RNA Methods and Protocols
Recent insight into the transcripts generated from the mammalian genome (i.e. the transcriptome) has revealed that transcription is a far more complex phenomenon than previously thought. In RNA: Methods and Protocols, expert researchers provide the proced
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MO L E C U L A R BI O L O G Y
Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For other titles published in this series, go to www.springer.com/series/7651
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RNA Methods and Protocols
Edited by
Henrik Nielsen University of Copenhagen, Denmark
Editor Henrik Nielsen, Ph.D. Department of Cellular and Molecular Medicine The Panum Institute University of Copenhagen Copenhagen DK-2200N, Denmark [email protected]
Additional material to this book can be downloaded from http://extras.springer.com. ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-58829-913-0 e-ISBN 978-1-59745-248-9 DOI 10.1007/978-1-59745-248-9 Springer New York Dordrecht Heidelberg London © 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. While the advice and information in this book are believed to be true and accurate at the date of going to press, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Humana Press is part of Springer Science+Business Media (www.springer.com)
Preface This is a book about the procedures and methods that are used to describe the structure of the messenger RNAs and non-coding RNAs that are transcribed as the immediate gene products by RNA polymerase II in mammalian cells. It is intended for researchers working on a biological problem that involves characterization of the expression of “gene X.” The book is focused on the structure of the RNA products of gene X and mapping of the proteins associated with these RNAs. The book is mainly intended for the non-specialist in RNA biology. Recent insight into the transcripts generated from the mammalian genome (i.e., the transcriptome) has revealed that transcription is a far more complex phenomenon than previously thought. In a sense, the present situation is comparable to the mid-1970s when the exon–intron organization of genes was discovered. Prior to that, it was generally believed that the mature mRNA was co-linear with the gene from which it was transcribed. This view was challenged by the extraordinary size of the genomes and the puzzling observation of very long nuc
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