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PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution

  • Zhipeng Lu
  • Jing Gong
  • Qiangfeng Cliff Zhang
Part of the Methods in Molecular Biology book series (MIMB, volume 1649)

Abstract

RNA has the intrinsic propensity to form base pairs, leading to complex intramolecular and intermolecular helices. Direct measurement of base pairing interactions in living cells is critical to solving transcriptome structure and interactions, and investigating their functions (Lu and Chang, Curr Opin Struct Biol 36:142–148, 2016). Toward this goal, we developed an experimental method, PARIS (Psoralen Analysis of RNA Interactions and Structures), to directly determine transcriptome-wide base pairing interactions (Lu et al., Cell 165(5):1267–1279, 2016). PARIS combines four critical steps, in vivo cross-linking, 2D gel purification, proximity ligation, and high-throughput sequencing to achieve high-throughput and near-base pair resolution determination of the RNA structurome and interactome in living cells. In this chapter, we aim to provide a comprehensive discussion on the principles behind the experimental and computational strategies, and a step-by-step description of the experiment and analysis.

Key words

Psoralen Cross-linking AMT (4′-aminomethyltrioxsalen hydrochloride) RNA structure RNA–RNA interaction 2D gel electrophoresis Proximity ligation High-throughput sequencing 

Notes

Acknowledgment

The authors wish to thank Dr. Howard Chang at Stanford University for his generous support and encouragement. Z.L. is a Layton Family Fellow of the Damon Runyon-Sohn Foundation Pediatric Cancer Fellowship Award (DRSG-14-15). This work was supported by the National Natural Science Foundation of China (31671355) and the National Thousand Young Talents Program of China to Q.C.Z., and by the Jump Start Award for Excellence in Research to Z.L. (Stanford University, award No. 106).

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  1. 1.Department of Dermatology, Center for Personal Dynamic RegulomesStanford UniversityStanfordUSA
  2. 2.MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life SciencesTsinghua UniversityHaidian, BeijingChina

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