PAR-CLIP background reads contain many T-to-C conversions that have G-rich motifs. A) Pie charts of all PARalyzer utilized reads from HuR PAR-CLIP and the three background gel slices (G45, G35 and G20) that contain T-to-C conversions, suggesting crosslinked events. PARalyzer utilized reads are defined as sequences containing 0, 1 or 2 T-to-C conversions that map uniquely to the human reference genome. B) Pie charts of genomic location where HuR, total RNA and background clusters map to in human reference genome. Background clusters are union of all three background samples. Total RNA was prepared from 4SU-containing, crosslinked lysates that were partially digested with RNase T1. C) Motif logo of top 25 occurring 8mer motifs by union of all three background samples. The G-rich motif is significantly enriched compared to shuffled sequences preserving di-nucleotide frequencies of the library (p-value = 7.04 × 10-8).
Friedersdorf and Keene Genome Biology 2014 15:R2 doi:10.1186/gb-2014-15-1-r2