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Regulation by non-coding RNAs Volume 2 Edited by Nicholas Delihas Printed Edition of the Special Issue Published in IJMS www.mdpi.com/journal/ijms Nicholas Delihas (Ed.) Regulation by non-coding RNAs Volume 2 This book is a reprint of the special issue that appeared in the online open access journal International Journal of Molecular Sciences (ISSN 1422-0067) in 2013 (available at: http://www.mdpi.com/journal/ijms/special_issues/regulation-by-non-coding-rnas). Guest Editor Nicholas Delihas Department of Molecular Genetics and Microbiology, School of Medicine, 158 Life Sciences Building, Stony Brook University, Stony Brook, NY 11794, USA Editorial Office MDPI AG Klybeckstrasse 64 Basel, Switzerland Publisher Shu-Kun Lin Managing Editor Rui Lu 1. Edition 2014 #Switzerland Volume 1 (ISBN 978-3-03842-010-1) Volume 2 (ISBN 978-3-03842-011-8) © 2014 by the authors; licensee MDPI, Basel, Switzerland. All articles in this volume are Open Access distributed under the Creative Commons Attribution 3.0 license (http://creativecommons.org/licenses/by/3.0/), which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. However, the dissemination and distribution of copies of this book as a whole is restricted to MDPI, Basel, Switzerland. I Table of Contents Volume 2 Nicholas Delihas Preface Guest Editor ....................................................................................................................... III Chapter 3. ncRNAs and hematopoietic and stem cell differentiation Franck Morceau, Sébastien Chateauvieux, Anthoula Gaigneaux, Mario Dicato and Marc Diederich Long and short non-coding RNAs as regulators of hematopoietic differentiation Reprinted from Int. J. Mol. Sci. 2013, 14(7), 14744–14770 ......................................................... 805 http://www.mdpi.com/1422-0067/14/7/14744 Alessandro Rosa and Ali H. Brivanlou Regulatory non-coding RNAs in pluripotent stem cells Reprinted from Int. J. Mol. Sci. 2013, 14(7), 14346–14373 ......................................................... 833 http://www.mdpi.com/1422-0067/14/7/14346 Marica Battista, Anna Musto, Angelica Navarra, Giuseppina Minopoli, Tommaso Russo and Silvia Parisi miR-125b Regulates the Early Steps of ESC Differentiation through Dies1 in a TGF-Independent Manner Reprinted from Int. J. Mol. Sci. 2013, 14(7), 13482–13496 ......................................................... 861 http://www.mdpi.com/1422-0067/14/7/13482 Chapter 4. Tendon adhesion and siRNAs Hongjiang Ruan, Shen Liu, Fengfeng Li, Xujun Li and Cunyi Fan Prevention of Tendon Adhesions by ERK2 Small Interfering RNAs Reprinted from Int. J. Mol. Sci. 2013, 14(2), 4361–4371 ............................................................. 877 http://www.mdpi.com/1422-0067/14/2/4361 Chapter 5. ncRNAs and laser therapy Toshihiro Kushibiki, Takeshi Hirasawa, Shinpei Okawa and Miya Ishihara Regulation of miRNA Expression by Low-Level Laser Therapy (LLLT) and Photodynamic Therapy (PDT) Reprinted from Int. J. Mol. Sci. 2013, 14(7), 13542–13558 ......................................................... 889 http://www.mdpi.com/1422-0067/14/7/13542 Chapter 6. CRISPR system Hagen Richter, Lennart Randau and André Plagens Exploiting CRISPR/Cas: Interference Mechanisms and Applications Reprinted from Int. J. Mol. Sci. 2013, 14(7), 14518–14531 ......................................................... 907 http://www.mdpi.com/1422-0067/14/7/14518 II Chapter 7. Plant and Fungal ncRNAs Mikhail M. Pooggin How Can Plant DNA Viruses Evade siRNA-Directed DNA Methylation and Silencing? Reprinted from Int. J. Mol. Sci. 2013, 14(8), 15233–15259 ......................................................... 921 http://www.mdpi.com/1422-0067/14/8/15233 Virginie Gébelin, Julie Leclercq, Songnian Hu, Chaorong Tang and Pascal Montoro Regulation of MIR Genes in Response to Abiotic Stress in Hevea brasiliensis Reprinted from Int. J. Mol. Sci. 2013, 14(10), 19587–19604 ....................................................... 949 http://www.mdpi.com/1422-0067/14/10/19587 Akihiro Matsui, Anh Hai Nguyen, Kentaro Nakaminami and Motoaki Seki Arabidopsis Non-Coding RNA Regulation in Abiotic Stress Responses Reprinted from Int. J. Mol. Sci. 2013, 14(11), 22642–22654 ....................................................... 967 http://www.mdpi.com/1422-0067/14/11/22642 Li-Ling Lin, Chia-Chi Wu, Hsuan-Cheng Huang, Huai-Ju Chen, Hsu-Liang Hsieh and Hsueh-Fen Juan Identification of MicroRNA 395a in 24-Epibrassinolide-Regulated Root Growth of Arabidopsis thaliana Using MicroRNA Arrays Reprinted from Int. J. Mol. Sci. 2013, 14(7), 14270–14286 ......................................................... 981 http://www.mdpi.com/1422-0067/14/7/14270 Yong Zhuang, Xiao-Hui Zhou and Jun Liu Conserved miRNAs and Their Response to Salt Stress in Wild Eggplant Solanum linnaeanum Roots Reprinted from Int. J. Mol. Sci. 2014, 15(1), 839–849 ................................................................. 999 http://www.mdpi.com/1422-0067/15/1/839 Francisco E. Nicolás and Rosa M. Ruiz-Vázquez Functional Diversity of RNAi-Associated sRNAs in Fungi Reprinted from Int. J. Mol. Sci. 2013, 14(8), 15348–15360 ....................................................... 1011 http://www.mdpi.com/1422-0067/14/8/15348 Chapter 8. 3' UTRs of mRNA Eva Michalova, Borivoj Vojtesek and Roman Hrstka Impaired Pre-mRNA Processing and Altered Architecture of 3' Untranslated Regions Contribute to the Development of Human Disorders Reprinted from Int. J. Mol. Sci. 2013, 14(8), 15681–15694 ....................................................... 1025 http://www.mdpi.com/1422-0067/14/8/15681 Reprinted from IJMS. Cite as: Curtale, G.; Citarella, F. Dynamic Nature of Noncoding RNA Regulation of Adaptive Immune Response. Int. J. Mol. Sci. 2013, 14, 17347-17377. III Preface These are exciting times for RNA molecular biologists! With the discovery of thousands of new non- coding RNA (ncRNA) transcripts in the last few years, and especially the new human genome transcripts, great opportunities and challenge are provided for determining functions in normal and disease states. This text is an outgrowth of a special issue of IJMS devoted to regulation by non-coding RNAs and contains both original research and review articles. In all there are 50 peer-reviewed articles presented that were submitted to the Journal within a period of 8 months. An attempt has been made to provide an up-to-date analysis of this very fast moving field and to cover regulatory roles of both microRNAs and long non-coding RNAs. Multifaceted functions of these RNAs in normal cellular processes, as well as in disease progression, are highlighted. We hope the readers will enjoy the articles and find the concepts presented challenging. Nicholas Delihas Guest Editor IV Chapter 3. ncRNAs and hematopoietic and stem cell differentiation 805 Reprinted from IJMS. Cite as: Morceau, F.; Chateauvieux, S.; Gaigneaux, A.; Dicato, M.; Diederich, M. Long and Short Non-Coding RNAs as Regulators of Hematopoietic Differentiation. Int. J. Mol. Sci. 2013, 14, 14744-14770. Review Long and Short Non-Coding RNAs as Regulators of Hematopoietic Differentiation Franck Morceau 1,†, Sébastien Chateauvieux 1,†, Anthoula Gaigneaux 1, Mario Dicato 1 and Marc Diederich 2,* 1 Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Kirchberg Hospital, 9 Rue Edward Steichen, 2540, Luxembourg; E-Mails: [email protected] (F.M.); [email protected] (S.C.); [email protected] (A.G.); [email protected] (M.D.) 2 Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul 151-742, Korea † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +82-2-880-8919. Received: 3 June 2013; in revised form: 5 July 2013 / Accepted: 9 July 2013 / Published: 15 July 2013 Abstract: Genomic analyses estimated that the proportion of the genome encoding proteins corresponds to approximately 1.5%, while at least 66% are transcribed, suggesting that many non-coding DNA-regions generate non-coding RNAs (ncRNAs). The relevance of these ncRNAs in biological, physiological as well as in pathological processes increased over the last two decades with the understanding of their implication in complex regulatory networks. This review particularly focuses on the involvement of two large families of ncRNAs, namely microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the regulation of hematopoiesis. To date, miRNAs have been widely studied, leading to a wealth of data about processing, regulation and mechanisms of action and more specifically, their involvement in hematopoietic differentiation. Notably, the interaction of miRNAs with the regulatory network of transcription factors is well documented whereas roles, regulation and mechanisms of lncRNAs remain largely unexplored in hematopoiesis; this review gathers current data about lncRNAs as well as both potential and confirmed roles in normal and pathological hematopoiesis. 806 Chapter 3. ncRNAs and hematopoietic and stem cell differentiation Keywords: ncRNA; miRNA; lncRNA; transcription factors; regulatory network; erythropoiesis; leukemia; lymphoma; differentiation 1. Introduction Hematopoiesis is the physiological process leading to the production of all circulating blood cells. Hematopoietic stem cells (HSCs) are pluripotent
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  • Annual Scientific Report 2013 on the Cover Structure 3Fof in the Protein Data Bank, Determined by Laponogov, I

    Annual Scientific Report 2013 on the Cover Structure 3Fof in the Protein Data Bank, Determined by Laponogov, I

    EMBL-European Bioinformatics Institute Annual Scientific Report 2013 On the cover Structure 3fof in the Protein Data Bank, determined by Laponogov, I. et al. (2009) Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases. Nature Structural & Molecular Biology 16, 667-669. © 2014 European Molecular Biology Laboratory This publication was produced by the External Relations team at the European Bioinformatics Institute (EMBL-EBI) A digital version of the brochure can be found at www.ebi.ac.uk/about/brochures For more information about EMBL-EBI please contact: [email protected] Contents Introduction & overview 3 Services 8 Genes, genomes and variation 8 Molecular atlas 12 Proteins and protein families 14 Molecular and cellular structures 18 Chemical biology 20 Molecular systems 22 Cross-domain tools and resources 24 Research 26 Support 32 ELIXIR 36 Facts and figures 38 Funding & resource allocation 38 Growth of core resources 40 Collaborations 42 Our staff in 2013 44 Scientific advisory committees 46 Major database collaborations 50 Publications 52 Organisation of EMBL-EBI leadership 61 2013 EMBL-EBI Annual Scientific Report 1 Foreword Welcome to EMBL-EBI’s 2013 Annual Scientific Report. Here we look back on our major achievements during the year, reflecting on the delivery of our world-class services, research, training, industry collaboration and European coordination of life-science data. The past year has been one full of exciting changes, both scientifically and organisationally. We unveiled a new website that helps users explore our resources more seamlessly, saw the publication of ground-breaking work in data storage and synthetic biology, joined the global alliance for global health, built important new relationships with our partners in industry and celebrated the launch of ELIXIR.