Plant Long Non-Coding RNAs

<p>Preface…<br>Table of Contents…<br>Contributing Authors…<br><br>1 An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK!<br>Hsiao-Lin V. Wang and Julia A. Chekanova<br><br>Part I Role of ncRNAs in Regulation of Gene Expression and Development in Plants<br><br>2 Analysis of siRNA Precursors Generated by RNA Polymerase IV and RNA-Dependent RNA Polymerase 2 in Arabidopsis<br>Todd Blevins, Ram Podicheti, and Craig S. Pikaard<br><br>3 Identification of Long Non-Coding RNAs in the Developing Endosperm of Maize<br>Eundeok Kim, Yuqing Xiong, Byung-Ho Kang, and Sibum Sung&nbsp;<br><br>4 RNA Isolation and Analysis of lncRNAs from Gametophytes of Maize<br>Linqian Han, Lin Li, Gary J. Muehlbauer, John E. Fowler, and Matthew M. S. Evans<br><br>Part II Studying the Tissue and Cell-Type Specific lncRNAs<br><br>5 Improved Method of RNA Isolation from Laser Capture Microdissection (LCM) Derived-Plant Tissues<br>Vibhav Gautam, Archita Singh, Sharmila Singh, Swati Verma, and Ananda K. Sarkar<br><br>6 Medium Throughput RNA In Situ Hybridization of Serial Sections from Paraffin-Embedded Tissue Microarrays<br>Edith Francoz, Philippe Ranocha, Christophe Dun, and Vincent Burlat<br><br>7 Purification and Functional Analysis of Plant Long Non-Coding RNAs (lncRNA)<br>Trung Do, Zhipeng Qu, and Iain Searle<br><br>Part III Studying lncRNAs Associated with Response to Abiotic and Biotic Stresses in Plants&nbsp;<br><br>8 The Involvement of Long Non-Coding RNAs in Response to Plant Stress<br>Akihiro Matsui and Motoaki Seki<br><br>9 Subcellular Localization and Functions of Plant lncRNAs in Drought and Salt Stress Tolerance<br>Tao Qin and Liming Xiong<br><br>10 Discovery, Identification, and Functional Characterization of Plant Long Intergenic Non-Coding RNAs after Virus Infection<br>Ruimin Gao, Peng Liu, Nadia Irwanto, De Rong Loh, and Sek-Man Wong<br><br>Part IV Identification and Functional Analysis of lncRNAs<br><br>11 Bioinformatics Approaches to Studying Plant Long Non-Coding RNAs (lncRNAs): Identification and Functional Interpretation of lncRNAs from RNA-seq Data Sets<br>Hai-Xi Sun and Nam-Hai Chua<br><br>12 Identification of Novel lincRNA and Co-Expression Network Analysis using RNA Sequencing Data in Plants<br>Song Qi, Shamima Akter, and Song Li<br><br>13 An Easy-to-Follow Pipeline for Long Non-Coding RNA Identification: A Case Study in Diploid Strawberry Fragaria vesca<br>Chunying Kang and Zhongchi Liu<br><br>14 Reference-Based Identification of Long Non-Coding RNAs in Plants with Strand-Specific RNA-Sequencing Data<br>Xiao Lin, Meng Ni, Zhixia Xiao, Ting-Fung Chan, and Hon-Ming Lam<br><br>15 NAMS: Non-Coding Assessment in Magnoliophyta Species<br>Gaurav Sablok, Kun Sun, and Hao Sun<br><br>16 De novo Plant Transcriptome Assembly and Annotation using Illumina RNA-seq Reads<br>Stephanie C. Kerr, Federico Gaiti, and Milos Tanurdzic<br><br>Part V Purification of lncRNAs and Ribonucleoprotein Complexes, RNA Secondary Structure, and RNA Modifications<br><br>17 Identification of Long Non-Coding RNA-Protein Interactions through In Vitro RNA Pull-Down Assay with Plant Nuclear Extracts<br>Jun Sung Seo and Nam-Hai Chua<br><br>18 Analysis of Interaction between Long Non-Coding RNAs and Protein by RNA-Immunoprecipitation in Arabidopsis<br>Jun Sung Seo and Nam-Hai Chua<br><br>19 Trimolecular Fluorescence Complementation (TriFC) Assay for Visualization of RNA-Protein Interaction in Plants<br>Jun Sung Seo and Nam-Hai Chua<br><br>20 In Vivo Genome-Wide RNA Structure Probing with Structure-seq2<br>Laura E. Ritchey, Zhao Su, Sarah M. Assmann, and Philip C. Bevilacqua<br><br>21 Using Protein Interaction Profile Sequencing (PIP-seq) to Identify RNA Secondary Structure and RNA-Protein Interaction Sites of Long Non-Coding RNAs in Plants<br>Marianne C. Kramer and Brian D. Gregory<br><br>22 Computationally Characterizing Protein Bound Long Non-Coding RNAs and their Secondary Structure using Protein Interaction Profile Sequencing (PIP-seq) in Plants<br>Mengge Shan, Zachary D. Anderson, and Brian D. Gregory<br><br>23 Stalking Structure in Plant Long Non-Coding RNAs<br>Karissa Y. Sanbonmatsu<br><br>24 Transcriptome-Wide Mapping 5-methylcytosine by m5C RNA Immunoprecipitation Followed by Deep Sequencing in Plant<br>Xiaofeng Gu and Zhe Liang&nbsp;<br><br>Part VI Databases of Plant lncRNAs and How to Use Them&nbsp;<br><br>25 A Walkthrough to the Use of GreeNC: The Plant lncRNA Database<br>Andreu Paytuví, Walter Sanseverino, and Riccardo Aiese Cigliano<br><br>26 CANTATAdb 2.0: Expanding the Collection of Plant Long Non-Coding RNAs<br>Michał Wojciech Szcześniak, Oleksii Bryzghalov, Joanna Ciomborowska-Basheer, and Izabela Makałowska<br><br>27 Experimentally Validated Plant lncRNAs in EVLncRNAs Database<br>Bailing Zhou, Huiying Zhao, Jiafeng Yu, Chengang Guo, Xianghua Dou, Feng Song, Guodong Hu, Zanxia Cao, Yuanxu Qu, Yuedong Yang, Yaoqi Zhou, Jihua Wang<br><br>Part VII Long-Range Chromatin Interactions and Chromosome Conformation Capture<br><br>28 In Situ Hi-C for Plants: An Improved Method to Detect Long-Range Chromatin Interactions<br>Sudharsan Padmarasu, Axel Himmelbach, Martin Mascher, and Nils Stein</p>