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. Author manuscript; available in PMC: 2016 Oct 18.
Published in final edited form as: Nat Chem Biol. 2015 Nov 17;11(12):933–941. doi: 10.1038/nchembio.1958

Figure 5. Outstanding challenges for understanding RNA structure inside living cells.

Figure 5

(a) Outline of an experiment for interrogating RNA structure formation during transcription. In such a case a modified nucleoside can be introduced into the cell and then used to enrich for co-transcriptionally probed RNA structure. (b) A schematic for the design of a dual-functioning chemical probe to measure RNA structure within unique subcellular compartments. (c) A depiction of how a chemical probe can be used to identify three-dimensional contacts within folded RNAs. The results are mapped to an interaction map, depicting the spatial relationship between two points in the RNA sequence. (d) A schematic for the recently developed method known as hiCLIP84. In hiCLIP non-contiguous reads are mapped to genes and represented by rainbow maps to connect primary sequence points through space.