MRP1 iCLIP analysis. (A) Schematic depiction of the MRP1 iCLIP workflow to purify UV-crosslinked RNA-MRP1 complexes and sequence the mRNAs. (B) Schematic representation of the problem of iCLIP mapping assignment ambiguity due to the presence of editing intermediates in the transcriptome. Many of the approximately 30 to 50 nt iCLIP tags can be attributed to a partially edited or to a pre/fully edited version of a transcript. Therefore, the editing state of a transcript from which an iCLIP tag was derived cannot be unambiguously defined. Small blue boxes depict editing events. (C) Illustration of the MRP1 iCLIP read mapping strategy. Preprocessed iCLIP reads were mapped against maxicircle-encoded mRNAs. (Top) iCLIP reads mapped to reference sequences existing on the maxicircle; namely, never-edited and pre-edited mRNA sequences. (Bottom) iCLIP reads mapped to fully edited sequences of edited mRNAs. Pan-, minimally, and never-edited mRNAs are marked in blue, gray, and black, respectively.
