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. Author manuscript; available in PMC: 2016 Nov 4.
Published in final edited form as: Curr Opin Plant Biol. 2015 Jun 26;27:36–43. doi: 10.1016/j.pbi.2015.05.021

Figure 1. Confounding factors in PIP-seq.

Figure 1

Diagrammatic representation of PIP-seq limitations in RNA secondary structure and RNA-protein interaction site probing. (A) A schematic of the ideal case in which a transcript has a large structural feature and distinct protein binding sites. (B) An example of a small bulge within a highly structured region, which may be undetectable by PIP-seq. (C) Multiple adjacent proteins, will likely undergo crosslinking during formaldehyde treatment and become represented as one large protein interaction site.