GGTACC, the enzyme binds and cleaves a number of noncanoni- tion. Should REases be highly specific for targeting the invading cal sequences (i.e., TGTACC, GTTACC, GATACC, GGAACC, foreign DNA? It is often considered to be the case. However, when GGTCCC, GGTATC, GGTACG, GGTACT), with the binding bacteria harboring a promiscuous or high-fidelity variant of the affinity ranging from 8 to 35 nM (14, 15). Accordingly, many of fi REase were challenged with bacteriophages, tness was maximal these sites are cleaved efficiently with kcat values varying from 0.06 − − under conditions of catalytic promiscuity. We also delineate pos- to 0.15 min 1 vs. 4.3 min 1 for canonical sites (15). The promis- sible mechanisms by which the REase recognizes the chromosome cuous activity of the enzyme is directed by a number of cofactors. as self at the noncanonical sites, thereby preventing lethal dsDNA In the presence of the physiological levels of Mg2+, the most breaks. -
Genetically Customized Generations—A Need for Increased Regulatory Control Over Gene Editing Technology in the United States
SMU Law Review Volume 73 Issue 3 Article 10 2020 Genetically Customized Generations—A Need for Increased Regulatory Control over Gene Editing Technology in the United States Morgan Mendicino Southern Methodist University, Dedman School of Law, [email protected] Follow this and additional works at: https://scholar.smu.edu/smulr Part of the Law Commons Recommended Citation Morgan Mendicino, Comment, Genetically Customized Generations—A Need for Increased Regulatory Control over Gene Editing Technology in the United States, 73 SMU L. REV. 585 (2020) https://scholar.smu.edu/smulr/vol73/iss3/10 This Comment is brought to you for free and open access by the Law Journals at SMU Scholar. It has been accepted for inclusion in SMU Law Review by an authorized administrator of SMU Scholar. For more information, please visit http://digitalrepository.smu.edu. GENETICALLY CUSTOMIZED GENERATIONS—A NEED FOR INCREASED REGULATORY CONTROL OVER GENE EDITING TECHNOLOGY IN THE UNITED STATES Morgan Mendicino* ABSTRACT Gene editing technology, once a far-fetched scientific fantasy, has be- come a tangible reality. One emerging form of gene editing in particular, human germline genome editing, possesses revolutionary capabilities that warrant cautious examination. Recent advancements in research have demonstrated that such biotechnology could be used to alter the genetic makeup of unborn children and the hereditary genes of future generations. This biotechnology may possess the ability to save countless human lives, but we must ask—What happens when the line between preventing disease and “playing God” becomes blurry? Human germline genome editing raises a multitude of widespread and deeply rooted questions surrounding the fate of humanity, all of which thwart justifying its present-day use. -
M1BP Cooperates with CP190 to Activate Transcription at TAD Borders and Promote Chromatin Insulator Activity
ARTICLE https://doi.org/10.1038/s41467-021-24407-y OPEN M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity Indira Bag 1,2, Shue Chen 1,2,4, Leah F. Rosin 1,2,4, Yang Chen 1,2, Chen-Yu Liu3, Guo-Yun Yu3 & ✉ Elissa P. Lei 1,2 1234567890():,; Genome organization is driven by forces affecting transcriptional state, but the relationship between transcription and genome architecture remains unclear. Here, we identified the Drosophila transcription factor Motif 1 Binding Protein (M1BP) in physical association with the gypsy chromatin insulator core complex, including the universal insulator protein CP190. M1BP is required for enhancer-blocking and barrier activities of the gypsy insulator as well as its proper nuclear localization. Genome-wide, M1BP specifically colocalizes with CP190 at Motif 1-containing promoters, which are enriched at topologically associating domain (TAD) borders. M1BP facilitates CP190 chromatin binding at many shared sites and vice versa. Both factors promote Motif 1-dependent gene expression and transcription near TAD borders genome-wide. Finally, loss of M1BP reduces chromatin accessibility and increases both inter- and intra-TAD local genome compaction. Our results reveal physical and functional inter- action between CP190 and M1BP to activate transcription at TAD borders and mediate chromatin insulator-dependent genome organization. 1 Nuclear Organization and Gene Expression Section, Bethesda, MD, USA. 2 Laboratory of Biochemistry and Genetics, Bethesda, MD, USA. 3 Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA. ✉ 4These authors contributed equally: Shue Chen, Leah F. -
NF1) Pseudogenes on Chromosomes 2, 14 and 22
European Journal of Human Genetics (2000) 8, 209–214 © 2000 Macmillan Publishers Ltd All rights reserved 1018–4813/00 $15.00 y www.nature.com/ejhg ARTICLE Mechanism of spreading of the highly related neurofibromatosis type 1 (NF1) pseudogenes on chromosomes 2, 14 and 22 Mirjam Luijten1, YingPing Wang2, Blaine T Smith2, Andries Westerveld1, Luc J Smink3, Ian Dunham3, Bruce A Roe2 and Theo JM Hulsebos1 1Department of Human Genetics, Academic Medical Center, University of Amsterdam, The Netherlands; 2Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA; 3Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, UK Neurofibromatosis type 1 (NF1) is a frequent hereditary disorder that involves tissues derived from the embryonic neural crest. Besides the functional gene on chromosome arm 17q, NF1-related sequences (pseudogenes) are present on a number of chromosomes including 2, 12, 14, 15, 18, 21, and 22. We elucidated the complete nucleotide sequence of the NF1 pseudogene on chromosome 22. Only the middle part of the functional gene but not exons 21–27a, encoding the functionally important GAP-related domain of the NF1 protein, is presented in this pseudogene. In addition to the two known NF1 pseudogenes on chromosome 14 we identified two novel variants. A phylogenetic tree was constructed, from which we concluded that the NF1 pseudogenes on chromosomes 2, 14, and 22 are closely related to each other. Clones containing one of these pseudogenes cross-hybridised with the other pseudogenes in this subset, but did not reveal any in situ hybridisation with the functional NF1 gene or with NF1 pseudogenes on other chromosomes.