A novel approach using aptamers for histone code analysis

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In this study, the development of new histone code analysis method was aimed by using aptamer based chromatin-affinity purification-mass spectrometry. First of all, three different histone modification (H3K4Me3, H3K9Me3, and H3K27Me3) was chosen as a target histone code since they are abundantly existed and are known as important histone PTMs by involving in gene regulations. Therefore, the first goal of this study was DNA aptamers development for those target histone PTMs.To address it, the SELEX (Systematic evolution of ligands by exponential enrichment) process was introduced by using a random DNA library and the histone modification peptide target coated magnetic beads (MBs). After several selection rounds, the final DNA pool was moved to next generation sequencing (NGS) step for DNA identification.Sequence-identified DNA aptamer candidates for each histone PTM targets were analyzed their binding affinity and target-specificity for verification of the aptamers. As a result of the characterization, aptamer 1336 has been found as H3K4Me3 specific aptamer with 13 nM of Kd. The best aptamers are ultimately applied to ISET platform for the affinity-purification and MALDI-MS analysis of histone code.