The authors have introduced a great method for identifying miRNA target sites through sequencing the 3' cleavage fragments and finding their potential miRNAs. The schematics of their method is shown below where they ligate a linker to the 3' cleavage fragments. Normal mRNAs would not be ligated due to the presence of a cap or lack of 5' phosphate. They subsequently amplify and sequence the ligated fragments. Their library has a great coverage and encompasses ~90% of the orfs in yeast. Their method captures 98 out 100 known miRNA target sites in arabidopsis. This batch of sequenced target sites were then used to identify the corresponding miRNA. They validate a set of their prediction which seems to work fine.
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