Proteomics reveals conserved features of histone biology in dinoflagellates
Current knowledge of DNA packaging in eukaryotic nuclei largely centers on its basic unit, the nucleosome. Multiple lineages have, however, diverged from this paradigm, most notably dinoflagellates. Among other molecular oddities, these enigmatic protists have enormous genomes, permanently condensed chromosomes and a foreign gene encoding Dinoflagellate Viral Nucleoprotein (DVNP), which is used…
A recent study utilizing proteomics has revealed conserved elements of histone biology across dinoflagellates, despite these protists typically being thought to lack histones entirely. The research focused on two dinoflagellate species, Oxyrrhis marina and Amphidinium carterae, both of which were found to possess all four core histone classes, alongside variants, and the foreign gene encoding Dinoflagellate Viral Nucleoprotein (DVNP).
Additionally, Amphidinium carterae exhibited Histone-like Proteins (HLPs), a trait acquired through lateral gene transfer from bacteria.
The findings confirm the presence of canonical histone genes within dinoflagellates, which were previously unrecognized. This discovery challenges the notion that these organisms lack histones and opens up new avenues for understanding the evolution of chromatin organization in eukaryotic cells. Furthermore, the identification of putative histone post-translational modifications found in canonical eukaryotes suggests that similar mechanisms of regulation are at play in these protists.
Comparative genomics also revealed a histone-handling and modification machinery in dinoflagellates, alongside an apparent reduction or diversification of machinery responsible for replication-dependent nucleosome deposition (CAF-1). This pattern is consistent with a predominantly transcription-associated role for nucleosomes in these organisms. The proteomics data further revealed modifications of DVNP and HLP, hinting at the possibility of these proteins co-opting histone machinery for their own purposes.
These revelations paint a new picture of a dinoflagellate chromatin, one that incorporates the localization of canonical nucleosomes to insulated chromatin territories (INTs). This model emphasizes the importance of understanding the unique evolutionary path taken by dinoflagellates in their chromatin organization, which diverges significantly from the more widely studied eukaryotic lineages.
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