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A methodology paper for histone variant peptide quantitation

Yu, Yanyan and chen , Jiajia and Gao, Jun and Liao, Rijing and Oyang, Counde and Li, En and Jin, Hong and Yang, Pengyuan and Zhou, Shaolian and Yi, Wei (2016) A methodology paper for histone variant peptide quantitation. Quantitative Profiling of Combinational K27/K36 Modifications on Histone H3 Variants in Mouse Organs..

Abstract

Co-existing Post-Translational Modifications (PTMs) on histone H3 were shown to have positive or negative interplay between each other, indicating their dependency and crosstalk in the epigenetic regulation pathways. Recent reports have shown that an important activating mark, H3K36 methylation, is antagonizing with PRC2 mediated K27 methylation with interesting crosstalk mechanism during transcription regulation.(1) Our previous study demonstrated that a multiple reaction monitoring (MRM) based LC-MS/MS method can be used to quantitatively profile global histone H3 post-translational modifications (PTMs) with stable isotopic labeled peptides as internal standards.(30) To further develop this method for in-depth understanding of different histone variants with distinct epigenetic roles, we herein report an integrated MRM method with RP/HILIC combination to analyze histone peptides, especially the combinatorial K27/K36 peptides of all three major H3 variants, from various mouse tissues/organs. Despite subtle biochemical differences in H3 variants, we successfully obtained decent separation and high sensitivity for histone H3.3 specific peptides and histone H3.1/3.2 specific peptides by optimizing the column selection and MS response in the combined HILIC/RP-MRM methods. Meanwhile, the sensitivity for low-abundant K4 methylation peptides was greatly improved. From the quantitative results of 4 mouse tissues/organs, we observed unique combinatorial K27/K36 modification patterns of histone variants indicating distinct histone codes in epigenetic regulation during cell differentiation and developmental process. The expression abundance of H3.3 was simultaneously measured in these mouse samples suggesting its different molecular functions in different functional organs.

Item Type: Article
Date Deposited: 27 Apr 2016 23:45
Last Modified: 27 Apr 2016 23:45
URI: https://oak.novartis.com/id/eprint/25034

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