Main description:

This second edition provides 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. Chapters guide readers through studies used to circular RNAs, RNA splicing, and 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.

Authoritative and cutting-edge, Long Non-Coding RNAs: Methods and Protocols,Second Edition aims to ensure successful results in the further study of this vital field.

Contents:

1. LncRNA pulldown Combined with Mass Spectrometry to Identify the Novel lncRNA-associated Proteins

Zhen Xing, Sergey Egranov, Chunru Lin, and Liuqing Yang

2. Cross-Linking Immunoprecipitation and qPCR (CLIP-qPCR) Analysis to Map Interactions of Long Noncoding RNAs with Canonical and Non-canonical RNA-binding Proteins

Jung-Hyun Cho, Ji Won Lee, Je-Hyun Yoon, and Kyung-Won Min

3. Characterization of Long Non-coding RNA Associated Proteins by RNA-immunoprecipitation

Junjie Jiang, Tianli Zhang, Yutian Pan, Zhongyi Hu, Jiao Yuan, Xiaowen Hu, Lin Zhang, and Youyou Zhang

4. Isolation of Protein Complexes Associated with Long Non-Coding RNAs

Min Li, Ying Xue, Ruiping He, and Qihong Huang

5. Detection of Long Noncoding RNA Expression by Real-time PCR

Rui Huang, Yihao Wang, Yaqi Deng, and Jianfeng Shen

6. Profiling Long Non-coding RNA expression using Custom-Designed Microarray

Xinna Zhang and George A. Calin

7. Long Non-coding RNA Expression Profiling using Arraystar LncRNA Microarrays

Yanggu Shi and Jindong Shang

8. Nuclear RNA Isolation and Sequencing

Navroop K Dhaliwal and Jennifer a Mitchell

9. Capturing Endogenous Long Noncoding RNAs and Their Binding Proteins Using Chromatin Isolation by RNA Purification

Jongchan Kim and Li Ma

10. Purification and Structural Characterization of the Long Noncoding RNAs

Allison Yankey, Sean C. Clark, Michael C. Owens, and Srinivas Somarowthu

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

12. Highly Resolved Detection of Long Non-coding RNAs In Situ

Megan Trotter, Clair Harris, Marissa Cloutier, Milan Samanta, and

Sundeep Kalantry

13. Detection of Long Non-coding RNA Expression by Non-radioactive Northern Blots

Yueying Wang, Mu Xu, Yuan Jiao, Zhongyi Hu, Youyou Zhang, Lin Zhang, and Xiaowen Hu

14. Assessment of in vivo siRNA Delivery in Cancer Mouse Models

Lingegowda S. Mangala, Cristian Rodriguez-Aguayo, Emine Bayraktar, Nicholas B. Jennings, Gabriel Lopez-Berestein, and Anil K. Sood

15. Genetic Editing of Long Non-Coding RNA Using CRISPR/Cas9 Technology

Kristina Larter, Bin Yi, and Yaguang Xi

16. Characterization of Circular RNAs

Yang Zhang, Li Yang, and Ling-Ling Chen

17. Identification of circRNA-Interacting Proteins by Affinity Pulldown

Jen-Hao Yang, Poonam R. Pandey, and Myriam Gorospe

18. Exploration to Circular RNA Interactomes by RNA Pull-Down Method

Mengshi Wu, Dan Peng, and Xiaomin Zhong

19. Methods for Characterization of Alternative RNA Splicing

Samuel E. Harvey, Jingyi Lyu, and Chonghui Cheng

20. Computational analysis of lncRNA from cDNA sequences

Susan Boerner and Karen M. McGinnis

21. Characterizing miRNA-lncRNA interplay

Dimitra Karagkouni, Anna Karavangeli, Maria D Paraskevopoulou, and Artemis G Hatzigeorgiou

22. Illuminating lncRNA Function through Target Prediction

Hua-Sheng Chiu, Sonal Somvanshi, Ting-Wen Chen, and Pavel Sumazin

23. Long Noncoding RNAs: An Overview

Dongmei Zhang, Mengshi Wu, Minmin Xiong, Congjian Xu, Peng Xiang, and Xiaomin Zhong