Histone sequence variation in divergent eukaryotes facilitates diversity in chromatin packaging

Abstract

The histone proteins defining nucleosome structure are highly conserved in common model organisms and are frequently portrayed as uniform chromatin building blocks. We surveyed over 1700 complete eukaryotic genomes and confirm that almost all encode recognisable canonical core histones. Nevertheless, divergent eukaryotes show unrecognised diversity in histone sequences and offer an opportunity to observe the potential for nucleosome variation. Recombinant histones for Plasmodium falciparum, Giardia lamblia, Encephalitozoon cuniculi and Leishmania major were prepared alongside those for human, Xenopus laevis and Saccharomyces cerevisiae. All could be assembled into nucleosomes in vitro on sequences known to direct positioning with metazoan histones. P. falciparum histones refolded into very stable nucleosomes consistent with a highly regulated transcriptional programme. In contrast, G. lamblia and E. cuniculi histones formed less stable nucleosomes and were prone to aggregation as H3-H4 tetramers. Inspection of the histone fold dimer interface residues suggested a potential to form tetrasomal arrays consistent with polymerisation. DNA binding preferences observed using systematic evolution of ligands by exponential enrichment (SELEX) for human, P. falciparum and E. cuniculi histone octamers were highly similar and reflect a shared capability to package diverse genomic sequences. This demonstrates that nucleosomal organisation is retained across eukaryotes and can accommodate genome variation, but histone protein sequences vary more than commonly recognised to provide the potential for diversity of chromatin features. Significance statementIt is widely assumed that eukaryotes package their genomes using equivalent nucleosome building blocks despite considerable variation in the composition and behaviour of cell nuclei. Our survey of available eukaryote genomes shows that histone proteins from divergent eukaryotes vary much more widely in sequence than is commonly recognised, even in histone fold dimer and DNA interaction interfaces. We demonstrate that divergent eukaryote histones nevertheless form nucleosomes on DNA sequences favoured in metazoans. These nucleosomes vary in stability but share broad DNA sequence preferences. This suggests that histone-dependent packaging does not constrain genome variation, and that chromatin behaviour can adapt by evolution of canonical core histone sequences in addition to other well-known mechanisms.