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Plasticity in Ploidy: a Generalized Response to Stress
Review Plasticity in ploidy: a generalized response to stress Daniel R. Scholes and Ken N. Paige School of Integrative Biology, University of Illinois at Urbana-Champaign, 515 Morrill Hall, 505 South Goodwin Avenue, Urbana, IL 61801, USA Endoreduplication, the replication of the genome with- or greater) are a general feature of endosperm and sus- out mitosis, leads to an increase in the cellular ploidy of pensor cells of seed across endopolyploid taxa [9]. Very low an organism over its lifetime, a condition termed ‘endo- (or the complete lack of) endopolyploidy across taxa is polyploidy’. Endopolyploidy is thought to play signifi- observed in a few cell types, including phloem companion cant roles in physiology and development through cells and stomatal guard cells, both of which serve highly cellular, metabolic, and genetic effects. While the occur- specialized functions that would possibly be disrupted by rence of endopolyploidy has been observed widely increased ploidy [7,9]. Because endoreduplication is a across taxa, studies have only recently begun to charac- somatic process, the embryo and meristematic cells terize and manipulate endopolyploidy with a focus on its (e.g., procambium, root and shoot apical meristems) also ecological and evolutionary importance. No compilation lack endopolyploidy [6,7,9]. Finally, mixed ploidy among of these examples implicating endoreduplication as a adjacent cells of the same type also occurs (e.g., leaf generalized response to stress has thus far been made, epidermal pavement cells range from 2C to 64C) [7,9]. despite the growing evidence supporting this notion. Although generalized patterns of endopolyploidy may We review here the recent literature of stress-induced be observed within and among plants, recent evidence endopolyploidy and suggest that plants employ endor- suggests that many plants that endoreduplicate can plas- eduplication as an adaptive, plastic response to mitigate tically increase their endopolyploidy beyond their ‘normal’ the effects of stress. -
Cell Cycle Arrest and DNA Endoreduplication Following P21waf1/Cip1 Expression
Oncogene (1998) 17, 1691 ± 1703 1998 Stockton Press All rights reserved 0950 ± 9232/98 $12.00 http://www.stockton-press.co.uk/onc Cell cycle arrest and DNA endoreduplication following p21Waf1/Cip1 expression Stewart Bates, Kevin M Ryan, Andrew C Phillips and Karen H Vousden ABL Basic Research Program, NCI-FCRDC, Building 560, Room 22-96, West 7th Street, Frederick, Maryland 21702-1201, USA p21Waf1/Cip1 is a major transcriptional target of p53 and there are an increasing number of regulatory mechan- has been shown to be one of the principal mediators of isms that serve to inhibit cdk activity. Primary amongst the p53 induced G1 cell cycle arrest. We show that in these is the expression of cdk inhibitors (CDKIs) that addition to the G1 block, p21Waf1/Cip1 can also contribute can bind to and inhibit cyclin/cdk complexes (Sherr to a delay in G2 and expression of p21Waf1/Cip1 gives rise and Roberts, 1996). These fall into two classes, the to cell cycle pro®les essentially indistinguishable from INK family which bind to cdk4 and cdk6 and inhibit those obtained following p53 expression. Arrest of cells complex formation with D-cyclins, and the p21Waf1/Cip1 in G2 likely re¯ects an inability to induce cyclin B1/cdc2 family that bind to cyclin/cdk complexes and inhibit kinase activity in the presence of p21Waf1/Cip1, although the kinase activity. inecient association of p21Waf1/Cip1 and cyclin B1 The p21Waf1/Cip1 family of CDKIs include p21Waf1/Cip1, suggests that the mechanism of inhibition is indirect. p27 and p57 and are broad range inhibitors of cyclin/ Cells released from an S-phase block were not retarded cdk complexes (Gu et al., 1993; Harper et al., 1993; in their ability to progress through S-phase by the Xiong et al., 1993; Firpo et al., 1994; Polyak et al., presence of p21Waf1/Cip1, despite ecient inhibition of 1994; Toyoshima and Hunter, 1994; Lee et al., 1995; cyclin E, A and B1 dependent kinase activity, suggesting Matsuoka et al., 1995). -
The Grammar of Transcriptional Regulation
Hum Genet (2014) 133:701–711 DOI 10.1007/s00439-013-1413-1 REVIEW PAPER The grammar of transcriptional regulation Shira Weingarten-Gabbay · Eran Segal Received: 11 June 2013 / Accepted: 24 December 2013 / Published online: 5 January 2014 © Springer-Verlag Berlin Heidelberg 2014 Abstract Eukaryotes employ combinatorial strategies to regulatory motifs (Levine and Tjian 2003) and exploit motif generate a variety of expression patterns from a relatively geometry as another dimension of combinatorial power small set of regulatory DNA elements. As in any other lan- for regulating transcription. Understanding the fundamen- guage, deciphering the mapping between DNA and expres- tal principles governing transcriptional regulation could sion requires an understanding of the set of rules that govern allow us to predict expression from DNA sequence, with basic principles in transcriptional regulation, the functional far-reaching implications. Most notably, in many human elements involved, and the ways in which they combine to diseases, genetic changes occur in non-coding regions such orchestrate a transcriptional output. Here, we review the cur- as gene promoters and enhancers. However, without under- rent understanding of various grammatical rules, including standing the grammar of transcriptional regulation, we the effect on expression of the number of transcription factor cannot tell which sequence changes affect expression and binding sites, their location, orientation, affinity and activity; how. For example, even for a single binding site, we do not co-association with different factors; and intrinsic nucleo- know the quantitative effects on expression of its location, some organization. We review different methods that are orientation, and affinity; whether these effects are general, used to study the grammar of transcription regulation, high- factor-specific, and/or promoter-dependent; and how they light gaps in current understanding, and discuss how recent depend on the intrinsic nucleosome organization. -
Gene Discovery and Functional Assessment of Rare Copy-Number Variants in Neurodevelopmental Disorders
bioRxiv preprint doi: https://doi.org/10.1101/011510; this version posted November 17, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Gene discovery and functional assessment of rare copy-number variants in neurodevelopmental disorders Janani Iyer and Santhosh Girirajan Corresponding author: Santhosh Girirajan, 205A Life Sciences Building, Departments of Biochemistry and Molecular Biology and Anthropology, The Pennsylvania State University, University Park, PA 16802, Tel: 814-865-0674, E-mail: [email protected], Word count: 4,608 AUTHOR BIOGRAPHY Janani Iyer is a postdoctoral fellow in the laboratory of Santhosh Girirajan at The Pennsylvania State University. She is studying the role of dosage sensitive genes within rare CNVs using Drosophila melanogaster. Santhosh Girirajan is an Assistant Professor of Biochemistry and Molecular Biology and Anthropology at The Pennsylvania State University. His laboratory is studying the molecular genetic basis of neurodevelopmental disorders by combining work on the discovery of genetic variants in affected children with functional characterization using model organisms. bioRxiv preprint doi: https://doi.org/10.1101/011510; this version posted November 17, 2014. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. ABSTRACT Rare copy-number variants (CNVs) are a significant cause of neurodevelopmental disorders. -
Cyclin-Dependent Kinase Inhibitors KRP1 and KRP2 Are Involved in Grain Filling and Seed Germination in Rice (Oryza Sativa L.)
International Journal of Molecular Sciences Article Cyclin-Dependent Kinase Inhibitors KRP1 and KRP2 Are Involved in Grain Filling and Seed Germination in Rice (Oryza sativa L.) Abolore Adijat Ajadi 1,2, Xiaohong Tong 1, Huimei Wang 1, Juan Zhao 1, Liqun Tang 1, Zhiyong Li 1, Xixi Liu 1, Yazhou Shu 1, Shufan Li 1, Shuang Wang 1,3, Wanning Liu 1, Sani Muhammad Tajo 1, Jian Zhang 1,* and Yifeng Wang 1,* 1 State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; [email protected] (A.A.A.); [email protected] (X.T.); [email protected] (H.W.); [email protected] (J.Z.); [email protected] (L.T.); [email protected] (Z.L.); [email protected] (X.L.); [email protected] (Y.S.); [email protected] (S.L.); [email protected] (S.W.); [email protected] (W.L.); [email protected] (S.M.T.) 2 Biotechnology Unit, National Cereals Research Institute, Badeggi, Bida 912101, Nigeria 3 College of Life Science, Yangtze University, Jingzhou 434025, China * Correspondence: [email protected] (J.Z.); [email protected] (Y.W.); Tel./Fax: +86-571-6337-0277 (J.Z.); +86-571-6337-0206 (Y.W.) Received: 21 November 2019; Accepted: 26 December 2019; Published: 30 December 2019 Abstract: Cyclin-dependent kinase inhibitors known as KRPs (kip-related proteins) control the progression of plant cell cycles and modulate various plant developmental processes. However, the function of KRPs in rice remains largely unknown. In this study, two rice KRPs members, KRP1 and KRP2, were found to be predominantly expressed in developing seeds and were significantly induced by exogenous abscisic acid (ABA) and Brassinosteroid (BR) applications. -
Involvement in Endoreduplication (Cell Cycle/Repa/Wheat Dwarf Virus) GIDEON GRAFI*T#, RONALD J
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 8962-8967, August 1996 Cell Biology A maize cDNA encoding a member of the retinoblastoma protein family: Involvement in endoreduplication (cell cycle/RepA/wheat dwarf virus) GIDEON GRAFI*t#, RONALD J. BURNETTr*, TIM HELENTJARIS*, BRIAN A. LARKINS*§, JAMES A. DECAPRIOt, WILLIAM R. SELLERSt, AND WILLIAM G. KAELIN, JR.t *Department of Plant Sciences, University of Arizona, Tucson AZ 85721; and tDana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115 Contributed by Brian A. Larkins, May 14, 1996 ABSTRACT Retinoblastoma (RB-1) is a tumor suppres- We identified a partial maize cDNA (ZmRB) that is pre- sor gene that encodes a 105-kDa nuclear phosphoprotein. To dicted to encode a protein with homology to members of the date, RB genes have been isolated only from metazoans. We pocket protein (Rb) family. Here we provide evidence that have isolated a cDNA from maize endosperm whose predicted ZmRb is a member of the retinoblastoma protein family and protein product (ZmRb) shows homology to the "pocket" A demonstrate its ability to bind the replication-associated pro- and B domains of the Rb protein family. We found ZmRb tein WDV RepA and its involvement in the process of DNA behaves as a pocket protein based on its ability to specifically endoreduplication during maize endosperm development. interact with oncoproteins encoded by DNA tumor viruses (E7, T-Ag, E1A). ZmRb can interact in vitro and in vivo with MATERIALS AND METHODS the replication-associated protein, RepA, encoded by the wheat dwarf virus. The maize Rb-related protein undergoes Plant Materials and Chemicals. -
Technical Glossary
WBVGL 6/28/03 12:00 AM Page 409 Technical Glossary abortive infection: Infection of a cell where there is no net increase in the production of infectious virus. abortive transformation: See transitory (transient or abortive) transformation. acid blob activator: A regulatory protein that acts in trans to alter gene expression and whose activity depends on a region of an amino acid sequence containing acidic or phosphorylated residues. acquired immune deficiency syndrome (AIDS): A disease characterized by loss of cell-mediated and humoral immunity as the result of infection with human immunodeficiency virus (HIV). acute infection: An infection marked by a sudden onset of detectable symptoms usually followed by complete or apparent recovery. adaptive immunity (acquired immunity): See immunity. adjuvant: Something added to a drug to increase the effectiveness of that drug. With respect to the immune system, an adjuvant increases the response of the system to a particular antigen. agnogene: A region of a genome that contains an open reading frame of unknown function; origi- nally used to describe a 67- to 71-amino acid product from the late region of SV40. AIDS: See acquired immune deficiency syndrome. aliquot: One of a number of replicate samples of known size. a-TIF: The alpha trans-inducing factor protein of HSV; a structural (virion) protein that functions as an acid blob transcriptional activator. Its specificity requires interaction with certain host cel- lular proteins (such as Oct1) that bind to immediate-early promoter enhancers. ambisense genome: An RNA genome that contains sequence information in both the positive and negative senses. The S genomic segment of the Arenaviridae and of certain genera of the Bunyaviridae have this characteristic. -
Unitary Structure of Palindromes in DNA
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.21.453288; this version posted July 22, 2021. 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. Unitary Structure of Palindromes in DNA Mehmet Ali Tibatan1, ∗ and Mustafa Sarısaman2, y 1Department of Biotechnology, Istanbul University, 34134, Vezneciler, Istanbul, Turkey 2Department of Physics, Istanbul University, 34134, Vezneciler, Istanbul, Turkey We investigate the quantum behavior encountered in palindromes within DNA structure. In par- ticular, we reveal the unitary structure of usual palindromic sequences found in genomic DNAs of all living organisms, using the Schwinger’s approach. We clearly demonstrate the role played by palin- dromic configurations with special emphasis on physical symmetries, in particular subsymmetries of unitary structure. We unveil the prominence of unitary structure in palindromic sequences in the sense that vitally significant information endowed within DNA could be transformed unchangeably in the process of transcription. We introduce a new symmetry relation, namely purine-purine or pyrimidine-pyrimidine symmetries (p-symmetry) in addition to the already known symmetry rela- tion of purine-pyrimidine symmetries (pp-symmetry) given by Chargaff’s rule. Therefore, important vital functions of a living organisms are protected by means of these symmetric features. It is un- derstood that higher order palindromic sequences could be generated in terms of the basis of the highest prime numbers that make up the palindrome sequence number. We propose that violation of this unitary structure of palindromic sequences by means of our proposed symmetries leads to a mutation in DNA, which could offer a new perspective in the scientific studies on the originand cause of mutation. -
Palindromes in DNA—A Risk for Genome Stability and Implications in Cancer
International Journal of Molecular Sciences Review Palindromes in DNA—A Risk for Genome Stability and Implications in Cancer Marina Svetec Mikleni´cand Ivan Krešimir Svetec * Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia; [email protected] * Correspondence: [email protected]; Tel.: +385-1483-6016 Abstract: A palindrome in DNA consists of two closely spaced or adjacent inverted repeats. Certain palindromes have important biological functions as parts of various cis-acting elements and protein binding sites. However, many palindromes are known as fragile sites in the genome, sites prone to chromosome breakage which can lead to various genetic rearrangements or even cell death. The ability of certain palindromes to initiate genetic recombination lies in their ability to form secondary structures in DNA which can cause replication stalling and double-strand breaks. Given their recombinogenic nature, it is not surprising that palindromes in the human genome are involved in genetic rearrangements in cancer cells as well as other known recurrent translocations and deletions associated with certain syndromes in humans. Here, we bring an overview of current understanding and knowledge on molecular mechanisms of palindrome recombinogenicity and discuss possible implications of DNA palindromes in carcinogenesis. Furthermore, we overview the data on known palindromic sequences in the human genome and efforts to estimate their number and distribution, as well as underlying mechanisms of genetic rearrangements specific palindromic sequences cause. Keywords: DNA palindromes; quasipalindromes; palindromic amplification; palindrome-mediated genetic recombination; carcinogenesis Citation: Svetec Mikleni´c,M.; Svetec, I.K. Palindromes in DNA—A Risk for Genome Stability and Implications in Cancer. -
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. -
B-Catenin Deficiency Causes Digeorge Syndrome-Like Phenotypes Through Regulation of Tbx1 Sung-Ho Huh and David M
RESEARCH ARTICLE 1137 Development 137, 1137-1147 (2010) doi:10.1242/dev.045534 © 2010. Published by The Company of Biologists Ltd b-catenin deficiency causes DiGeorge syndrome-like phenotypes through regulation of Tbx1 Sung-Ho Huh and David M. Ornitz* SUMMARY DiGeorge syndrome (DGS) is a common genetic disease characterized by pharyngeal apparatus malformations and defects in cardiovascular, craniofacial and glandular development. TBX1 is the most likely candidate disease-causing gene and is located within a 22q11.2 chromosomal deletion that is associated with most cases of DGS. Here, we show that canonical Wnt–b-catenin signaling negatively regulates Tbx1 expression and that mesenchymal inactivation of b-catenin (Ctnnb1) in mice caused abnormalities within the DGS phenotypic spectrum, including great vessel malformations, hypoplastic pulmonary and aortic arch arteries, cardiac malformations, micrognathia, thymus hypoplasia and mislocalization of the parathyroid gland. In a heterozygous Fgf8 or Tbx1 genetic background, ectopic activation of Wnt–b-catenin signaling caused an increased incidence and severity of DGS- like phenotypes. Additionally, reducing the gene dosage of Fgf8 rescued pharyngeal arch artery defects caused by loss of Ctnnb1. These findings identify Wnt–b-catenin signaling as a crucial upstream regulator of a Tbx1–Fgf8 signaling pathway and suggest that factors that affect Wnt–b-catenin signaling could modify the incidence and severity of DGS. KEY WORDS: b-catenin, Tbx1, Fgf8, Pharyngeal arch, DiGeorge syndrome INTRODUCTION is expressed in the pharyngeal arch endoderm, core mesoderm, DiGeorge syndrome (DGS) is one of the most common genetic anterior heart field and head mesenchyme, but is absent in neural disorders with an incidence of 1 in 4000 live births. -
Perspectives
CopyTight 0 1997 by the Genetics Society of America Perspectives Anecdotal, Historical And Critical Commentaries on Genetics Edited by James F. Crow and William F. Dove Chromosome Changes in Cell Differentiation Orlando J. Miller Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201 N a recent “Perspectives” article, EEVA THEW the H19 gene. The maternal H19 allele is expressed, I (1995) called attention to a variety of alterations and its cis-acting, nontranslatable RNA product inhibits in chromosomes that occur regularly in differentiating the expression of the maternal alleles of the other three cells, have been known for many years, and are still genes, mash-2, Ins-2, and I@. The paternal H19 allele poorly understood. Theseincludedfacultatiue heterochro- is methylated and notexpressed, so the paternal alleles matinization, polyploidization by endoreduplication, under- of the other three genes are expressed. Imprinting of replication ofsome sequences inpolytene chromosomes, the Inns-2 and I@ genes is disrupted by maternal inheri- and gene amplijication. The related programmed DNA tance of a targeted deletion of the H19 gene and its loss phenomena called chromatin diminutionand chromo- flanking sequence, while paternal inheritance has no some eliminationalso belong tothis group of highly regu- effect, reflecting the normally silent state of the pater- lated developmental chromosomechanges. Here Ishall nal HI 9 allele (LEIGHTONet al. 1995). There is also a briefly review these changes, with particular emphasis cluster of several genes on human chromosome 15 that on thecell and molecular genetic approaches thathave are expressed exclusively on thepaternal chromosome; provided, or could provide, insights into the signaling these may play a role in thePrader-Willi syndrome.