MicroRNAs: From Basic Science to Disease Biology

Sidney  Altman; Victor R. Ambros

doi:10.1017/CBO9780511541766

MicroRNAs (miRNAs) are RNA molecules, conserved by evolution, that regulate gene expressions and their discovery has revolutionised both basic biomedical research and drug discovery. Expression levels of miRNAs have been found to vary between tissues and with developmental stages and hence evaluation of the global expression of miRNAs potentially provides opportunities to identify regulatory points for many different biological processes. This wide-ranging reference work, written by leading experts from both academia and industry, will be an invaluable resource for all those wishing to use miRNA techniques in their own research, from graduate students, post-docs and researchers in academia to those working in R&D in biotechnology and pharmaceutical companies who need to understand this emerging technology. From the discovery of miRNAs and their functions to their detection and role in disease biology, this volume uniquely integrates the basic science with industry application towards drug validation, diagnostic and therapeutic development.

'… comprehensive and detailed … compiled logically … informative and easy to read.'

Source: Microbiology Today

'… a useful reference guide for those interested in miRNA …'

Source: Immunology News

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Contents

Frontmatter
pp i-iv
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Contents
pp v-vii
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List of contributors
pp viii-xxiv
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Foreword by Sidney Altman
pp xxv-xxvi
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Foreword by Victor R. Ambros
pp xxvii-xxviii
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Introduction
pp 1-4
- By Krishnarao Appasani, GeneExpression Systems, Inc. PO Box 540170 Waltham, MA 02454USA
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I - Discovery of microRNAs in various organisms
pp 5-6
- By Krishnarao Appasani, Founder and Chief Executive Officer GeneExpression Systems, Inc. PO Box 540170 Waltham, MA 02454 USA
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1 - The microRNAs of C. elegans
pp 7-21
- By Ines Alvarez-Garcia, The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road Cambridge CB2 1QN, United Kingdom, Eric A. Miska, The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road Cambridge CB2 1QN, United Kingdom
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2 - Non-coding RNAs – development of man-made vector-based intronic microRNAs (miRNAs)
pp 22-41
- By Shao-Yao Ying, Department of Cell and Neurobiology Keck School of Medicine, University of Southern California 1333 San Pablo Street, BMT-403 Los Angeles, CA 90033-9112 USA, Joseph D. Miller, Department of Cell and Neurobiology Keck School of Medicine, University of Southern California 1333 San Pablo Street, BMT-403 Los Angeles, CA 90033-9112 USA, Shi-Lung Lin, Department of Cell and Neurobiology Keck School of Medicine, University of Southern California 1333 San Pablo Street, BMT-403 Los Angeles, CA 90033-9112 USA
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3 - Seeing is believing: strategies for studying microRNA expression
pp 42-57
- By Joshua W. Hagen, Memorial Sloan-Kettering Institute Department of Developmental Biology 521 Rockefeller Research Labs 1275 York Avenue, Box 252 New York, NY 10021 USA, Eric C. Lai, Memorial Sloan-Kettering Institute Department of Developmental Biology 521 Rockefeller Research Labs 1275 York Avenue, Box 252 New York, NY 10021 USA
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4 - MicroRNAs in limb development
pp 58-69
- By Danielle M. Maatouk, Department of Molecular Genetics & Microbiology, University of Florida College of Medicine 1600 SW Archer Road Gainesville, FL 32610-0266 USA, Jason R. Rock, Department of Molecular Genetics & Microbiology, University of Florida College of Medicine 1600 SW Archer Road Gainesville, FL 32610-0266 USA, Brian D. Harfe, Department of Molecular Genetics & Microbiology, University of Florida College of Medicine 1600 SW Archer Road Gainesville, FL 32610-0266 USA
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5 - Identification of miRNAs in the plant Oryza sativa
pp 70-82
- By Hui Zhou, Biotechnology Research Center Key Laboratory of Gene Engineering of the Ministry of Education Zhongshan University Guangzhou, 510275 People's Republic of China, Yue-Qin Chen, Biotechnology Research Center Key Laboratory of Gene Engineering of the Ministry of Education Zhongshan University Guangzhou, 510275 People's Republic of China, Yu-Chun Luo, Biotechnology Research Center Key Laboratory of Gene Engineering of the Ministry of Education Zhongshan University Guangzhou, 510275 People's Republic of China, Jia-Fu Wang, Biotechnology Research Center Key Laboratory of Gene Engineering of the Ministry of Education Zhongshan University Guangzhou, 510275 People's Republic of China, Liang-Hu Qu, Biotechnology Research Center Key Laboratory of Gene Engineering of the Ministry of Education Zhongshan University Guangzhou, 510275 People's Republic of China
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II - MicroRNA functions and RNAi-mediated pathways
pp 83-84
- By Krishnarao Appasani, Founder and Chief Executive Officer GeneExpression Systems, Inc. PO Box 540170 Waltham, MA 02454 USA
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6 - Inhibition of translation initiation by a microRNA
pp 85-101
- By David T. Humphreys, Molecular Genetics Program Victor Chang Cardiac Research Institute 384 Victoria Street, Darlinghurst Sidney, NSW 2010 Australia, Belinda J. Westman, Molecular Genetics Program Victor Chang Cardiac Research Institute 384 Victoria Street, Darlinghurst Sidney, NSW 2010 Australia, David I. K. Martin, Molecular Genetics Program Victor Chang Cardiac Research Institute 384 Victoria Street, Darlinghurst Sidney, NSW 2010 Australia, Thomas Preiss, Molecular Genetics Program Victor Chang Cardiac Research Institute 384 Victoria Street, Darlinghurst Sidney, NSW 2010 Australia
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7 - In situ analysis of microRNA expression during vertebrate development
pp 102-114
- By Diana K. Darnell, Department of Cell Biology and Anatomy University of Arizona PO Box 245044 Life Sciences North 462 1501 N. Campbell Avenue Tucson, AZ 85724-5044 USA, Stacey Stanislaw, Department of Cell Biology and Anatomy University of Arizona PO Box 245044 Life Sciences North 462 1501 N. Campbell Avenue Tucson, AZ 85724-5044 USA, Simran Kaur, Department of Cell Biology and Anatomy University of Arizona PO Box 245044 Life Sciences North 462 1501 N. Campbell Avenue Tucson, AZ 85724-5044 USA, Tatiana A. Yatskievych, Department of Cell Biology and Anatomy University of Arizona PO Box 245044 Life Sciences North 462 1501 N. Campbell Avenue Tucson, AZ 85724-5044 USA, Sean Davey, Department of Cell Biology and Anatomy University of Arizona PO Box 245044 Life Sciences North 462 1501 N. Campbell Avenue Tucson, AZ 85724-5044 USA, Jay H. Konieczka, Department of Cell Biology and Anatomy University of Arizona PO Box 245044 Life Sciences North 462 1501 N. Campbell Avenue Tucson, AZ 85724-5044 USA, Parker B. Antin, Department of Cell Biology and Anatomy University of Arizona PO Box 245044 Life Sciences North 462 1501 N. Campbell Avenue Tucson, AZ 85724-5044 USA
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8 - MicroRNA function in the nervous system
pp 115-128
- By Gerhard Schratt, University of Heidelberg Interdisciplinary Center for Neurosciences Im Neuenheimer Feld 345, Room 160 D-69120 Heidelberg Germany, Michael Greenberg, Department of Neurobiology Children's Hospital, 300 Longwood Avenue Harvard Medical School Boston, MA 02115 USA
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9 - MicroRNA expression that controls the amount of branched chain α-ketoacid dehydrogenase in mitochondria of human cells
pp 129-136
- By Dean J. Danner, Department of Human Genetics Emory University 615 Michael Street, Room 305C Atlanta, GA 30322 USA, John Barnes, Department of Human Genetics Emory University 615 Michael Street Atlanta, GA 30322 USA, Benjamin Mersey, Department of Human Genetics Emory University 615 Michael Street Atlanta, GA 30322USA
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10 - MicroRNAs and the regulation of leaf shape
pp 137-154
- By Ramiro E. Rodriguez, Molecular Biology Division IBR – Institute of Molecular and Cellular Biology of Rosario Suipacha 531 2000 Rosario Argentina, Carla Schommer, Department of Molecular Biology Max Plank Institute for Developmental Biology Tubingen 72076 Germany, Javier F. Palatnik, Molecular Biology Division IBR – Institute of Molecular and Cellular Biology of Rosario Suipacha 531 2000 Rosario Argentina
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III - Computational biology of microRNAs
pp 155-156
- By Krishnarao Appasani, Founder and Chief Executive Officer GeneExpression Systems, Inc. PO Box 540170 Waltham, MA 02454 USA
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11 - miRBase: a database of microRNA sequences, targets and nomenclature
pp 157-171
- By Anton J. Enright, Computational and Functional Genomics The Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA United Kingdom, Sam Griffiths-Jones, Computational and Functional Genomics The Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA United Kingdom
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12 - Computational prediction of microRNA targets in vertebrates, fruitflies and nematodes
pp 172-186
- By Dominic Grün, Center for Functional Comparative Genomics Department of Biology, NYU, 1009 Main Building 100 Washington Square East New York, NY 10003-6688 USA, Nikolaus Rajewsky, Assistant Prof. of Biology and Mathematics New York University Center for Functional Comparative Genomics Department of Biology, NYU, 1009 Main Building 100 Washington Square East New York, NY 10003-6688 USA
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13 - Computational approaches to elucidate miRNA biology
pp 187-198
- By Praveen Sethupathy, University of Pennsylvania Center for Bioinformatics 1407 Blockley Hall/6021 Philadelphia, PA 19104-6021 USA, Molly Megraw, University of Pennsylvania Center for Bioinformatics 1407 Blockley Hall/6021 Philadelphia, PA 19104-6021 USA, Artemis G. Hatzigeorgiou, University of Pennsylvania Center for Bioinformatics 1407 Blockley Hall/6021 Philadelphia, PA 19104-6021 USA
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14 - The RNAhybrid approach to microRNA target prediction
pp 199-209
- By Marc Rehmsmeier, Universität Bielefeld Center for Biotechnology (CeBiTec) 33594 Bielefeld Germany
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15 - Machine learning predicts microRNA target sites
pp 210-220
- By Pål Sætrom, Jr., Interagon AS Laboratoriesenteret Medisinsk Teknisk Senter NO-7489 Trondheim Norway, Ola Snøve, Interagon AS Laboratoriesenteret Medisinsk Teknisk Senter NO-7489 Trondheim Norway
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16 - Models of microRNA–target coordination
pp 221-226
- By Neil R. Smalheiser, University of Illinois at Chicago Psychiatric Institute 1601 W. Taylor Street Chicago, IL 60612 USA, Vetle I. Torvik, University of Illinois at Chicago Psychiatric Institute 1601 W. Taylor Street Chicago, IL 60612 USA
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IV - Detection and quantitation of microRNAs
pp 227-228
- By Krishnarao Appasani, Founder and Chief Executive Officer GeneExpression Systems, Inc. PO Box 540170 Waltham, MA 02454 USA
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17 - Detection and analysis of microRNAs using LNA (locked nucleic acid)-modified probes
pp 229-241
- By Sakari Kauppinen, Wilhelm Johannsen Centre for Functional Genome Research Institute of Medical Biochemistry and Genetics University of Copenhagen Blegdamsvej 3 DK-2200 Copenhagen NorthDenmark; Santaris Pharma Boge Alle 3 Horshol DK-2970 Denmark
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18 - Detection and quantitation of microRNAs using the RNA Invader® assay
pp 242-254
- By Hatim T. Allawi, Third Wave Technologies, Inc. 502 S. Rosa Rd Madison, WI 53719-1256 USA, Victor I. Lyamichev, Third Wave Technologies, Inc. 502 S. Rosa Rd Madison, WI 53719-1256 USA
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19 - A single molecule method to quantify miRNA gene expression
pp 255-268
- By Sonal Patel, US Genomics, Inc. 12 Gill Street, Suite 4700 Woburn, MA 01801 USA, Joanne Garver, US Genomics, Inc. 12 Gill Street, Suite 4700 Woburn, MA 01801 USA, Michael Gallo, Epic Therapeutics, Inc. 220 Norwood Park Norwood, MA 02062 USA, Maria Hackett, Novartis Institutes for Biomedical Research 250 Massachusetts Avenue Cambridge, MA 02139 USA, Stephen McLaughlin, US Genomics, Inc. 12 Gill Street, Suite 4700 Woburn, MA 01801 USA, Steven R. Gullans, RxGen, Inc. New Haven, CT USA, Mark Nadel, US Genomics, Inc. 12 Gill Street, Suite 4700 Woburn, MA 01801 USA, John Harris, US Genomics, Inc. 12 Gill Street, Suite 4700 Woburn, MA 01801 USA, Duncan Whitney, US Genomics, Inc. 12 Gill Street, Suite 4700 Woburn, MA 01801 USA, Lori A. Neely, Technology & Pre-Development Millipore Corp. 80 Ashby Rd. Bedford, MA 01730 USA
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20 - Real-time quantification of microRNAs by TaqMan® assays
pp 269-282
- By Yu Liang, Research & Development Applied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404 USA, Linda Wong, Research & Development Applied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404USA, Ruoying Tan, Research & Development Applied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404 USA, Caifu Chen, Research & Development Applied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404 USA
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MicroRNAs

From Basic Science to Disease Biology

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