Nuclear Functions in Plant Transcription, Signaling and Development PDF
Preview Nuclear Functions in Plant Transcription, Signaling and Development
Nuclear Functions in Plant Transcription, Signaling and Development Olga Pontes • Hailing Jin Editors Nuclear Functions in Plant Transcription, Signaling and Development 1 3 Editors Olga Pontes Hailing Jin Shanghai Center for Plant Stress Biology Plant Pathology and Microbiology (PSC) University of California Shanghai Riverside China California USA ISBN 978-1-4939-2385-4 ISBN 978-1-4939-2386-1 (eBook) DOI 10.1007/978-1-4939-2386-1 Library of Congress Control Number: 2015933016 Springer New York Heidelberg Dordrecht London © Springer Science+Business Media New York 2015 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 Springer is part of Springer Science+Business Media (www.springer.com) Preface for Nuclear Functions (eds. Pontes and Jin) Plants provide us with food and are the source of several other by-products such as compounds used in pharmaceutics or biofuels. Therefore, it comes as no surprise that plants are crucial in solving major challenges now facing humanity, namely, food productivity/security, increasing energy demands, and environmental changes. There has been a dramatic increase for plant-derived food and feed products as the world population grows exponentially. Plants are also playing a role in filling our ever-increasing energy needs and these bio-energy crops are expected to provide a sustainable, CO -neutral emission solution in the near future. Yet such crops will 2 need to be compatible with food and feed agriculture production and must preserve Earth’s ecosystems. So the question is: how can we face all of these challenges? To meet our planet’s needs, we need to improve and further develop sustainable methods for plant production by incorporating both biotechnology and sustainable agricultural practices. In this context, we must first establish a baseline understand- ing of different molecular and cellular mechanisms underlying plant development and response to stress, so we can then apply it to practical advances in plant produc- tion across the globe. Surprisingly, the biological networks underpinning plant yield are still poorly understood, particularly regarding the master regulator of cellular function: the nucleus. The nucleus harbors the large majority of the plant’s DNA, the linear sequence of which is the blueprint of every living organism. However, this is only the beginning: how this DNA is expressed and regulated depends on a variety of other interacting factors that play crucial roles in shaping its organization and function. With the sequencing of several plant genomes and recent advances in high-throughput tech- nologies, plant nuclear biologists have been able to unveil many of the mechanisms underlying genome regulation. For instance, epigenetic modifications, such as histone post-translational modifi- cations and DNA methylation, directly impact gene expression and genome defense by regulating the organization and function of the genome. Importantly, while evolu- tionary processes take place at a timescale that does not allow plants to respond and adapt to climate-induced stress, we are starting to recognize that epigenetic mecha- nisms can confer phenotypic plasticity. Epigenetics enables a heritable control of v vi Preface for Nuclear Functions (eds. Pontes and Jin) phenotypes that can change rapidly in response to environmental cues—sometimes over the course of just two to three generations. This epigenetic timescale of change has tremendous implications for how environmentally altered phenotypes are ac- quired and inherited at the organism and eventually at the population levels. Another exciting recent discovery that came about through plant biology re- search is the previously unacknowledged role of noncoding small RNAs in gene expression. These small molecules have been increasingly recognized as players in the establishment of epigenetic modifications, as well as in genome defense and integrity. Noncoding small RNAs impact normal growth, development, and stress responses in diverse plant species, including staple crops such as rice and maize. Small noncoding RNAs are already playing key roles in plant biotechnology appli- cations including directing the specific and enhanced expression of selected genes. These molecules are therefore of great interest in the context of bioengineering, and have enormous potential for enhancing crop productivity in a wide range of ecosys- tems. Yet, there is still a great deal left to learn about how small noncoding RNAs are integrated into plants’ feedback loops, which direct epigenetic modifications throughout development and the stress response process. Finally, genomes are dynamic structures as their functional properties are strong- ly determined by their spatial organization over time. Similarly, changes in higher order nuclear organization alter the functional properties of genomic regions. Vari- ous types of subcellular physical domains have been identified in the nucleus, the known nuclear bodies or subcompartments, and these structures are associated with transcription factors, RNA-processing proteins, and epigenetic regulators. Interest- ingly, these nuclear domains display different behaviors in response to the environ- ment, yet it is still a matter of debate how nuclear organization functionally relates to plant biological processes. The mechanisms and processes described above make it clear that a true un- derstanding of genome function requires integrating the genomic sequence with what we are still discovering about how epigenetics, small noncoding RNAs, and dynamic nuclear organization modify genomes. It is the goal of this book to compile a series of landmark discussions on the recent advances in plant nuclear biology re- search and offer new perspectives into the functional relevance of the arrangement of genomes and nuclear processes that impact plant physiology and development. The following chapters will provide insights as to how genes are switched on/off and are tuned to specific expression levels, which will allow us to better predict plant phenotypes. Overall, a better understanding of the fundamentals of plant gene expression will aid in the more efficient design of numerous biotechnological ap- plications and plant-breeding programs. This new knowledge will thus provide a foundation for solving both agricultural and environmental problems as well as de- veloping practices that enable global sustainability. Lastly, plant biology is also rel- evant to human biology as several aspects of underlying mechanisms are conserved between both organisms. Understanding this shared biology will shed light on hu- man diseases and could lead to better therapies for cancer and genetic diseases. O. Pontes H. Jin Contents 1 RNA-Directed DNA Methylation and Transcriptional Silencing in Arabidopsis ............................................................................ 1 Xian-Yang Deng and Xin-Jian He 2 T he Role of DNA Methylation in Transposable Element Silencing and Genomic Imprinting ......................................................... 13 Yoko Ikeda and Taisuke Nishimura 3 Nuclear Bodies and Responses to the Environments ............................. 31 Yin Liu and Yuda Fang 4 Plasticity of Chromatin Organization in the Plant Interphase Nucleus ............................................................... 57 Ana Paula Santos, Rita Abranches, Margarida Oliveira and Peter Shaw 5 Role of Epigenetic Modifications in Plant Responses to Environmental Stresses ........................................................................ 81 Xuncheng Liu, Ming Luo, Songguang Yang and Keqiang Wu 6 Setting the Stage for the Next Generation: Epigenetic Reprogramming During Sexual Plant Reproduction ............................ 93 Leonor C. Boavida, Marcela Hernandez-Coronado and Jörg D. Becker 7 Epigenetic Modifications at Developmental Transitions in Arabidopsis ............................................................................................. 119 Heike Wollmann and Frédéric Berger 8 Mechanisms of Transposable Element Evolution in Plants and Their Effects on Gene Expression .................................................... 133 Lisa M. Smith vii viii Contents 9 Population Epigenetics ............................................................................. 165 Christy M. Foust, Aaron W. Schrey and Christina L. Richards Index ................................................................................................................. 181 Contributors Rita Abranches Plant Cell Biology laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal Jörg D. Becker Instituto Gulbenkian de Ciencia, Oeiras, Portugal Frédéric Berger Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Republic of Singapore Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore Leonor C. Boavida Instituto Gulbenkian de Ciencia, Oeiras, Portugal Xian-Yang Deng National Institute of Biological Sciences, Beijing, China Yuda Fang National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China Christy M. Foust Department of Integrative Biology, University of South Florida, Tampa, FL, USA Xin-Jian He National Institute of Biological Sciences, Beijing, China Marcela Hernandez-Coronado Instituto Gulbenkian de Ciencia, Oeiras, Portugal Yoko Ikeda Institute of Plant Science and Resources, Okayama University, Okayama, Japan Xuncheng Liu South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China Yin Liu National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China ix x Contributor Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China Ming Luo Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China Taisuke Nishimura PRESTO, Japanese Science and Technology Agency, Tokyo, Japan Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan Nagaoka University of Technology, Nagaoka, Japan Margarida Oliveira Genomics of Plant Stress Unit, Instituto de Biologia Experimental e Tecnológica, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal Christina L. Richards Department of Integrative Biology, University of South Florida, Tampa, FL, USA Ana Paula Santos Genomics of Plant Stress Unit, Instituto de Biologia Experimental e Tecnológica, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal Aaron W. Schrey Department of Biology, Armstrong State University, Savannah, GA, USA Peter Shaw Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK Lisa M. Smith Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK Heike Wollmann Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Republic of Singapore Genome Institute of Singapore, Singapore, Republic of Singapore Keqiang Wu Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan Songguang Yang South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
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