RNA Technologies Nikolaus Rajewsky Stefan Jurga Jan Barciszewski Editors Plant Epigenetics RNA Technologies More information about this series at http://www.springer.com/series/8619 Nikolaus Rajewsky • Stefan Jurga • Jan Barciszewski Editors Plant Epigenetics Editors Nikolaus Rajewsky Stefan Jurga Max Delbrück Center for Nanobiomedical Center Molecular Medicine Adam Mickiewicz University Berlin Institute for Medical Poznan´, Poland Systems Biology Berlin-Buch, Berlin Germany Jan Barciszewski Polish Academy of Sciences Institute of Bioorganic Chemistry Poznan´, Poland ISSN 2197-9731 ISSN 2197-9758 (electronic) RNA Technologies ISBN 978-3-319-55519-5 ISBN 978-3-319-55520-1 (eBook) DOI 10.1007/978-3-319-55520-1 Library of Congress Control Number: 2017937907 © Springer International Publishing AG 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. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Preface Plant Epigenetics: From Genotype to Phenotype The Last Unicellular Common Ancestor (LUCA) has existed more than 1 billion years ago. During that time, the plant and animal kingdoms have evolved separately and adopted a multicellular system, with sophisticated pathways of development and capability for perfect adaptation to the environment. Today, in the era of genomics it is known that many developmental processes of plants and animals are similar, although they have evolved independently. The carriers of the logic in these two major lineages are different and show a complicated network of ancient protein and nucleic acid domains, but at the same time a very high conservation and similarity of chromatin proteins and regulatory mechanisms is observed. This, however, does not exclude differences of structure and functions of chromatin that exist between plants and animals. They have evolved very efficient and flexible but different adaptation mechanisms to the local environment in order to ensure survival and reproduction. The specific differences connected to lineage-specific features may provide strong information on the general mechanisms underlying the complexity and regulatory and integratory role of chromatin in all eukaryotes. During a movement towards their final differentiated states, various changes occur in cells due to genetic and environmental factors. Resulted altered properties of the cells have been memorized after each cell division. Recent technological advances allow genome-wide analysis of DNA and histone modifications, which affect their structures, and have the potential to reveal the regulation mechanisms in plants on the level above nucleotide sequence. Those chemical changes allow the manifestation of multiple phenotypes encoded in the same DNA sequence. In this way, chromatin modifications contribute to variation at multiple levels, ranging from the expression of individual genes, to the differen- tiation of cell types, to population-level phenotypic diversity. In other words, that is epigenetics. v vi Preface Formally, the term epigenetics is a combination of two words ‘epigenesis’ and ‘genetics’ and has been coined 75 years ago (Brilliant Jubilee) in 1942 by Conrad H. Waddington. He proposed epigenetics as the branch of biology that studies the causal interaction genes and their products, which brings the phenotype into being, and proposed the concept of the epigenetic landscape as a metaphor for cell differentiation. Currently, epigenetics is interpreted as the study of mitotically and/or meiotically heritable changes in patterns of gene expression that occur without alterations in DNA sequence. Generally, epigenetic studies are focused on chemical modifications of chromatin and their roles in transcriptional silencing. Epigenetic modifications contribute to phenotypic variation at multiple levels, from gene regulation to development, stress response, and population level phenotypic diversity and evolution. A lot of epigenomic features have been comprehensively profiled in health and disease across cell types, tissues and individuals. Plant development particularly depends on epigenetics. They integrate various environmental signals into different phenotypic or growth responses. Therefore, an understanding of mechanisms of how epigenetic modifications affect the expression of genotype into phenotype in plants is of prime interest. There are a number of epigenetic phenomena discovered in plants: (i) paramutation which describes the heritable change in expression status of an allele upon its exposure to an allele with the same sequence but displays a different expression status, (ii) nucleolar dominance that is a selective silencing of the ribosomal RNA genes inherited from one progenitor of a genetic hybrid, (iii) imprinting which is character- ized by selective expression of genes inherited from only the maternal or the paternal parent, (iv) vernalization which induces flowering in plants in response to cold, (v) RNA-mediated homology-dependent technologies that have important contribu- tions for plant genetic engineering, (vi) RNA-mediated DNA methylation that leads to gene downregulation and (vii) RNA-mediated mRNA degradation or inactivation. Nowadays, genome sequences for Arabidopsis, rice, poplar, maize and many other plants are known and thus facilitate genome-wide analyses of DNA methyl- ation and histone modifications and their relationships to coding as well as short (miRNAs, siRNAs) and long noncoding RNAs, which can function as epigenetic marks of transcriptional gene silencing and also a defence against transposable elements and viruses. Thus, plants are good model systems and stay as first line of discoveries in the fields of epigenetics. To deeply discuss and present the frontiers of plant epigenetics, we brought together a diverse group of experts from academia, who working both from the bottom (mechanism) up and top (phenotype) down. We believe that these comple- mentary approaches enable high-impact science. In the book, there are 26 chapters, which present the current state of epigenomic profiling, and how functional information can be indirectly inferred is discussed. New approaches that promise functional answers, collectively referred to as epigenome editing, are also described. The book highlights the latest important advances in our understanding of the functions of plant epigenomics or new technologies for the study of epigenomic marks and mechanisms in plants. Topics include the deposition or removal of chromatin modifications and histone variants, Preface vii the role of epigenetics in development and response to environmental signals, natural variation and ecology, and applications for epigenetics in crop improve- ment. The chapters in this book are variable in nature, ranging from the complex regulation of stress and heterosis to the precise mechanisms of DNA and histone modifications, providing breakthroughs in the explanation of complex phenotypic phenomena. We hope that the chapters in this book present outstanding significance and will capture broad interest. Berlin Nikolaus Rajewsky Poznan´ Stefan Jurga Poznan´ Jan Barciszewski January 2017 Contents Conservation, Divergence, and Abundance of MiRNAs and Their Effect in Plants ................................................. 1 Flor de Fa´tima Rosas-Ca´rdenas and Stefan de Folter The Role of MiRNAs in Auxin Signaling and Regulation During Plant Development ............................................. 23 Clelia De-la-Pena,~ Geovanny I. Nic-Can, Johny Avilez-Montalvo, Jose´ E. Cetz-Chel, and Vı´ctor M. Loyola-Vargas Growing Diversity of Plant MicroRNAs and MIR-Derived Small RNAs .............................................. 49 Mariyana Gozmanova, Vesselin Baev, Elena Apostolova, Gaurav Sablok, and Galina Yahubyan An Evolutionary View of the Biogenesis and Function of Rice Small RNAs .............................................. 69 Tian Tang, Ming Wen, Pei Lin, and Yushuai Wang Small RNAs: Master Regulators of Epigenetic Silencing in Plants .... 89 Sarma Rajeev Kumar, Safia, and Ramalingam Sathishkumar Small RNA Biogenesis and Degradation in Plants ................. 107 Qiming Yu, Yaling Liu, Mu Li, and Bin Yu Plant Epigenetics: Non-coding RNAs as Emerging Regulators ....... 129 Juan Sebastian Ramirez-Prado, Federico