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

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FIGURE 3.
FIGURE 3.

Discrimination between bound and unbound sites as a function of the accessibility threshold Pcutoff and of the length n of the nucleation region. (A) Discrimination D is shown as a function of Pcutoff for all possible lengths n. (B) Fraction of the accessible among bound sites [P(A|B)] plotted as a function of Pcutoff for all lengths n. (C) Fraction of the accessible among unbound sites [P(A|B)] plotted as a function of Pcutoff for all lengths n. (D) Discrimination is shown as a function of the length of the nucleation region while maintaining the same total number of accessible sites. For each length n, we show the cases for which approximately 10 or 13 million accessible sites were obtained. In each case, the corresponding value of Pcutoff is indicated above the bar. Statistical significance was evaluated with the unpaired one-sided t-test.

This Article

  1. RNA 18: 1760-1770