RBP crosslinking sites exhibit global sequence conservation. (a) Average ribosome depleted mRNA-seq and gPAR-CLIP read distributions across 5' UTR, CDS, and 3' UTR regions for all libraries. Error bar: 1 standard deviation. RPKM: reads per million mapped reads per kilobase. (b) Cumulative distribution of CLS values from wild-type (WT) libraries. (c) Proportion of Ts in crosslinking site binned by crosslinking site coverage (reads per million mapped reads (RPM)). The dashed red line indicates average T content of all crosslinking sites. (d) Number of conserved blocks in 3' and 5' UTRs overlapping 100% with WT gPAR-CLIP crosslinking sites (χ2 P-values indicated). Control blocks were randomly generated within 3' and 5' UTRs to match the number and size of conserved blocks. (e) Two major gPAR-CLIP crosslinking sites in ATG8 3' UTR (top) and TOM40 3' UTR (bottom) overlapping conserved blocks. (f) Mean phastCons scores for Ts ranked and binned by CLS. Control lines represent mean phastCons scores of randomly ranked and binned Ts with no CLS, repeated ten times.
Freeberg et al. Genome Biology 2013 14:R13 doi:10.1186/gb-2013-14-2-r13