Long Non-Coding Rnas: Methods and Protocols

ISBN-13: 9781493933761 / Angielski / Twarda / 2016 / 298 str.

Yi Feng; PH.D . Lin Zhang

Opis

This volume assembles a broad spectrum of methods used in long non-coding RNAs (lncRNA) research, ranging from computational annotation of lncRNA genes to molecular and cellular analyses of the function of individual lncRNA. Long Non-Coding RNAs: Methods and Protocols also discusses methods used to study circular RNAs and RNA splicing, as well as influential findings on lncRNA in human diseases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Thorough and cutting-edge, Long Non-Coding RNAs: Methods and Protocols is a must-have for molecular biologists, cell and developmental biologists, specialists who conduct disease-oriented research, and bioinformatics experts who seek a better understanding on lncRNA expression and function by computational analysis of the massive sequencing data that are rapidly accumulating in recent years.

Spis treści

1.       LncRNA Pulldown Combined with Mass Spectrometry to Identify the Novel LncRNA-Associated Proteins
Zhen Xing, Chunru Lin, and Liuqing Yang

2.       Cross-Linking Immunoprecipitation and qPCR (CLIP-qPCR) Analysis to Map Interactions between Long Non-Coding RNAs and RNA-Binding Proteins
Je-Hyun Yoon and Myriam Gorospe

3.       Characterization of Long Non-Coding RNA Associated Proteins by RNA-Immunoprecipitation

Youyou Zhang, Yi Feng, Zhongyi Hu, Xiaowen Hu, Chao-Xing Yuan, Yi Fan, Lin Zhang

4.       Isolation of Protein Complexes Associated with Long Non-Coding RNAs
Kiranmai Gumireddy, Jinchun Yan, and Qihong Huang

5.       Profiling Long Non-Coding RNA Expression Using Custom-Designed Microarray
Xinna Zhang, Gabriel Lopez-Berestein, Anil K. Sood, and George A. Calin

6.       Long Non-Coding RNA Expression Profiling Using Arraystar LncRNA Microarrays
Yanggu Shi and Jindong Shang

7.       Nuclear RNA Isolation and Sequencing
Navroop K. Dhaliwal and Jennifer A. Mitchell

8.       Targeted LncRNA Sequencing with the SeqCap RNA Enrichment System
John C. Tan, Venera D. Bouriakov, Liang Feng, Todd A. Richmond, and Daniel Burgess

9.       ChIP-Seq: Library Preparation and Sequencing
Karyn L. Sheaffer and Jonathan Schug

10.   Stellaris ® RNA Fluorescence In Situ Hybridization for the Simultaneous detection of Immature and Mature Long Non-Coding RNAs in Adherent Cells
Arturo V. Orjalo, Jr., and Hans E. Johansson

11.   Simultaneous RNA-DNA FISH
Lan-Tian Lai, Zhenyu Meng, Fangwei Shao & Li-Feng Zhang

12.   Visualizing Long Non-Coding RNAs on Chromatin
Michael Hinten, Emily Maclary, Srimonta Gayen, Clair Harris, and Sundeep Kalantry

13.   Non-Isotopic Method for In Situ LncRNA Visualization and Quantitation
Botoul Maqsodi and Corina Nikoloff

14.   Detection of Long Non-Coding RNA Expression by Non-Radioactive Northern Blots
Xiaowen Hu, Yi Feng, Zhongyi Hu, Youyou Zhang, Chao-Xing Yuan, Xiaowei Xu, and Lin Zhang

15.   Assessment of In Vitro SiRNA Delivery in Cancer Mouse Models
Hiroto Hatakeyama, Sherry Y. Wu, Lingegowda S. Mangala, Gabriel Lopez-Berestein, and Anil K. Sood

16.   Targeting Long Non-Coding RNA with Antisense Oligonucleotide Technology as Cancer Therapeutics
Tianyuan Zhou, Youngsoo Kim, and A. Robert Macleod

17.   Characterization of Circular RNAs
Yang Zhang, Li Yang, and Ling-Ling Chen

18.

   Methods for Characterization of Alternative RNA Splicing
Samuel E. Harvey and Chonghui Cheng

19.   NONCODEv4: Annotation of Non-Coding RNAs with Emphasis on Long Non-Coding RNAs
Yi Zhao, Jiao Yuan, and Runsheng Chen

20.   Computational Analysis of LncRNA from cDNA Sequences
Susan Boerner and Karen M. McGinnis

21.   Analyzing MiRNA: LncRNA Interactions
Maria D. Paraskevopoulou and Artemis G. Hatzigeoriou

22.   Long Non-Coding RNAs: An Overview
Dongmei Zhang, Minmin Xiong, Congjian Xu, Peng Xiang, and Xiaomin Zhong