Breaking Boundaries in Histone Modification MS-based Detection: A Tailored Search Strategy for Unrestricted identification of novel epigenetic marks

ABSTRACT: Histone post-translational modifications (PTMs) are crucial for gene expression regulation and DNA maintenance, and their aberrations are linked to multiple diseases, like cancer. While functions related to lysine acetylation and methylation have been well-studied, recent studies have uncovered additional PTMs that also contribute significantly to chromatin structure and function. Mass Spectrometry (MS) is the most effective analytical method for studying histone PTMs, but computational limitations often restrict the analysis to common modifications. Unrestrictive search strategies hold the potential for an in-depth characterization of the histone modifications landscape. In this work, we carry out a systematic assessment of the application of unrestrictive search approaches to histone data. We assess the limitations of these approaches, and we implement and test an optimized bioinformatics workflow, HiP-Frag (Histone PTMs analysis with FragPipe), which allows the identification of 201 sites modified by uncommon modifications (127 of these were previously unreported) on core histones and 82 modified sites on the linker histones purified form human cell lines and primary samples, greatly contributing to the expansion of the catalogue of histone modifications. The comprehensive analysis of histone PTMs enabled by this strategy is one of the first to leverage previously unexplored epigenetic information in MS raw data. This approach opens the door to identifying uncommon, difficult-to-detect, and yet unannotated histone modifications, leading to a more complete annotation of the histone code and a potential deeper understanding of the roles of novel, less-characterized histone marks in both physiological and disease conditions.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Breast, Cell Culture

SUBMITTER: Alessandro Vai  

LAB HEAD: Tiziana Bonaldii

PROVIDER: PXD061934 | Pride | 2025-11-11

REPOSITORIES: Pride