Secondary analysis of a public UPF1 iCLIP data set. We analyzed the data sets of UPF1-iCLIP experiments on untreated HeLa cells and cells treated with puromycin (Zünd et al. 2013) to determine whether UPF1 associated with histone mRNAs. (A) A representative histone mRNA, HIST1H2AL, is shown. The RPMM across the histone mRNA (top) and the reverse transcriptase (RT) termini, which give the site of crosslinking (bottom) are plotted. (B) Our SLBP HITS-CLIP data for the HIST1H2AL gene are shown. The RPMM (top), the single nucleotide deletion (1D) rate (middle), and the fragment termini (bottom) determined using our cleavage-mapping algorithm, are plotted in the 3.0 GU Mnase SLBP HITS-CLIP data from two specified size ranges. (C) The HIST1H2AL gene model graphic is shown below with the CDS and UTRs indicating CDS boundaries. (D) The phyloP (Pollard et al. 2010) placental mammal conservation score (Meyer et al. 2013) is shown for each nucleotide of the mature HIST1H2AL mRNA. (E) A cartoon depicting the potential arrangement of proteins on a generic RD-histone mRNA 3′ end (Isken and Maquat 2008).
