Observation of DNA Intertwining Along Authentic Budding Yeast Chromosomes
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Ability of the Hydrophobic FGF and Basic TAT Peptides To
Ability of the hydrophobic FGF and basic TAT peptides to promote cellular uptake of recombinant Cre recombinase: A tool for efficient genetic engineering of mammalian genomes Michael Peitz, Kurt Pfannkuche, Klaus Rajewsky*, and Frank Edenhofer† Institute for Genetics, University of Cologne, Weyertal 121, 50931 Cologne, Germany Contributed by Klaus Rajewsky, February 5, 2002 Conditional mutagenesis is a powerful tool to analyze gene func- sive mouse breeding causing the experiments to be time con- tions in mammalian cells. The site-specific recombinase Cre can be suming and costly. The leakiness of the system represents a used to recombine loxP-modified alleles under temporal and spa- critical factor because a Cre recombinase that is undesirably tial control. However, the efficient delivery of biologically active active before induction often leads to unwanted side effects such Cre recombinase to living cells represents a limiting factor. In this as mosaic recombination and͞or selection of recombined or study we compared the potential of a hydrophobic peptide mod- nonrecombined cells both in vivo and in vitro (9, 17, 18). ified from Kaposi fibroblast growth factor with a basic peptide Moreover, the widely used inducers IFN, hydroxy-tamoxifen, derived from HIV-TAT to promote cellular uptake of recombinant and doxycycline are known to display toxic side effects (19, 20) Cre. We present the production and characterization of a Cre and͞or induce also unwanted physiological effects that may protein that enters mammalian cells and subsequently performs interfere with the experimental phenotype of the conditional recombination with high efficiency in a time- and concentration- mutation to be analyzed (21, 22). -
Establishment of Sister Chromatid Cohesion During Dna Replication in Saccharomyces Cerevisiae
ESTABLISHMENT OF SISTER CHROMATID COHESION DURING DNA REPLICATION IN SACCHAROMYCES CEREVISIAE Vanessa de Sousa Ferreira Borges Thesis submitted for the degree of Doctor of Philosophy to University College London Supervisor: Dr. Frank Uhlmann September 2012 Chromosome Segregation Laboratory Cancer Research UK, London Research Institute 44 Lincoln’s Inn Fields London WC2A 3LY United Kingdom Declaration I, Vanessa de Sousa Ferreira Borges, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. 2 Acknowledgements One day scientific research became part of me, a world of puzzles, challenges and open questions waiting to be answered. Four years ago this decision brought me to London to do my PhD and many people became part of this exciting adventure and helped me through it in so many different ways. For this I would like to thank… …My supervisor Frank Uhlmann, for his continuous support, guidance and excellent scientific advice throughout the last 4 years. For always having the door of his office opened and time to discuss important or trivial questions about my project. For his contagious enthusiasm about science and for everything he taught me during my PhD. For being a great supervisor. …Everyone in the Chromosome and Segregation Laboratory for a very stimulating working environment and for making it such a nice place to work. I would like to thank Maria for all her help around the lab, Sebastian who taught me a lot in the beginning of my PhD, Adrian, Thomas, Celine, Molly, Rahul, Sandra, Lesia, Yasuto and Yasu. -
An Overview of Tyrosine Site-Specific Recombination: from an Flp Perspective
An Overview of Tyrosine Site-specific Recombination: From an Flp Perspective MAKKUNI JAYARAM,1 CHIEN-HUI MA,1 AASHIQ H KACHROO,1 PAUL A ROWLEY,1 PIOTR GUGA,2 HSUI-FANG FAN,3 and YURI VOZIYANOV4 1Department of Molecular Biosciences, UT Austin, Austin, TX 78712; 2Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bio-organic Chemistry, Lodz, Poland; 3Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan; 4School of Biosciences, Louisiana Tech University, Ruston, LA 71272 ABSTRACT Tyrosine site-specific recombinases (YRs) are prokaryotes. They were thought to be nearly absent widely distributed among prokaryotes and their viruses, and among eukaryotes, the budding yeast lineage (Saccharo- fi were thought to be con ned to the budding yeast lineage mycetaceae) being an exception in that a subset of its among eukaryotes. However, YR-harboring retrotransposons members houses nuclear plasmids that code for YRs (the DIRS and PAT families) and DNA transposons (Cryptons) have been identified in a variety of eukaryotes. The YRs utilize (1, 2). However, YR-harboring DIRS and PAT families a common chemical mechanism, analogous to that of type IB of retrotransposons and presumed DNA transposons topoisomerases, to bring about a plethora of genetic classified as Cryptons have now been identified in a rearrangements with important physiological consequences large number of eukaryotes (3, 4). The presence of in their respective biological contexts. A subset of the tyrosine functional YRs encoded in Archaeal genomes has been recombinases has provided model systems for analyzing the established by a combination of comparative genomics chemical mechanisms and conformational features of the and modeling complemented by biochemical and struc- recombination reaction using chemical, biochemical, topological, structural, and single molecule-biophysical tural analyses (5, 6). -
SMC Complexes Orchestrate the Mitotic Chromatin Interaction Landscape
Curr Genet DOI 10.1007/s00294-017-0755-y REVIEW SMC complexes orchestrate the mitotic chromatin interaction landscape Yasutaka Kakui1 · Frank Uhlmann1 Received: 13 September 2017 / Revised: 14 September 2017 / Accepted: 16 September 2017 © The Author(s) 2017. This article is an open access publication Abstract Chromatin is a very long DNA–protein complex Keywords Chromosome condensation · SMC complex · that controls the expression and inheritance of the genetic Chromatin · Cell cycle · Hi-C information. Chromatin is stored within the nucleus in interphase and further compacted into chromosomes dur- ing mitosis. This process, known as chromosome condensa- Introduction tion, is essential for faithful segregation of genomic DNA into daughter cells. Condensin and cohesin, members of How chromatin is spatially organized within the cell nucleus the structural maintenance of chromosomes (SMC) fam- and within chromosomes is a fundamental question in cell ily, are fundamental for chromosome architecture, both biology. Centimeter-long DNA molecules change their spa- for establishment of chromatin structure in the interphase tial chromatin organization within micrometer-sized cells nucleus and for the formation of condensed chromosomes during cell cycle progression. In interphase, chromatin is in mitosis. These ring-shaped SMC complexes are thought distributed throughout the nucleus to express the genetic to regulate the interactions between DNA strands by topo- information. When cells enter mitosis, chromatin becomes logically entrapping DNA. How this activity shapes chro- compacted to form mitotic chromosomes. Chromosome mosomes is not yet understood. Recent high throughput condensation, the gross morphological change of spatial chromosome conformation capture studies revealed how chromatin organization in mitosis, is indispensable for chromatin is reorganized during the cell cycle and have the faithful inheritance of genetic information. -
3718 Issue63july2010 1.Pdf
Issue 63.qxd:Genetic Society News 1/10/10 14:41 Page 1 JULYJULLYY 2010 | ISSUEISSUE 63 GENETICSGENNETICSS SOCIETYSOCIEETY NENEWSEWS In this issue The Genetics Society NewsNewws is edited by U Genetics Society PresidentPresident Honoured Honoured ProfProf David Hosken and items ittems for future future issues can be sent to thee editor,editor, preferably preferably U Mouse Genetics Meeting by email to [email protected],D.J.Hosken@@exeter.ac.uk, or U SponsoredSponsored Meetings Meetings hardhard copy to Chair in Evolutionary Evoolutionary Biology, Biology, UniversityUniversity of Exeter,Exeter, Cornwall Cornnwall Campus, U The JBS Haldane LectureLecture Tremough,Tremough, Penryn, TR10 0 9EZ UK.UK. The U Schools Evolutionn ConferenceConference Newsletter is published twicet a year,year, with copy dates of 1st June andand 26th November.November. U TaxiTaxi Drivers The British YeastYeaste Group Group descend on Oxford Oxford for their 2010 meeting: m see the reportreport on page 35. 3 Image © Georgina McLoughlin Issue 63.qxd:Genetic Society News 1/10/10 14:41 Page 2 A WORD FROM THE EDITOR A word from the editor Welcome to issue 63. In this issue we announce a UK is recognised with the award of a CBE in the new Genetics Society Prize to Queen’s Birthday Honours, tells us about one of Welcome to my last issue as join the medals and lectures we her favourite papers by Susan Lindquist, the 2010 editor of the Genetics Society award. The JBS Haldane Mendel Lecturer. Somewhat unusually we have a News, after 3 years in the hot Lecture will be awarded couple of Taxi Drivers in this issue – Brian and seat and a total of 8 years on annually to recognise Deborah Charlesworth are not so happy about the committee it is time to excellence in communicating the way that the print media deals with some move on before I really outstay aspects of genetics research to scientific issues and Chris Ponting bemoans the my welcome! It has been a the public. -
EMBO Facts & Figures
excellence in life sciences Reykjavik Helsinki Oslo Stockholm Tallinn EMBO facts & figures & EMBO facts Copenhagen Dublin Amsterdam Berlin Warsaw London Brussels Prague Luxembourg Paris Vienna Bratislava Budapest Bern Ljubljana Zagreb Rome Madrid Ankara Lisbon Athens Jerusalem EMBO facts & figures HIGHLIGHTS CONTACT EMBO & EMBC EMBO Long-Term Fellowships Five Advanced Fellows are selected (page ). Long-Term and Short-Term Fellowships are awarded. The Fellows’ EMBO Young Investigators Meeting is held in Heidelberg in June . EMBO Installation Grants New EMBO Members & EMBO elects new members (page ), selects Young EMBO Women in Science Young Investigators Investigators (page ) and eight Installation Grantees Gerlind Wallon EMBO Scientific Publications (page ). Programme Manager Bernd Pulverer S Maria Leptin Deputy Director Head A EMBO Science Policy Issues report on quotas in academia to assure gender balance. R EMBO Director + + A Conducts workshops on emerging biotechnologies and on H T cognitive genomics. Gives invited talks at US National Academy E IC of Sciences, International Summit on Human Genome Editing, I H 5 D MAN 201 O N Washington, DC.; World Congress on Research Integrity, Rio de A M Janeiro; International Scienti c Advisory Board for the Centre for Eilish Craddock IT 2 015 Mammalian Synthetic Biology, Edinburgh. Personal Assistant to EMBO Fellowships EMBO Scientific Publications EMBO Gold Medal Sarah Teichmann and Ido Amit receive the EMBO Gold the EMBO Director David del Álamo Thomas Lemberger Medal (page ). + Programme Manager Deputy Head EMBO Global Activities India and Singapore sign agreements to become EMBC Associate + + Member States. EMBO Courses & Workshops More than , participants from countries attend 6th scienti c events (page ); participants attend EMBO Laboratory Management Courses (page ); rst online course EMBO Courses & Workshops recorded in collaboration with iBiology. -
Pp2acdc55 Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation
Article PP2ACdc55 Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation Graphical Abstract Authors Molly Godfrey, Sandra A. Touati, Meghna Kataria, Andrew Jones, Ambrosius P. Snijders, Frank Uhlmann Correspondence [email protected] In Brief The eukaryotic cell cycle comprises a robustly ordered series of phosphorylation events. Godfrey et al. show that the phosphatase PP2ACdc55 counteracts and thereby delays cell-cycle phosphorylation by cyclin-dependent kinase specifically on threonine, but not serine, phosphorylation sites. This reveals an ordering principle that might be also relevant in other signaling networks. Highlights d The phosphatase PP2ACdc55 counteracts Cdk phosphorylation during the cell cycle d It does so specifically on threonine, but not serine, phosphorylation sites d Consequently, threonine phosphorylation is a late event in the cell cycle d Thereby, PP2ACdc55 contributes to setting the timing of mitosis Godfrey et al., 2017, Molecular Cell 65, 393–402 February 2, 2017 ª 2016 The Author(s). Published by Elsevier Inc. http://dx.doi.org/10.1016/j.molcel.2016.12.018 Molecular Cell Article PP2ACdc55 Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation Molly Godfrey,1,3 Sandra A. Touati,1 Meghna Kataria,1 Andrew Jones,2 Ambrosius P. Snijders,2 and Frank Uhlmann1,4,* 1Chromosome Segregation Laboratory 2Mass Spectrometry Proteomics Science Technology Platform The Francis Crick Institute, London NW1 1AT, UK 3Present address: Developmental Biology Division, Department of Biology, Utrecht University, 3584 CH Utrecht, the Netherlands 4Lead Contact *Correspondence: [email protected] http://dx.doi.org/10.1016/j.molcel.2016.12.018 SUMMARY before mitosis, is not well understood. -
Chimeras of the Flp and Cre Recombinases: Tests of the Mode of Cleavage by Flp and Cre A
doi:10.1006/jmbi.2000.3967 available online at http://www.idealibrary.com on J. Mol. Biol. (2000) 302, 27±48 Chimeras of the Flp and Cre Recombinases: Tests of the Mode of Cleavage by Flp and Cre A. C. Shaikh and Paul D. Sadowski* Department of Molecular and The Flp and Cre recombinases are members of the integrase family of Medical Genetics, University of tyrosine recombinases. Each protein consists of a 13 kDa NH2-terminal Toronto, Toronto, M5S 1A8 domain and a larger COOH-terminal domain that contains the active site Canada of the enzyme. The COOH-terminal domain also contains the major determinants for the binding speci®city of the recombinase to its cognate DNA binding site. All family members cleave the DNA by the attach- ment of a conserved nucleophilic tyrosine residue to the 30-phosphate group at the sites of cleavage. In order to gain further insights into the determinants of the binding speci®city and modes of cleavage of Flp and Cre, we have made chimeric proteins in which we have fused the NH2-terminal domain of Flp to the COOH-terminal domain of Cre (``Fre'') and the NH2-terminal domain of Cre to the COOH-terminal domain of Flp (``Clp''). These chimeras have novel binding speci®cities in that they bind strongly to hybrid sites con- taining elements from both the Flp and Cre DNA targets but poorly to the native target sites. In this study we have taken advantage of the unique binding speci®ci- ties of Fre and Clp to examine the mode of cleavage by Cre, Flp, Fre and Clp. -
Trustees' Annual Report and Financial Statements 31 March 2016
THE FRANCIS CRICK INSTITUTE LIMITED A COMPANY LIMITED BY SHARES TRUSTEES’ ANNUAL REPORT AND FINANCIAL STATEMENTS 31 MARCH 2016 Charity registration number: 1140062 Company registration number: 6885462 The Francis Crick Institute Accounts 2016 CONTENTS INSIDE THIS REPORT Trustees’ report (incorporating the Strategic report and Directors’ report) 1 Independent auditor’s report 12 Consolidated statement of financial activities 13 Balance sheets 14 Cash flow statements 15 Notes to the financial statements 16 1 TRUSTEES’ REPORT (INCORPORATING THE STRATEGIC REPORT AND DIRECTORS’ REPORT) The trustees present their annual directors’ report together with the consolidated financial statements for the charity and its subsidiary (together, ‘the Group’) for the year ended 31 March 2016, which are prepared to meet the requirements for a directors’ report and financial statements for Companies Act purposes. The financial statements comply with the Charities Act 2011, the Companies Act 2006, and the Statement of Recommended Practice applicable to charities preparing their accounts in accordance with the Financial Reporting Standard applicable in the UK (FRS102) effective 1 January 2015 (Charity SORP). The trustees’ report includes the additional content required of larger charities. REFERENCE AND ADMINISTRATIVE DETAILS The Francis Crick Institute Limited (‘the charity’, ‘the Institute’ or ‘the Crick) is registered with the Charity Commission, charity number 1140062. The charity has operated and continues to operate under the name of the Francis Crick -
Analysis of 3D Genomic Interactions Identifies Candidate Host Genes That Transposable Elements Potentially Regulate Ramya Raviram1,2,3†, Pedro P
Raviram et al. Genome Biology (2018) 19:216 https://doi.org/10.1186/s13059-018-1598-7 RESEARCH Open Access Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate Ramya Raviram1,2,3†, Pedro P. Rocha1,4†, Vincent M. Luo1,2, Emily Swanzey5, Emily R. Miraldi2,6,7,8, Edward B. Chuong9, Cédric Feschotte10, Richard Bonneau2,6,7 and Jane A. Skok1* Abstract Background: The organization of chromatin in the nucleus plays an essential role in gene regulation. About half of the mammalian genome comprises transposable elements. Given their repetitive nature, reads associated with these elements are generally discarded or randomly distributed among elements of the same type in genome-wide analyses. Thus, it is challenging to identify the activities and properties of individual transposons. As a result, we only have a partial understanding of how transposons contribute to chromatin folding and how they impact gene regulation. Results: Using PCR and Capture-based chromosome conformation capture (3C) approaches, collectively called 4Tran, we take advantage of the repetitive nature of transposons to capture interactions from multiple copies of endogenous retrovirus (ERVs) in the human and mouse genomes. With 4Tran-PCR, reads are selectively mapped to unique regions in the genome. This enables the identification of transposable element interaction profiles for individual ERV families and integration events specific to particular genomes. With this approach, we demonstrate that transposons engage in long-range intra-chromosomal interactions guided by the separation of chromosomes into A and B compartments as well as topologically associated domains (TADs). In contrast to 4Tran-PCR, Capture-4Tran can uniquely identify both ends of an interaction that involve retroviral repeat sequences, providing a powerful tool for uncovering the individual transposable element insertions that interact with and potentially regulate target genes. -
Reverse Transcriptase Activity Innate to DNA Polymerase I and DNA
Reverse transcriptase activity innate to DNA SEE COMMENTARY polymerase I and DNA topoisomerase I proteins of Streptomyces telomere complex Kai Bao*† and Stanley N. Cohen*‡§ Departments of *Genetics and ‡Medicine, Stanford University School of Medicine, Stanford, CA 94305-5120 Edited by Nicholas R. Cozzarelli, University of California, Berkeley, CA, and approved August 10, 2004 (received for review June 18, 2004) Replication of Streptomyces linear chromosomes and plasmids gation and, remarkably, that both of these eubacterial enzymes -proceeds bidirectionally from a central origin, leaving recessed 5 can function efficiently as RTs in addition to having the bio termini that are extended by a telomere binding complex. This chemical properties predicted from their sequences. We further complex contains both a telomere-protecting terminal protein show that the Streptomyces coelicolor and Streptomyces lividans (Tpg) and a telomere-associated protein that interacts with Tpg TopA proteins are prototypes for a subfamily of bacterial and the DNA ends of linear Streptomyces replicons. By using topoisomerases whose catalytic domains contain a unique Asp– histidine-tagged telomere-associated protein (Tap) as a scaffold, Asp doublet motif that is required for their RT activity and which we identified DNA polymerase (PolA) and topoisomerase I (TopA) is essential also to the RNA-dependent DNA polymerase func- proteins as other components of the Streptomyces telomere com- tions of HIV RT and eukaryotic cell telomerases (16, 17). plex. Biochemical characterization of these proteins indicated that both PolA and TopA exhibit highly efficient reverse transcriptase Materials and Methods (RT) activity in addition to their predicted functions. Although RT Plasmid and Bacterial Strains. -
Development of Adenoviral Vectors for Monitoring Telomerase Activity in Living Cells
Development of adenoviral vectors for monitoring telomerase activity in living cells Edqvist, Anna 2007 Link to publication Citation for published version (APA): Edqvist, A. (2007). Development of adenoviral vectors for monitoring telomerase activity in living cells. Genetics. Total number of authors: 1 General rights Unless other specific re-use rights are stated the following general rights apply: Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Read more about Creative commons licenses: https://creativecommons.org/licenses/ Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. LUND UNIVERSITY PO Box 117 221 00 Lund +46 46-222 00 00 Download date: 05. Oct. 2021 DEVELOPMENT OF ADENOVIRAL VECTORS FOR MONITORING TELOMERASE ACTIVITY IN LIVING CELLS ANNA HELENA EDQVIST 2007 DEPARTMENT OF CELL AND ORGANISM BIOLOGY LUND UNIVERSITY SWEDEN A doctoral thesis at a university in Sweden is produced either as a monograph or as a collection of papers. In the latter case, the introductory part constitutes the formal thesis, which summarises the accompanying papers.