Identification of crosslinking-induced mutations (CIMs) in CLASH data at piRNA and miRNA targeting sites. (A) A model illustrating the CLASH experimental procedure of PIWI and Argonaute complexes and the production of CIMs during cDNA synthesis. (B) A flowchart of MUTACLASH analysis pipeline for identifying small RNA–mRNA hybrids and for analyzing CIMs from PIWI and Argonaute CLASH data. (C) The distribution of deletions (left) and substitutions (middle) on targeting mRNAs identified from hybrid reads from ALG-1 Argonaute iCLIP data (let-7 and lin-14) or PRG-1 PIWI CLASH data (21ur-1563 and 21ur-4863). The base-pairing between miRNA (let-7 and lin-14) or piRNA (21ur-1563 and 21ur-4863) and the targeting mRNAs is shown (right). The seed region of miRNA (let-7 and lin-14) or piRNA (21ur-1563 and 21ur-4863) is underlined.
