RNA and DNA Editing Methods and Protocols
The recent expansion in diversity of RNA and DNA editing types has stimulated the development of many unique genetic, molecular, biochemical, and computational approaches to biological issues. In RNA and DNA Editing: Methods and Protocols, leading e
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Molecular Biology™
Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
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RNA and DNA Editing Methods and Protocols Edited by
Ruslan Aphasizhev Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, USA
Editor Ruslan Aphasizhev, Ph.D. Department of Microbiology and Molecular Genetics School of Medicine University of California Irvine, CA 92697 USA [email protected]
ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-61779-017-1 e-ISBN 978-1-61779-018-8 DOI 10.1007/978-1-61779-018-8 Springer New York Heidelberg London Dordrecht Library of Congress Control Number: 2011921338 © Springer Science+Business Media, LLC 2011 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper Humana Press is part of Springer Science+Business Media (www.springer.com)
Foreword RNA editing is a disparate field held together by history and friendships between the researchers. The term was coined by Robb Benne in his 1986 Cell paper in which he described the presence of four nonencoded uridylyl nucleotides in the middle of the mRNA for cytochrome oxidase subunit II in the trypanosomatid protist, Crithidia fasciculata. The striking thing was that these precise U-insertions at the RNA level precisely compensated for or “edited” an encoded −1 frameshift in the mitochondrial maxicircle DNA encoded gene. In 1989, Janet Shaw and I tried to define RNA editing as “any modification of the sequence of an mRNA molecule within coding regions, except for splicing of introns.” This definition encompassed a single C to U substitution in the mRNA for mammalian apolipoprotein B (apoB), specific A to I modifications in the mRNA for the glutamate receptor, multiple C to U substitutions in plant chloroplast and mitochondrial mRNAs, and even insertions of G residues within coding regions of negative strand RNA viruses. But it failed to cover specific nucleotide changes in tRNAs from Acanthamoeba and marsupials, and the most diverse and striking phenomenon of all, specific insertions of multiple C and dinucleotide residues and other modifications in all mitochondrial transcripts in Physarum, including rRNAs. The sexy term, RNA editing, was hijacked (just joki
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