Technologies to probe functions and mechanisms of long noncoding RNAs

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Thousands of long noncoding RNAs (lncRNAs) have been discovered, but their functional characterization has been slowed by a limited set of research tools. Here we review emerging RNA-centric methods to interrogate the intrinsic structure of lncRNAs as well as their genomic localization and biochemical partners. Understanding these technologies, including their advantages and caveats, and developing them in the future will be essential to progress from description to comprehension of the myriad roles of lncRNAs.

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Figure 1: ChIRP sequencing (ChIRP-seq) and its applications.
Figure 2: Workflow of high-throughput RNA structure and RNA-protein analysis.
Figure 3: Knowledge gained by the use of various technologies can accelerate the virtuous cycle of developing biological insights and RNA engineering iteratively.


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We thank members of our laboratory for thoughtful discussions. This work was supported by the Singapore Agency for Science, Technology, and Research (A*STAR to C.C.), the A.P. Giannini Foundation (R.C.S.) and the US National Institutes of Health (H.Y.C.). H.Y.C. is supported as an Early Career Scientist of the Howard Hughes Medical Institute.

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Correspondence to Robert C Spitale or Howard Y Chang.

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Competing interests

C.C. and H.Y.C. are inventors of a patent on ChIRP technology held by Stanford University. R.C.S. and H.Y.C. are inventors of a patent on SHAPE probes held by Stanford University.

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Chu, C., Spitale, R. & Chang, H. Technologies to probe functions and mechanisms of long noncoding RNAs. Nat Struct Mol Biol 22, 29–35 (2015) doi:10.1038/nsmb.2921

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