The RNA Base-Pairing Problem and Base-Pairing Solutions

RNA molecules are folded into structures and complexes to perform a wide variety of functions. Determination of RNA structures and their interactions is a fundamental problem in RNA biology. Most RNA molecules in living cells are large and dynamic, posing unique challenges to structure analysis. Here we review progress in RNA structure analysis, focusing on methods that use the "cross-link, proximally ligate, and sequence" principle for high-throughput detection of base-pairing interactions in living cells. Beginning with a comparison of commonly used methods in structure determination and a brief historical account of psoralen cross-linking studies, we highlight the important features of cross-linking methods and new biological insights into RNA structures and interactions from recent studies. Further improvement of these cross-linking methods and application to previously intractable problems will shed new light on the mechanisms of the "modern RNA world." Outline 1 The everlasting RNA structure problem and ever-evolving solutions 2 Historical use of psoralen to analyze RNA structures and interactions 3 The next generation: Cross-linking with proximity ligation and high-throughput sequencing 4 Basic analysis of RNA structure cross-linking data 5 Prevalent long-range structures in the transcriptome 6 Conservation analysis of the RNA structures 7 Dynamic and complex structures: Catching RNA in action 8 Architecture of the XIST RNP: Modular structures for modular functions 9 Novel RNA-RNA interactions: The molecular social network 10 Limitations of the psoralen cross-linking methods and future directions 11 Integrating methods to solve complex RNA structures and interactions References