Chromatin Remodeling Methods and Protocols
Chromatin is of central importance to gene regulation in eukaryotes. Reflecting this singular role for chromatin, numerous approaches have evolved in the laboratory over the past three decades to study chromatin structure and its alterations. Method
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IN
MOLECULAR BIOLOGY™
Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes: http://www.springer.com/series/7651
Chromatin Remodeling Methods and Protocols
Edited by
Randall H. Morse Wadsworth Center, New York State Department of Health, Albany, NY, USA
Editor Randall H. Morse Wadsworth Center New York State Department of Health Albany, NY, USA [email protected]
ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-61779-476-6 e-ISBN 978-1-61779-477-3 DOI 10.1007/978-1-61779-477-3 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2011943306 © Springer Science+Business Media, LLC 2012 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)
Preface No modern molecular biologist needs convincing of the central importance of chromatin to gene regulation in eukaryotes. From large-scale domains to individual gene promoters, gene expression is regulated by histone modifications and histone variants, nucleosome positioning, and nucleosome stability. A panoply of approaches has evolved in the laboratory over the past three decades to study chromatin structure and its alterations, and methods of investigating chromatin remodeling – changes in nucleosome structure or position with respect to the incorporated DNA, or in histone modifications – have progressed rapidly over the past 10 years. Here are presented a wide array of protocols for studying chromatin remodeling. We include methods for investigating chromatin remodeling in vitro and in vivo, in yeast, plants, and mammalian cells, and at local and global levels. Both genespecific and genome-wide approaches are covered, and in recognition of the increasing prevalence of the latter type of study, the final two chapters focus on bioinformatic/ computational approaches to analyzing genome-wide data on chromatin structure. We hope that this volume will be used by readers in more than way. The obvious utility is as a direct guide to a multitude of techniques, served up as recipes with introductions and special “Notes” sections. These latter sections, which provide extra tips and background for the user, have been an especially appreciated feature of these volumes over the years. We
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