Analysis of the accessibility of CLIP bound sites reveals that nucleation of the miRNA:mRNA pairing occurs preferentially at the 3′-end of the seed match

Comparison of accessibility (P_u) and other thermodynamic features as predictors of site functionality. Discrimination D based on the accessibility is shown for different lengths and locations of the nucleation region: n = 7 (labeled as P_u (7-mer)), n = 4 restricted to the 3′-end (labeled as P_u (3′ 4-mer)), and n = 4 restricted to the 5′-end (labeled as P_u (5′ 4-mer)). Discrimination values based on hybridization (E_hybrid), opening (E_open), and interaction (E_interaction) energies are also shown (see Materials and Methods). Statistical significance was evaluated with the unpaired one-sided t-test. Results are based on the PAR-CLIP data set.