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Genetic and Epigenetic Mechanisms of the Regulation of Mouse Embryonic Stem Cells Self-Renewal by the Pluripotency Transcription Factor Nanog
Genetic and epigenetic mechanisms of the regulation of mouse embryonic stem cells self-renewal by the pluripotency transcription factor Nanog Victor HEURTIER Thèse de doctorat de Biologie Dirigée par Pablo NAVARRO GIL Laboratoire Epigénétique des cellules souches – Institut Pasteur Sorbonne Université Ecole doctorale Complexité du Vivant (ED 515) Présentée et soutenue publiquement le 18/09/2018 Devant un jury composé de : Président : Pr MOUCHEL-VIELH Emmanuèle, Professeur Rapporteur : Dr SAVATIER Pierre, Directeur de Recherche Rapporteur : Dr RADA-IGLESIAS Alvaro, Chef d’équipe Examinateur : Dr AZUARA Veronique, Maître de conférences Examinateur : Dr PINSKAYA Marina, Maître de conférences Directeur de thèse : Dr NAVARRO GIL Pablo, Chef d’équipe Abstract Mouse embryonic stem (ES) cells are derived from the pre-implantation blastocyst and are able to maintain their pluripotent state through virtually limitless cell divisions in vitro. The study of the mechanisms regulating the specific features of ES cells led to the discovery of the transcription factors (TFs) governing their unique transcriptome. Among those TFs, Nanog plays a central role in the gene regulatory network that supports ES cells self-renewal. However, the molecular mechanisms by which Nanog exerts its functions are not fully elucidated. We adapted an inducible CRISPR activation (CRISPRa) system in mouse ES cells and demonstrated its functionality to stimulate transcription at endogenous loci. We then accurately determined the list of Nanog responsive genes using gain (CRISPRa cell line) and loss of function experiments and total RNA sequencing. Moreover, the DNA binding profiles of distinct pluripotency TFs were assessed genome-wide by chromatin immunoprecipitation (ChIP) and sequencing upon Nanog depletion and revealed the importance of the latter in the regulation of the pluripotency network activity at thousands of loci. -
Looking at Earth: an Astronaut's Journey Induction Ceremony 2017
american academy of arts & sciences winter 2018 www.amacad.org Bulletin vol. lxxi, no. 2 Induction Ceremony 2017 Class Speakers: Jane Mayer, Ursula Burns, James P. Allison, Heather K. Gerken, and Gerald Chan Annual David M. Rubenstein Lecture Looking at Earth: An Astronaut’s Journey David M. Rubenstein and Kathryn D. Sullivan ALSO: How Are Humans Different from Other Great Apes?–Ajit Varki, Pascal Gagneux, and Fred H. Gage Advancing Higher Education in America–Monica Lozano, Robert J. Birgeneau, Bob Jacobsen, and Michael S. McPherson Redistricting and Representation–Patti B. Saris, Gary King, Jamal Greene, and Moon Duchin noteworthy Select Prizes and Andrea Bertozzi (University of James R. Downing (St. Jude Chil- Barbara Grosz (Harvard Univer- California, Los Angeles) was se- dren’s Research Hospital) was sity) is the recipient of the Life- Awards to Members lected as a 2017 Simons Investi- awarded the 2017 E. Donnall time Achievement Award of the gator by the Simons Foundation. Thomas Lecture and Prize by the Association for Computational American Society of Hematology. Linguistics. Nobel Prize in Chemistry, Clara D. Bloomfield (Ohio State 2017 University) is the recipient of the Carol Dweck (Stanford Univer- Christopher Hacon (University 2017 Robert A. Kyle Award for sity) was awarded the inaugural of Utah) was awarded the Break- Joachim Frank (Columbia Univer- Outstanding Clinician-Scientist, Yidan Prize. through Prize in Mathematics. sity) presented by the Mayo Clinic Di- vision of Hematology. Felton Earls (Harvard Univer- Naomi Halas (Rice University) sity) is the recipient of the 2018 was awarded the 2018 Julius Ed- Nobel Prize in Economic Emmanuel J. -
2011 Annual Report
Memorial Sloan-Kettering Cancer Center 2011 Annual Report 10 steps closer 10 steps closer Letter from the Chairman and the President 1 1 | First effective treatments for advanced melanoma 5 2 Genomic analysis offers clues to most common | type of ovarian cancer 7 3 Breast cancer surgery: practice-changing | findings for some patients 9 4 New drugs offer survival benefit for men | with metastatic prostate cancer 11 5 | Insights into DNA damage and repair 13 6 Novel stem cell technique shows promise | in treating disease 15 7 Combination therapy may prevent spread | of nasopharyngeal tumors 17 8 Algorithm can predict shape of proteins, | speeding basic cancer research 19 9 Two of 2011’s top five advances in cancer | research led by MSKCC physician-scientists 21 10 | The Josie Robertson Surgery Center 23 The Campaign for Memorial Sloan-Kettering 25 Statistical Profile 27 Financial Summary 29 Boards of Overseers and Managers 31 www.mskcc.org/annualreport Letter from the Chairman and the President The year 2011 was a strong one at Memorial Sloan-Kettering. We continued to lead across “Our success as an institution is due in the spectrum of patient care, research, and training, and laid the groundwork for important progress in the years ahead. great measure to our remarkable staff… We want to begin by saying that our success as an institution is due in great measure to our remarkable staff. On a daily basis, we are inspired by their dedication and compassion, and We are inspired by their dedication Douglas A. Warner III are grateful for the work they do in the service of our patients and our mission. -
Resubmission JBC Frescas and De Lange
Cell Biology: Binding of TPP1 Protein to TIN2 Protein Is Required for POT1a,b Protein-mediated Telomere Protection David Frescas and Titia de Lange J. Biol. Chem. 2014, 289:24180-24187. doi: 10.1074/jbc.M114.592592 originally published online July 23, 2014 Downloaded from Access the most updated version of this article at doi: 10.1074/jbc.M114.592592 http://www.jbc.org/ Find articles, minireviews, Reflections and Classics on similar topics on the JBC Affinity Sites. Alerts: • When this article is cited • When a correction for this article is posted at Rockefeller University Library on August 31, 2014 Click here to choose from all of JBC's e-mail alerts This article cites 29 references, 13 of which can be accessed free at http://www.jbc.org/content/289/35/24180.full.html#ref-list-1 THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 289, NO. 35, pp. 24180–24187, August 29, 2014 © 2014 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. Binding of TPP1 Protein to TIN2 Protein Is Required for POT1a,b Protein-mediated Telomere Protection* Received for publication, June 30, 2014, and in revised form, July 22, 2014 Published, JBC Papers in Press, July 23, 2014, DOI 10.1074/jbc.M114.592592 David Frescas and Titia de Lange1 From the Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10065 Background: Chromosome ends require the TPP1/POT1 heterodimers for protection. Results: A TIN2 mutant that fails to bind TPP1 resulted in phenotypes associated with TPP1/POT1 deletion. -
Bulletin the Canadian Society for Molecular Biosciences La Société Canadienne Pour Les Biosciences Moléculaires
Bulletin The Canadian Society for Molecular Biosciences La Société Canadienne pour les Biosciences Moléculaires 2013 www.csmb-scbm.ca Bulletin The Canadian Society for Molecular Biosciences La Société Canadienne pour les Biosciences Moléculaires 2013 www.csmb-scbm.ca Cover images were provided by Dr. Benoit Chabot (see article standing on p32). 2 CSMB | SCBM Bulletin 2013 CSMB Board for 2013 ...............................................................................................................................................................5 President’s Report 2013 .........................................................................................................................................................7 Incoming Member of the Executive Board Martin Bisaillon, Councillor ...............................................................................................................................................9 Minutes of the 56th Annual General Meeting 2013 ...................................................................................................10 Financial Statement 2013 ....................................................................................................................................................12 56th Annual Meeting, Niagara-on-the Lake Meeting Schedule ..............................................................................................................................................................17 Scenes from the Meeting .................................................................................................................................................25 -
Editorial Board
MOLECULAR AND CELLULAR BIOLOGY VOLUME 29 ● JULY 2009 ● NUMBER 13 Roger J. Davis, Editor in Chief (2012) B. Franklin Pugh, Editor (2012) University of Massachusetts Medical School Pennsylvania State University Antony M. Carr, Editor (2012) J. Wade Harper, Editor (2013) Anjana Rao, Editor (2012) University of Sussex Harvard Medical School Immune Disease Institute, Inc. John L. Cleveland, Editor (2014) David E. Levy, Editor (2012) Joel D. Richter, Editor (2013) Scripps Florida New York University School of Medicine University of Massachusetts Medical School James Douglas Engel, Editor (2012) James L. Manley, Editor (2013) Andrey S. Shaw, Editor (2013) University of Michigan Medical School Columbia University Washington University School of Medicine Mark E. Ewen, Editor (2014) Christopher J. Marshall, Editor (2012) Ali Shilatifard, Editor (2012) Dana-Farber Cancer Institute Institute of Cancer Research Stowers Institute for Medical Research Leonard P. Freedman, Editor (2011) Jeremy W. Thorner, Editor (2013) Thomas Jefferson University University of California, Berkeley EDITORIAL BOARD Cory Abate-Shen (’09) Sharon Y. R. Dent (’10) Peter M. Howley (’09) Aaron P. Mitchell (’09) Edward Seto (’09) Peter D. Adams (’11) Melvin L. DePamphilis (’10) Kazuhiko Igarashi (’09) Cornelis Murre (’09) Andrew D. Sharrocks (’11) Dario Alessi (’10) Channing J. Der (’09) Anton Jetten (’09) Carol Newlon (’09) Ramin Shiekhattar (’11) Marisa Bartolomei (’11) Robert N. Eisenman (’09) Roland Kanaar (’10) Timothy Nilsen (’09) M. Celeste Simon (’11) Michelle C. Barton (’11) Sarah C. R. Elgin (’09) Gerard Karsenty (’09) Tomoo Ogi (’11) David Stern (’09) Claudio Basilico (’09) Scott Emr (’09) Michael B. Kastan (’09) Eric N. Olson (’10) Philip Stork (’10) Anton Bennett (’11) Gen-Sheng Feng (’11) Andrius Kazlauskas (’10) Moshe Oren (’11) Brian D. -
DNA Replication
Cold Spring Harbor Laboratory Press Fall 2013 Catalog TEXTBOOKS TABLE OF CONTENTS TEXTBOOKS Genome Science D1 Evolution D4 DNA Science D2 Epigenetics D5 Molecular Biology of the Gene, 7th Ed. D3 ADVANCED TEXTBOOKS Introduction to Protein-DNA Interactions D6 Angiogenesis D24 Bacterial Pathogenesis D7 The Biology of Alzheimer Disease D26 Cell Survival and Cell Death D8 Extracellular Matrix Biology D28 Cystic Fibrosis D9 HIV D29 DNA Repair , Mutagenesis, and Parkinson’s Disease D31 Other Responses to DNA Damage D10 Protein Synthesis and Translational Control D32 DNA Replication D11 Type 1 Diabetes D33 The Endoplasmic Reticulum D13 The Synapse D34 Hemoglobin and Its Diseases D14 Wnt Signaling D35 Immune Tolerance D16 An Introduction to Animal Behavior D37 Mitochondria D17 Means to an End D38 Signaling by Receptor Tyrosine Kinases D18 RNA Worlds D39 Transplantation D20 Yeast Intermediary Metabolism D40 Addiction D22 Price changes and sale prices on selected titles may not be reflected in this catalog. Please visit our website for current pricing www.cshlpress.org. Please visit our Sale Shelf for special discounts on selected items. www.cshlpress.org 1-855-452-6793 Cold Spring Harbor Laboratory Press Fall 2013 Catalog TEXTBOOKS TABLE OF CONTENTS ADVANCED TEXTBOOKS (Continued) Essentials of Glycobiology, Second Edition D41 A Genetic Switch D44 Untangling the Double Helix D42 Index (Subject Areas) D45 An Introduction to Nervous Systems D43 Price changes and sale prices on selected titles may not be reflected in this catalog. Please visit our website for current pricing www.cshlpress.org. Please visit our Sale Shelf for special discounts on selected items. www.cshlpress.org 1-855-452-6793 TEXTBOOKS Genome Science A Practical and Conceptual Introduction to Molecular Genetic Analysis in Eukaryotes By David Micklos, Cold Spring Harbor Laboratory, Bruce Nash, Cold Spring Harbor Laboratory, and Uwe Hilgert, University of Arizona enome Science is a textbook and laboratory manual for advanced secondary and post-sec - G ondary education. -
March 2004 ASCB Newsletter
Bioethics Shake-Up ................... 1 Annual Meeting Keynote ......... 1 LETTERPresident’s Column .................. 2 Annual Meeting Program ........ 5 VOLUME 27, NUMBER 3 March 2004 Cytokinesis Meeting .................. 6 LAC Meeting ............................... 7 Bush Fires Blackburn from WICB ............................................. 8 Call for Nominations .............. 10 Bioethics Council Public Policy Briefing ............. 11 Member Profile .........................14 Renowned cell biologist Elizabeth Blackburn of the University of Cali- fornia, San Francisco, who served as ASCB President in 1998, was Members in the News .............17 abruptly terminated from the President’s Council on Bioethics with a Gifts..............................................17 phone call from the White House. Letters to the Editor ............... 17 Blackburn had been outspoken in her insistence that the Council Grants & Opportunities ........ 18 consider the moral cost of forgoing potentially lifesaving research, and Classifieds..................................19 was frequently at odds with the Council Chairman, Leon Kass over how that science should be presented. Calendar .....................................20 Elizabeth Blackburn Blackburn and William May of Southern Methodist University, who had joined Blackburn in the opinion that stem cell research is an important and promising field of research that should be funded by the Federal government with appropriate oversight, were replaced by three new members. They include a doctor who has called for more religion in public life, a political scientist Micrographs who has effusively and publicly praised Kass and has called research in which embryos are destroyed, “the evil of willful destruction of innocent human life” and a Needed professor of government at Berry College in Georgia who warned in a conservative The ASCB is producing a publication that if citizens of the U.S. do not realize that abortion is wrong, then cell biology calendar to com- women will be compelled to abort genetically defective babies. -
TELOMERE EXTENSION USING MODIFIED TERT Mrna TO
TELOMERE EXTENSION USING MODIFIED TERT mRNA TO LENGTHEN HEALTHSPAN A DISSERTATION SUBMITTED TO THE NEUROSCIENCES PROGRAM AND THE COMMITTEE ON GRADUATE STUDIES OF STANFORD UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY John Ramunas May 2014 © 2014 by John Ramunas. All Rights Reserved. Re-distributed by Stanford University under license with the author. This work is licensed under a Creative Commons Attribution- Noncommercial 3.0 United States License. http://creativecommons.org/licenses/by-nc/3.0/us/ This dissertation is online at: http://purl.stanford.edu/vb798wq6556 ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Helen Blau, Primary Adviser I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Michael Longaker I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Juan Santiago I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Robert Sapolsky Approved for the Stanford University Committee on Graduate Studies. Patricia J. Gumport, Vice Provost for Graduate Education This signature page was generated electronically upon submission of this dissertation in electronic format. An original signed hard copy of the signature page is on file in University Archives. -
Dissertation Published Version
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2018 Biochemical and regulatory aspects of DNA double-strand break repair Godau, Julia Eileen Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-170542 Dissertation Published Version Originally published at: Godau, Julia Eileen. Biochemical and regulatory aspects of DNA double-strand break repair. 2018, University of Zurich, Faculty of Science. Biochemical and Regulatory Aspects of DNA Double-Strand Break Repair Dissertation zur Erlangung der naturwissenschaftlichen Doktorwürde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftlichen Fakultät der Universität Zürich von Julia Eileen Godau aus Deutschland Promotionskommission Prof. Dr. Alessandro A. Sartori (Vorsitz und Leitung der Dissertation) Prof. Dr. Joao Matos PD. Dr. Pavel Janscak Prof. Dr. Matthias Altmeyer Zürich, 2018 Contents Abbreviations v Summary vii Zusammenfassung ix 1 Introduction 1 1.1 Genome instability - A hallmark of cancer . 1 1.2 DNA damage response . 2 1.3 DNA repair . 3 1.3.1 DSB repair . 4 1.3.2 Meiotic recombination . 6 1.3.3 Fanconi anemia pathway of ICL repair . 7 1.4 Post-translational modifications . 10 1.5 CtIP . 11 1.5.1 Sae2/Ctp1/CtIP protein family . 11 1.5.2 CtIP promotes DNA-end resection . 13 1.5.3 Regulation of CtIP by PTMs . 15 1.5.4 CtIP and its connection to cancer development and therapy . 18 1.6 SLX4 - A nuclease scaffold . 19 1.7 PIN1 . 22 1.7.1 PIN1 - A molecular switch regulating diverse pathways . -
GEOFFREY BEENE CANCER RESEARCH CENTER 10 Year Report, 2007–2017
GEOFFREY BEENE CANCER RESEARCH CENTER 10 Year Report, 2007–2017 10 YEAR REPORT | 2007–2017 2 COVER IMAGES, CLOCKWISE FROM TOP LEFT: Tumor- and stromal cell-derived cathepsin S expression in primary breast cancer. Shown here is an immunofluorescence image of a human breast cancer specimen stained for the cysteine protease cathepsin S in red, and tumor cells in green. Cathepsin S expression, which is typically associated with immune cells such as macrophages, is expressed in a subset of breast carcinoma cells, and may endow them with the ability to metastasize to the brain The Iacobuzio lab and Kellan Lutz, an ambassador for the Geoffrey Beene Foundation Epifluorescent imaging of transparent casper zebrafish transplanted with the human-derived PC3 prostate cancer cell line exhibits dissemination solely to the spinal column Epifluorescent imaging of transparent casper zebrafish transplanted with the zebrafish- derived ZMEL1 melanoma cell line exhibits widely disseminated tumors to the skin, eyes, muscles, and brain. Image by Isabella Kim of the White lab Ping Chi and lab members Confocal microscopy shows that the nucleolar structure of hematopoietic stem cells is altered with Stag2 loss of function. Image by Aaron Viny of the Levine lab Scott Lowe and lab member 3 GEOFFREY BEENE CANCER RESEARCH CENTER CONTENTS Welcome . .2 Supporting Innovation through the Years . 5. Milestones . 6 Highlights of Breakthrough Projects . 8 Retreats and Special Conferences . 14. Supporting Novel Research . .16 Faculty . 18. Graduate Students . .19 Q&A with Barry Taylor . .19 Financial Statistics . 20 Research Grants . 21 Publications . 38 Shown are intestinal organoids derived from transgenic shRen mice in which renilla luciferase is suppressed by doxycycline . -
Celebrating 40 Years of Rita Allen Foundation Scholars 1 PEOPLE Rita Allen Foundation Scholars: 1976–2016
TABLE OF CONTENTS ORIGINS From the President . 4 Exploration and Discovery: 40 Years of the Rita Allen Foundation Scholars Program . .5 Unexpected Connections: A Conversation with Arnold Levine . .6 SCIENTIFIC ADVISORY COMMITTEE Pioneering Pain Researcher Invests in Next Generation of Scholars: A Conversation with Kathleen Foley (1978) . .10 Douglas Fearon: Attacking Disease with Insights . .12 Jeffrey Macklis (1991): Making and Mending the Brain’s Machinery . .15 Gregory Hannon (2000): Tools for Tough Questions . .18 Joan Steitz, Carl Nathan (1984) and Charles Gilbert (1986) . 21 KEYNOTE SPEAKERS Robert Weinberg (1976): The Genesis of Cancer Genetics . .26 Thomas Jessell (1984): Linking Molecules to Perception and Motion . 29 Titia de Lange (1995): The Complex Puzzle of Chromosome Ends . .32 Andrew Fire (1989): The Resonance of Gene Silencing . 35 Yigong Shi (1999): Illuminating the Cell’s Critical Systems . .37 SCHOLAR PROFILES Tom Maniatis (1978): Mastering Methods and Exploring Molecular Mechanisms . 40 Bruce Stillman (1983): The Foundations of DNA Replication . .43 Luis Villarreal (1983): A Life in Viruses . .46 Gilbert Chu (1988): DNA Dreamer . .49 Jon Levine (1988): A Passion for Deciphering Pain . 52 Susan Dymecki (1999): Serotonin Circuit Master . 55 Hao Wu (2002): The Cellular Dimensions of Immunity . .58 Ajay Chawla (2003): Beyond Immunity . 61 Christopher Lima (2003): Structure Meets Function . 64 Laura Johnston (2004): How Life Shapes Up . .67 Senthil Muthuswamy (2004): Tackling Cancer in Three Dimensions . .70 David Sabatini (2004): Fueling Cell Growth . .73 David Tuveson (2004): Decoding a Cryptic Cancer . 76 Hilary Coller (2005): When Cells Sleep . .79 Diana Bautista (2010): An Itch for Knowledge . .82 David Prober (2010): Sleeping Like the Fishes .