Enhancer RNAs Methods and Protocols
This volume provides a comprehensive overview of the experimental and computational methodologies used to study the function of long non-coding RNA (ncRNAs) expressed from enhancers. Chapter detail both wet-lab and dry-lab techniques and annotating long n
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Ulf Andersson Ørom Editor
Enhancer RNAs Methods and Protocols
METHODS
IN
MOLECULAR BIOLOGY
Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes: http://www.springer.com/series/7651
Enhancer RNAs Methods and Protocols
Edited by
Ulf Andersson Ørom Max Planck Institute for Molecular Genetics, Berlin, Germany
Editor Ulf Andersson Ørom Max Planck Institute for Molecular Genetics Berlin, Germany
ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-4033-2 ISBN 978-1-4939-4035-6 (eBook) DOI 10.1007/978-1-4939-4035-6 Library of Congress Control Number: 2016949091 © Springer Science+Business Media New York 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper This Humana Press imprint is published by Springer Nature The registered company is Springer Science+Business Media LLC New York
Preface Long noncoding RNAs (long ncRNAs) are being continuously studied as more and more functions are described and they are found to be involved in several processes. Since the discovery that enhancer RNA (eRNA) and enhancer-like long ncRNAs are transcribed from enhancers and contribute to the activity of enhancers [11, 15] and are widely expressed from active enhancers [1, 3, 8, 13, 21], a substantial number of papers have elaborated further on their importance and mechanisms [11, 16]. With this series issue on enhancer-associated RNA, the techniques for both individual transcript studies and genome-wide and transcriptome-wide analyses are provided. The ever-increasing demand for high-throughput data creates a need to understand and apply both wet-lab and drylab techniques to explore the full potential of how long ncRNAs can provide functionality in enhancer function. RNA localization is important for the function of the transcript. While many mRNAs are predominantly localized to the cytoplasm, long ncRNAs are often enriched in
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