Genomic position and motif preferences for subcellular HuR. (A) Metagene profiles for HuR binding for input CLIP or coCLIP under mock or arsenite conditions centered on indicated mRNA features: transcription starts, start codons, 5′ and 3′ splice sites, 3′-UTR starts, and 3′-UTR ends. The number of peaks for each metagene profile is shown in the upper left corner. (B) Correlation matrix for HuR peak binding for all CLIP experiments by type. (Frac CLIP) Fractionation CLIP. (C) HuR binding motif ranks for all CLIP and coCLIP experiments ordered by PAR-CLIP rankings from Mukherjee et al. (2011). (D) Motif density within HuR peaks (top) and cumulative distribution for frequency of the UUUUU motif (bottom) in input CLIP or coCLIP in mock or stress conditions. (E) Motif density within HuR peaks (top) and cumulative distribution for frequency of the AAAAA motif (bottom) as in D. Indicated P-values calculated by Kolmogorov–Smirnov test.
