Main description:

This detailed volume explores the continuing techniques of
studying RNA-protein complexes and interactions as research in these areas
expand. After an introductory chapter,
the book continues with ways to purify RNA-protein complexes assembled in cells
or in isolated cellular extracts, methods for measuring various biochemical
activities of RNA-interacting proteins or ribonucleoproteins, biochemical
methods for measuring direct RNA-protein contact, as well as various new or
innovative methods pertinent to the subject. Written for the highly successful Methods in Molecular Biology series,
chapters contain brief 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 up-to-date, RNA-Protein
Complexes and Interactions: Methods and Protocols provides a set of useful
protocols, both basic and advanced, designed to inspire researchers working
with RNA and RNA-interacting proteins.

Contents:

1. Characterization of RNA-Protein
Interactions: Lessons from Two RNA-Binding Proteins, SRSF1 and SRSF2

Lindsey
Skrdlant and Ren-Jang Lin

2. Identification of mRNA-Interacting Factors by
MS2-TRAP (MS2-Tagged RNA Affinity Purification)

Je-Hyun Yoon and Myriam Gorospe

3. Biotin-Streptavidin Affinity Purification of
RNA-Protein Complexes Assembled In Vitro

Shuai Hou, Lei Shi, and
Haixin Lei

4. Detecting RNA-Protein Interaction Using End-Labeled Biotinylated
RNA Oligonucleotides and Immunoblotting

Xuexiu Zheng, Sunghee Cho, Heegyum
Moon, Tiing Jen Loh, Hana Jang, and Haihong Shen

5. Purification of RNA-Protein Splicing Complexes Using a
Tagged Protein from In Vitro Splicing Reaction Mixture

Naoyuki Kataoka

6. Loading of Argonaute Protein with Small
Duplex RNA in Cellular Extracts

Keith T. Gagnon

7. In Vitro Analysis of Ribonucleoprotein Complex
Remodeling and Disassembly

Hua-Lin Zhou and Hua Lou

8. Single-Turnover Kinetics of Methyl
Transfer to tRNA by Methyltransferases

Ya-Ming Hou

9. Purification and Functional Reconstitution of Box
H/ACA Ribonucleoprotein Particles

Chao Huang, Guowei Wu, and Yi-Tao Yu

10. Northwestern Blot Analysis: Detecting RNA-Protein
Interaction After Gel Separation of Protein Mixture

Shangbing Zang and Ren-Jang Lin

11. Measuring mRNA Translation by Polysome Profiling

Marek Kudla and Fedor V. Karginov

12. Genome-Wide Profiling of RNA-Protein
Interactions Using CLIP-Seq

Cheryl Stork and Sika Zheng

13. Identification of Endogenous mRNA-Binding Proteins in
Yeast Using Crosslinking and PolyA Enrichment

Sarah F. Mitchell and Roy Parker

14. Ribo-Proteomics Approach to Profile RNA-Protein and
Protein-Protein Interaction Networks

Hsin-Sung Yeh, Jae-Woong Chang, and
Jeongsik Yong

15. Detection of Protein-Protein Interaction Within an
RNA-Protein Complex Via Unnatural-Amino-Acid-Mediated Photochemical
Crosslinking

Fu-Lung Yeh, Luh Tung,
and Tien-Hsien Chang

16. Evolution of Cell-Type-Specific RNA
Aptamers Via Live Cell-Based SELEX

Jiehua Zhou and John J. Rossi

17. mCarts: Genome-Wide Prediction of Clustered Sequence
Motifs as Binding Sites for RNA Binding Proteins

Sebastien M. Weyn-Vanhentenryck and
Chaolin Zhang

18. Design of RNA-Binding Proteins:
Manipulate Alternative Splicing in Human Cells with Artificial Splicing Factors

Yang Wang and Zefeng Wang

19. Informational Suppression to Probe RNA:RNA
Interactions in the Context of Ribonucleoproteins: U1 and 5' Splice-Site
Base-Pairing

Jiazi Tan and Xavier Roca

20. Analysis of Alternative Pre-RNA Splicing in the Mouse
Retina Using a Fluorescent Reporter

Daniel Murphy, Saravanan
Kolandaivelu, Visvanathan Ramamurthy, and Peter Stoilov