The aim was to characterize histone variants and PTMs in mutant plants with histone chaperone dysfunction using mass spectrometry-based approach. We found that the maintenance of genome stability via chromatin remodelling depends on a two-tiered process. The first level relies on a highly flexible mechanism that involves alterations in histone marks while the second adaptive level requires assistance of histone chaperones for the replacement of specific histone variants which is a more time-consuming process.