Nuclear bodies and noncoding RNAs: methods and protocols / ed. by S.Nakagawa, T.Hirose. - New York: Springer Science+Business Media: Humana press, 2015. - xii, 351 p.: ill. - (Methods in molecular biology; 1262) (Springer protocols). - Bibliogr. at the end of the chapters. - Ind.: p.349-351. - ISBN 978-1-4939-2252-9; ISSN 1064-3745 Шифр: (Pr 852/N 1262) 02  Место хранения:   02 | Отделение ГПНТБ СО РАН | Новосибирск

Оглавление / Contents

Preface ........................................................ v Contributors .................................................. ix Part I. Imaging of Noncoding RNAs and Nuclear Bodies 1 Visualization of IncRNA by Single-Molecule Fluorescence In Situ Hybridization ........................................ 3 Margaret Dunagin, Moran N. Cabili, John Rinn, and Arjun Raj 2 Super-Resolution Imaging of Nuclear Bodies by STED Microscopy .................................................. 21 Yasushi Okada and Shinichi Nakagawa 3 High-Resolution 3D DNA FISH Using Plasmid Probes and Computational Correction of Optical Aberrations to Study Chromatin Structure at the Sub-megabase Scale ............... 37 Luca Giorgetti, Tristan Piolot, and Edith Heard 4 Time-Lapse Imaging of Nuclear Bodies ........................ 55 Saskia Hutten, Samuel Swift, and Angus I. Lamond 5 Visualization of Nucleic Acids with Synthetic Exciton- Controlled Fluorescent Oligonucleotide Probes ............... 69 Dan Ohtan Wang and Akimitsu Okamoto 6 Live CLEM Imaging to Analyze Nuclear Structures at High Resolution .................................................. 89 Tokuko Haraguchi, Hiroko Osakada, and Takako Koujin 7 Ultrastructural Analysis of Nuclear Bodies Using Electron Microscopy ................................................. 105 Sylvie Souquere and Gérard Pierron 8 Analyses of Nuclear Proteins and Nucleic Acid Structures Using Atomic Force Microscopy .............................. 119 Jamie L. Gilmore, Aiko Yoshida, Hirohide Takahashi, Katashi Deguchi, Toshiro Kobori, Emilie Louvet, Masahiro Kumeta, Shige H. Yoshimura, and Kunio Takeyasu 9 Genome-Wide Co-Localization Screening of Nuclear Body Components Using a Fluorescently Tagged FLI cDNA Clone Library .................................................... 155 Tetsuro Hirose and Naoki Goshima Part II. Biochemical Analysis of Noncoding RNAs and Nuclear Bodies 10 Purification of Specific Chromatin Regions Using Oligonucleotides: Capture Hybridization Analysis of RNA Targets ( CHART) ..... 167 Christopher P. Davis and Jason A. West 11 RNA Antisense Purification (RAP) for Mapping RNA Interactions with Chromatin ................................ 183 Jesse Engreitz, Eric S. Lander, and Mitchell Guttman 12 In Situ Dissection of RNA Functional Subunits by Domain- Specific Chromatin Isolation by RNA Purification (dChIRP) .. 199 Jeffrey J. Quinn and Howard Y. Chang 13 Extracting, Enriching, and Identifying Nuclear Body Sub- Complexes Using Label-Based Quantitative Mass Spectrometry ............................................... 215 Archa Fox, Virja Mehta, Severine Boulon, and Laura Trinkle-Mulcahy 14 Studying RNA-Binding Protein Interactions with Target mRNAs in Eukaryotic Cells: Native Ribonucleoprotein Immunoprecipitation (RIP) Assays ........................... 239 Joseph A. Cozzitorto, Masaya Jimbo, Saswati Chand, Fernando Blanco, Shruti Lal, Melissa Gilbert, Jordan M. Winter, Myriam Gorospe, and Jonathan R. Brody 15 Cross-Linking and Immunoprecipitation of Nuclear RNA-Binding Proteins ....................................... 247 Quan Li, Yuri Ventura, and Yukio Kawahara 16 Purification of Noncoding RNA and Bound Proteins Using FLAG Peptide-Conjugated Antisense-Oligonucleotides ... 265 Shungo Adachi and Tohru Natsume Part III. Cell and Molecular Biological Approach Toward the Analysis of Noncoding RNAs and Nuclear Bodies 17 MMCT-Mediated Chromosome Engineering Technique Applicable to Functional Analysis of IncRNA and Nuclear Dynamics ...... 277 Makiko Meguro-Horike and Shin-ichi Horike 18 Reconstitution of Nucleocytoplasmic Transport Using Digitonin-Permeabilized Cells .............................. 291 Shingo Kose, Tomoko Funakoshi, and Naoko Imamoto 19 Genome-Wide Analysis of Long Noncoding RNA Turnover ........ 305 Hidenori Tani, Naoto Imamachi, Rena Mizutani, Katsutoshi Imamura, Yeondae Kwon, Satoru Miyazaki, Sho Maekawa, Yutaka Suzuki, and Nobuyoshi Akimitsu 20 Knockdown of Nuclear-Retained Long Noncoding RNAs Using Modified DNA Antisense Oligonucleotides .............. 321 Xinying Zong, Lulu Huang, Vidisha Tripathi, Raechel Peralta, Susan M. Freier, Shuling Guo, and Kannanganattu V. Prasanth 21 siRNA Screening of Nuclear Proteins ........................ 333 Yuko Hasegawa and Shinichi Nakagawa Index ......................................................... 349