Histone protein profiling in rice reveals a correlation between canonical and noncanonical function and evolution

Histones epitomize the key protein module of chromatin and act as important signatures for many biological processes, such as replication, cell cycle regulation, transcription, translation, and apoptosis. The past decade has seen major advances in our understanding of histone and nucleosome structure, function, and dynamics in plants, but it is restricted to a few species. The major challenge is to isolate high-quality histone and its variants due to the presence of cell walls and to identify novel protein variants and isoforms. Here, we optimized the histone extraction protocol for rice tissue and developed the histone proteome map by 1-DE and LC–MS/MS analysis. A total of 19 histones and their variants were identified, encompassing core and linker histones. Using rigorous statistical algorithms, we outline different motifs, domains, and families of identified histones related to their functionality. Chromosome distribution of histones revealed that dispersed gene clusters and gene duplication events have evolutionary implications. To establish a correlation between protein chemistry and function, the physicochemical analysis was performed using web-based tools. Functional cataloging uncovered known and novel roles of histones, including nucleosome assembly, DNA recombination, chromatin silencing, double fertilization, development, and gene expression regulation. Phylogenetic studies guided by statistical analysis pointed out that histone genes undergo concerted evolution to maintain sequence homogeneity. Taken together, these results provide insights into rice histone dynamics, including sequence variation, conservation, gene structure, function, and diversification events during the evolution.