A 20S Complex Containing CDC27 and CDC16 Catalyzes the Mitosis-Specific Conjugation of Ubiquitin to Cyclin B
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A New Genetic Method for Isolating Functionally Interacting Genes
Copyright 2000 by the Genetics Society of America A New Genetic Method for Isolating Functionally Interacting Genes: High plo1؉-Dependent Mutants and Their Suppressors De®ne Genes in Mitotic and Septation Pathways in Fission Yeast C. Fiona Cullen,*,² Karen M. May,* Iain M. Hagan,³ David M. Glover²,§ and Hiroyuki Ohkura*,² *Institute of Cell and Molecular Biology, The University of Edinburgh, Edinburgh EH9 3JR, United Kingdom, ²Department of Anatomy and Physiology, Medical Sciences Institute, The University of Dundee, Dundee DD1 4HN, United Kingdom, ³School of Biological Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom and §Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom Manuscript received February 2, 2000 Accepted for publication April 10, 2000 ABSTRACT We describe a general genetic method to identify genes encoding proteins that functionally interact with and/or are good candidates for downstream targets of a particular gene product. The screen identi®es mutants whose growth depends on high levels of expression of that gene. We apply this to the plo1ϩ gene that encodes a ®ssion yeast homologue of the polo-like kinases. plo1ϩ regulates both spindle formation and septation. We have isolated 17 high plo1ϩ-dependent (pld) mutants that show defects in mitosis or septation. Three mutants show a mitotic arrest phenotype. Among the 14 pld mutants with septation defects, 12 mapped to known loci: cdc7, cdc15, cdc11 spg1, and sid2. One of the pld mutants, cdc7-PD1, was selected for suppressor analysis. As multicopy suppressors, we isolated four known genes involved in septation in ®ssion yeast: spg1ϩ, sce3ϩ, cdc8ϩ, and rho1ϩ, and two previously uncharacterized genes, mpd1ϩ and mpd2ϩ. -
Analysis of Gene Expression Data for Gene Ontology
ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins. -
New Approaches to Functional Process Discovery in HPV 16-Associated Cervical Cancer Cells by Gene Ontology
Cancer Research and Treatment 2003;35(4):304-313 New Approaches to Functional Process Discovery in HPV 16-Associated Cervical Cancer Cells by Gene Ontology Yong-Wan Kim, Ph.D.1, Min-Je Suh, M.S.1, Jin-Sik Bae, M.S.1, Su Mi Bae, M.S.1, Joo Hee Yoon, M.D.2, Soo Young Hur, M.D.2, Jae Hoon Kim, M.D.2, Duck Young Ro, M.D.2, Joon Mo Lee, M.D.2, Sung Eun Namkoong, M.D.2, Chong Kook Kim, Ph.D.3 and Woong Shick Ahn, M.D.2 1Catholic Research Institutes of Medical Science, 2Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, Seoul; 3College of Pharmacy, Seoul National University, Seoul, Korea Purpose: This study utilized both mRNA differential significant genes of unknown function affected by the display and the Gene Ontology (GO) analysis to char- HPV-16-derived pathway. The GO analysis suggested that acterize the multiple interactions of a number of genes the cervical cancer cells underwent repression of the with gene expression profiles involved in the HPV-16- cancer-specific cell adhesive properties. Also, genes induced cervical carcinogenesis. belonging to DNA metabolism, such as DNA repair and Materials and Methods: mRNA differential displays, replication, were strongly down-regulated, whereas sig- with HPV-16 positive cervical cancer cell line (SiHa), and nificant increases were shown in the protein degradation normal human keratinocyte cell line (HaCaT) as a con- and synthesis. trol, were used. Each human gene has several biological Conclusion: The GO analysis can overcome the com- functions in the Gene Ontology; therefore, several func- plexity of the gene expression profile of the HPV-16- tions of each gene were chosen to establish a powerful associated pathway, identify several cancer-specific cel- cervical carcinogenesis pathway. -
Mouse Cdc27 Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Cdc27 Knockout Project (CRISPR/Cas9) Objective: To create a Cdc27 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Cdc27 gene (NCBI Reference Sequence: NM_145436 ; Ensembl: ENSMUSG00000020687 ) is located on Mouse chromosome 11. 19 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 19 (Transcript: ENSMUST00000093923). Exon 2~7 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from about 1.13% of the coding region. Exon 2~7 covers 32.93% of the coding region. The size of effective KO region: ~8408 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 7 19 Legends Exon of mouse Cdc27 Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 2 is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 1285 bp section downstream of Exon 7 is aligned with itself to determine if there are tandem repeats. -
Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia. -
WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT (51) International Patent Classification: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, C12Q 1/68 (2018.01) A61P 31/18 (2006.01) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, C12Q 1/70 (2006.01) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (21) International Application Number: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, PCT/US2018/056167 OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (22) International Filing Date: SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 16 October 2018 (16. 10.2018) TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (30) Priority Data: UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 62/573,025 16 October 2017 (16. 10.2017) US TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, ΓΕ , IS, IT, LT, LU, LV, (71) Applicant: MASSACHUSETTS INSTITUTE OF MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TECHNOLOGY [US/US]; 77 Massachusetts Avenue, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, Cambridge, Massachusetts 02139 (US). -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
C/Ebpδ Targets Cyclin D1 for Proteasome-Mediated Degradation Via Induction of CDC27/APC3 Expression
C/EBPδ targets cyclin D1 for proteasome-mediated degradation via induction of CDC27/APC3 expression Snehalata A. Pawara,1,2, Tapasree Roy Sarkara,2, Kuppusamy Balamurugana, Shikha Sharana, Jun Wanga, Youhong Zhanga, Steven F. Dowdyb, A-Mei Huanga,3, and Esta Sternecka,4 aCenter for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201; and bDepartment of Cellular and Molecular Medicine, Howard Hughes Medical Institute, University of California, San Diego School of Medicine, La Jolla, CA 92093-0686 Edited* by George F. Vande Woude, Van Andel Research Institute, Grand Rapids, MI, and approved April 15, 2010 (received for review December 3, 2009) The transcription factor CCAAT/enhancer binding protein δ (C/EBPδ, breast tumor cell lines including MCF-7 (16). Addressing the CEBPD, NFIL-6β) has tumor suppressor function; however, the molecu- possibility of a causal relationship, we found that exogenous lar mechanism(s) by which C/EBPδ exerts its effect are largely unknown. C/EBPδ alone down-regulated endogenous cyclin D1 but not Here, we report that C/EBPδ induces expression of the Cdc27 (APC3) cyclin E2 in MCF-7 cells (Fig. 1A). An inverse correlation of C/ subunit of the anaphase promoting complex/cyclosome (APC/C), which EBPδ and cyclin D1 protein expression was also observed in MEFs results in the polyubiquitination and degradation of the prooncogenic from wild-type and Cebpd null mice (Fig. S1A). Next, we tested the cell cycle regulator cyclin D1, and also down-regulates cyclin B1, Skp2, role of target gene regulation by introducing an R198A mutation andPlk-1.InC/EBPδ knockout mouse embryo fibroblasts (MEF) Cdc27 into the DNA binding domain (C/EBPδ-R198A), which does levels were reduced, whereas cyclin D1 levels were increased even in not affect nuclear localization (17) but prevents DNA binding of the presence of activated GSK-3β. -
Protein Engineering of a Ubiquitin-Variant Inhibitor of APC/C Identifies a Cryptic K48 Ubiquitin Chain Binding Site
Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site Edmond R. Watsona,b, Christy R. R. Gracea, Wei Zhangc,d,2, Darcie J. Millera, Iain F. Davidsone, J. Rajan Prabub, Shanshan Yua, Derek L. Bolhuisf, Elizaveta T. Kulkof, Ronnald Vollrathb, David Haselbache,g, Holger Starkg, Jan-Michael Peterse,h, Nicholas G. Browna,f, Sachdev S. Sidhuc,1, and Brenda A. Schulmana,b,1 aDepartment of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105; bDepartment of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; cDonnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5S3E1; dDepartment of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S3E1; eResearch Institute of Molecular Pathology, Vienna BioCenter, 1030 Vienna, Austria; fDepartment of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599; gMax Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; and hMedical University of Vienna, 1090 Vienna, Austria Contributed by Brenda A. Schulman, June 24, 2019 (sent for review February 19, 2019; reviewed by Kylie Walters and Hao Wu) Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism the type of catalytic domain. E3s harboring “HECT” and “RBR” used by eukaryotic cells to maintain homeostasis and protein catalytic domains promote ubiquitylation through 2-step reac- quality, and to control timing in biological processes. Two essential tions involving formation of a thioester-linked intermediate be- aspects of Ub regulation are conjugation through E1-E2-E3 enzy- tween the E3 and Ub’s C terminus: First, Ub is transferred from matic cascades and recognition by Ub-binding domains. -
Ultraconserved Elements Are Associated with Homeostatic Control of Splicing Regulators by Alternative Splicing and Nonsense-Mediated Decay
Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay Julie Z. Ni,1 Leslie Grate,1 John Paul Donohue,1 Christine Preston,2 Naomi Nobida,2 Georgeann O’Brien,2 Lily Shiue,1 Tyson A. Clark,3 John E. Blume,3 and Manuel Ares Jr.1,2,4 1Center for Molecular Biology of RNA and Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA; 2Hughes Undergraduate Research Laboratory, University of California at Santa Cruz, Santa Cruz, California 95064, USA; 3Affymetrix, Inc., Santa Clara, California 95051, USA Many alternative splicing events create RNAs with premature stop codons, suggesting that alternative splicing coupled with nonsense-mediated decay (AS-NMD) may regulate gene expression post-transcriptionally. We tested this idea in mice by blocking NMD and measuring changes in isoform representation using splicing-sensitive microarrays. We found a striking class of highly conserved stop codon-containing exons whose inclusion renders the transcript sensitive to NMD. A genomic search for additional examples identified >50 such exons in genes with a variety of functions. These exons are unusually frequent in genes that encode splicing activators and are unexpectedly enriched in the so-called “ultraconserved” elements in the mammalian lineage. Further analysis show that NMD of mRNAs for splicing activators such as SR proteins is triggered by splicing activation events, whereas NMD of the mRNAs for negatively acting hnRNP proteins is triggered by splicing repression, a polarity consistent with widespread homeostatic control of splicing regulator gene expression. -
A Novel Function for HSF1-Induced Mitotic Exit Failure and Genomic Instability Through Direct Interaction Between HSF1 and Cdc20
Oncogene (2008) 27, 2999–3009 & 2008 Nature Publishing Group All rights reserved 0950-9232/08 $30.00 www.nature.com/onc ORIGINAL ARTICLE A novel function for HSF1-induced mitotic exit failure and genomic instability through direct interaction between HSF1 and Cdc20 YJ Lee1, HJ Lee1, JS Lee2, D Jeoung3, CM Kang1, S Bae1, SJ Lee2, SH Kwon4, D Kang4 and YS Lee1 1Division of Radiation Effect, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea; 2Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea; 3College of Natural Sciences, Kangwon National University, Chunchon, Korea and 4Korea Basic Science Institute, Chunchon Center, Chunchon, Korea Although heat-shock factor (HSF) 1 is a known highly aneuploid, however, the molecular mechanisms transcriptional factor of heat-shock proteins, other path- underlying the development of aneuploidy have not wayslike production of aneuploidy and increasedprotein been fully defined, although mutations in mitotic stability of cyclin B1 have been proposed. In the present checkpoint genes have been identified in a subset of study, the regulatory domain of HSF1 (amino-acid human cancers and cell lines (Lengauer et al., 1997; sequence 212–380) was found to interact directly with Cahill et al., 1998). the amino-acid sequence 106–171 of Cdc20. The associa- Enhanced heat-shock protein (HSP) expression in tion between HSF1 and Cdc20 inhibited the interaction response to various stimuli is regulated by heat-shock between Cdc27 and Cdc20, the phosphorylation of Cdc27 factors (HSFs), the functional relevance of which is now and the ubiquitination activity of anaphase-promoting emerging. -
An Architectural Map of the Anaphase-Promoting Complex
Downloaded from genesdev.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press An architectural map of the anaphase-promoting complex Brian R. Thornton,1,3 Tessie M. Ng,1,3 Mary E. Matyskiela,2 Christopher W. Carroll,2 David O. Morgan,2 and David P. Toczyski1,4 1Cancer Research Institute, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94115, USA; 2Department of Physiology, University of California, San Francisco, California 94143-2200, USA The anaphase-promoting complex or cyclosome (APC) is an unusually complicated ubiquitin ligase, composed of 13 core subunits and either of two loosely associated regulatory subunits, Cdc20 and Cdh1. We analyzed the architecture of the APC using a recently constructed budding yeast strain that is viable in the absence of normally essential APC subunits. We found that the largest subunit, Apc1, serves as a scaffold that associates independently with two separable subcomplexes, one that contains Apc2 (Cullin), Apc11 (RING), and Doc1/Apc10, and another that contains the three TPR subunits (Cdc27, Cdc16, and Cdc23). We found that the three TPR subunits display a sequential binding dependency, with Cdc27 the most peripheral, Cdc23 the most internal, and Cdc16 between. Apc4, Apc5, Cdc23, and Apc1 associate interdependently, such that loss of any one subunit greatly reduces binding between the remaining three. Intriguingly, the cullin and TPR subunits both contribute to the binding of Cdh1 to the APC. Enzymatic assays performed with APC purified from strains lacking each of the essential subunits revealed that only cdc27⌬ complexes retain detectable activity in the presence of Cdh1.