Advances in Experimental Medicine and Biology 907 Gene W. Yeo Editor RNA Processing Disease and Genome-wide Probing Advances in Experimental Medicine and Biology Volume 907 Editorial Board: IRUN R. COHEN, The Weizmann Institute of Science, Rehovot, Israel ABEL LAJTHA, N.S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA JOHN D. LAMBRIS, University of Pennsylvania, Philadelphia, PA, USA RODOLFO PAOLETTI, University of Milan, Milan, Italy More information about this series at h ttp://www.springer.com/series/5584 Gene W. Yeo Editor RNA Processing Disease and Genome-wide Probing Editor Gene W. Yeo, Ph.D., M.B.A. Department of Cellular and Molecular Medicine Institute for Genomic Medicine Stem Cell Program University of California, San Diego La Jolla , CA , USA ISSN 0065-2598 ISSN 2214-8019 (electronic) Advances in Experimental Medicine and Biology ISBN 978-3-319-29071-3 ISBN 978-3-319-29073-7 (eBook) DOI 10.1007/978-3-319-29073-7 Library of Congress Control Number: 2016936562 © Springer International Publishing Switzerland 2016 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms 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 specifi c 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 Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG Switzerland Pref ace Ribonucleic acid (RNA) binding proteins currently number in the thousands, and defects in their function are at the heart of diseases such as cancer and neurodegen- eration. RNA-binding proteins have become implicated in the intricate control of surprisingly diverse biological settings, such as circadian rhythm, stem cell self- renewal, oncogenesis, and germ cell development. RNA-binding proteins bind to diverse RNA substrates to mediate aspects of the life cycle of RNA processing, including alternative splicing, stability, export, trans- port, and translation, as well as the assembly and disassembly of RNA granules. Understanding the roles of RNA-binding proteins requires multidisciplinary approaches: characterization of their targets, single-molecule approaches to unveil- ing their modes of interaction, and computational considerations of the tremendous amounts of data associated with analysis of their activities. Given the success of the volume S ystems Biology of RNA Binding Proteins , I have assembled this second volume with chapters focused on cutting-edge methods to study aspects of RNA-binding protein-RNA function that were not previously covered and introduce the most recent exciting biology related to RNA-binding proteins. The content of this book surveys a range of genome-wide and systems approaches to studying RNA-binding proteins and the importance of RNA-binding proteins in development, cancer, and circadian rhythm. These chapters provide opportunities for open questions and new areas of inquiry into posttranscriptional processing. With the combination of high-throughput short-read sequencing with biochemi- cal methods such as RNA immunoprecipitation and RNA cross-linking and immu- noprecipitation, transcriptome-wide maps of sites of interaction between RNA-binding proteins and their RNA targets have proved useful in elucidating novel molecular and cellular functions of RNA-binding proteins. Eric Van Nostrand and Stephanie Huelga in my laboratory discuss challenges associated with large- scale identifi cation and analysis of RNA-binding protein-RNA interactions. RNA does not exist as simple linear sequences in vivo. Gregory and colleagues present a review of genome-wide approaches to determining RNA structure in the v vi Preface transcriptome. RNA structure discovery is a fundamentally important aspect of understanding the protein-RNA landscape. With the increasing number of proteins thought to have RNA-binding capacity, Tomas Bos, Julia Nussbacher, and Stefan Aigner in my laboratory review how teth- ered function assays can be utilized to reveal novel molecular functions of candi- date RNA-binding proteins. To truly understand the stepwise interactions of proteins onto RNA substrates, Moore and Serebrov discuss single-molecule approaches that shed light on deep mechanistic insights into interrogating RNA-binding protein function. The following chapters deal with exciting areas in biology that have become entwined with RNA-binding proteins. Circadian control has recently become associated with posttranscriptional con- trol of gene expression. Panda and colleagues recount circadian control of RNA by RNA-binding proteins. Posttranscriptional and translation regulation is particularly important in germ cell biology. Licatalosi summarizes the role of RNA-binding proteins in male germ cell development. Ito and colleagues present the importance of RNA-binding proteins in stem cell biology and oncogenesis. Self-renewal of stem cells is key to our understanding of development and cancer. How RNA-binding proteins control stem cell fate and oncogenesis is a topic of hot debate. Hundley and Washburn feature the roles of RNA-binding proteins in RNA edit- ing. Uncovering how enzymes affect RNA editing is critically important in our dissection of human diseases. It is still unknown how many and which RNA-binding proteins can regulate A-to-I editing in vivo. Bejar clarifi es the recent fi ndings that splicing factors are commonly mutated in cancer. Recurrent somatic mutations of genes encoding core subunits of the spliceo- some have been identifi ed in several different cancer types and will be discussed in this review, avenues for novel cancer therapeutic strategies. C alarco and colleagues discuss how tissue-specifi c alternative splicing is con- trolled and the utility of the model organism C . elegans in aiding in its elucidation. Leung and Fan present exciting fi ndings of the roles of RNA-binding proteins in RNA granules, particularly in neurodegenerative diseases such as ALS and FTLD. Massirer and colleagues emphasize the importance of posttranslational modifi - cations on RNA-binding proteins, an area poorly understood but with tremendous potential for understanding diseases such as neurodegeneration. The contributors of this book are internationally recognized leaders in the arena of technology development, RNA processing, and biology relevant to RNA-binding proteins, and we envision that this book will serve as a valuable resource for both experts and nonexperts. Advanced undergraduate students and entering graduate students in biology, chemistry, molecular engineering, computer science, and bio- informatics, as well as medical students and postdoctoral fellows who are new to the arena of posttranscriptional gene regulation, should fi nd this book accessible. We hope the chapters in this volume will stimulate interest and appreciation of the complexity and importance of posttranscriptional gene regulation to its readers and Preface vii even lead them to pose new solutions to the enormous challenges that lie ahead in comprehending how RNA-binding proteins affect gene regulation. I sincerely express my greatest gratitude to the contributors to this book: Stefan Aigner, Rafael Bejar, Giorgia Benegiamo, Mario Bengtson, Nathan Berkowitz, Tomas Bos, Steven Brown, Kristina Buac, John Calarco, Alexander Fan, Sager Gosai, Xicotencatl Gracida, Brian Gregory, Ayuna Hattori, Stephanie Huelga, Heather Hundley, Takahiro Ito, Anthony Leung, Donny Licatalosi, Michael Lovci, Katlin Massirer, Melissa Moore, Adam Norris, Julia Nussbacher, Satchidananda Panda, Victor Serebrov, Ian Silverman, Eric Van Nostrand, and Michael Washburn. La Jolla, CA, USA Gene W. Yeo Contents 1 Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions .......................................... 1 Eric L. Van Nostrand , Stephanie C. Huelga , and Gene W. Yeo 2 Genome-Wide Approaches for RNA Structure Probing ..................... 29 Ian M. Silverman , Nathan D. Berkowitz , Sager J. Gosai , and Brian D. Gregory 3 Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins .................................... 61 Tomas J. Bos , Julia K. Nussbacher , Stefan Aigner , and Gene W. Yeo 4 Single Molecule Approaches in RNA-Protein Interactions ................. 89 Victor Serebrov and Melissa J. Moore 5 RNA Dynamics in the Control of Circadian Rhythm .......................... 107 Giorgia Benegiamo , Steven A. Brown , and Satchidananda Panda 6 Roles of RNA-Binding Proteins and Post- transcriptional Regulation in Driving Male Germ Cell Development in the Mouse ............................................................................................. 123 Donny D. Licatalosi 7 Regulation of Stem Cell Self-Renewal and Oncogenesis by RNA-Binding Proteins ....................................................................... 153 Ayuna Hattori , Kristina Buac , and Takahiro Ito 8 Controlling the Editor: The Many Roles of RNA-Binding Proteins in Regulating A-to-I RNA Editing .......................................... 189 Michael C. Washburn and Heather A. Hundley 9 Splicing Factor Mutations in Cancer .................................................... 215 Rafael Bejar ix