Computational protocol: The Characterization of microRNA-Mediated Gene Regulation as Impacted by Both Target Site Location and Seed Match Type

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Protocol publication

[…] Site accessibility has been used to measure the degree of difficulty in opening the mRNA sequences for miRNA targeting and binding. We used the accessibility energy ΔΔG introduced by to measure the site accessibility for miRNA target sites of different seed match types and located in different gene regions. The metrics incorporates both the binding energy of forming the miRNA-target duplex (ΔGduplex), and the energy cost of making the target site accessible (ΔGopen), including the cost of unpairing additional bases flanking downstream and upstream of the target site. The accessibility energy ΔΔG is the difference between the binding energy ΔGduplex, calculated by RNAhybrid , and the free energy to unpair the target site nucleotides ΔGopen, calculated by RNAfold . Each target site consists of 21 nucleotides bound to miRNAs, 17 flank upstream nucleotides and 10 flank downstream nucleotides. In this study, we used the Z-score of ΔΔG to measure the extent to which the site accessibility deviates from random expectation, similar to that in . The Z-score of ΔΔG is defined in ). (1) Here, is site accessibility for the naturally occurring target region under consideration. is the mean of which is for the target region in the ith permuted sequence. n is the total number of permuted sequences, and is equal to 1,000 in this study. […]

Pipeline specifications

Software tools RNAhybrid, RNAfold
Application RNA structure analysis