Figure 2

Protein occupancy profiling in MCF7 cells. (A, B) Nucleotide mismatches in read mappings for both MCF7 replicate experiments. From left to right: total number of mapped reads, number of reads with zero mismatches and number of reads with exactly one mismatch followed by the occurrence of individual transitions. A high number of T-C transitions relative to perfect matching reads are indicative of efficient protein-RNA crosslinking. (C, D) Distribution of reads mapping to different RNA types for each individual MCF7 replicate experiment. (E, F) Browser view of the genomic region encoding MYC (E) and the 3' UTR of cyclin D1 (CCND1) mRNA (F). The consensus T-C transition track (in black, number of T-C transitions) and sequence coverage track (orange) of protein occupancy profiles from MCF7 cells are shown on top of each other. PhastCons conservation scores across placental mammals are shown in blue.