Abstract
Histones are the principal constituents of eukaryotic chromatin. The four core histones (H2A, H2B, H3 and H4) are conserved across sequenced eukaryotic genomes and therefore thought to be universal to eukaryotes. In the early 1980s, however, a series of biochemical investigations failed to find evidence for histones or nucleosomal structures in the microscopic green alga Nanochlorum eucaryotum. If true, derived histone loss in this lineage would constitute an exceptional case that might help us further understand the principles governing eukaryotic gene regulation. To substantiate these earlier reports of histone loss in N. eucaryotum, we sequenced, assembled and quantified its transcriptome. Following a systematic search for histone-fold domains in the assembled transcriptome, we detect orthologues to all four core histones. We also find histone mRNAs to be highly expressed, comparable to the situation in other eukaryotes. Finally, we obtain characteristic protection patterns when N. eucaryotum chromatin is subjected to micrococcal nuclease digestion, indicating widespread formation of nucleosomal complexes in vivo. We conclude that previous reports of missing histones in N. eucaryotum were mistaken. By all indications, Nanochlorum eucaryotum has histone-based chromatin characteristic of most eukaryotes.
Highlights
Nucleosomes are the fundamental repeat units of eukaryotic chromatin; four core histones (H3, H4, H2A and H2B) assembled into octameric complexes that wrap approximately 150 bp of DNA
To establish whether histones are present in N. eucaryotum we obtained strain SAG 55.87 from the Culture Collection of Algae at the University of Göttingen (Sammlung von Algenkulturen der Universität Göttingen, SAG)
This strain is identical to strain UTEX 2502 in the Culture Collection of Algae at the University of Texas at Austin [20], even though the associated species designations are not. Both phylogenetic and morphological, triggered a veritable bonanza of valid and invalid taxonomic revisions, as Nanochlorum eucaryotum became variously known as Nannochloris eucaryotum [21], the name still associated with UTEX 2502, and Pseudochloris wilhelmii, the name currently associated with SAG 55.87 [20]
Summary
Nucleosomes are the fundamental repeat units of eukaryotic chromatin; four core histones (H3, H4, H2A and H2B) assembled into octameric complexes that wrap approximately 150 bp of DNA. All four core histones were present in the last common ancestor of eukaryotes [1,2], have since been retained along distant eukaryotic lineages, and are considered part of the universal, indispensable molecular toolkit of eukaryotes In a series of papers in the early 1980s, histones and nucleosomal structures were reported absent from the microscopic green alga Nanochlorum eucaryotum [13,14]. This claim has gone unchallenged since and been reiterated decades later [15,16] as a potential example of deviant eukaryotic chromatin architecture. Based on this evidence we conclude that N. eucaryotum is not a unicorn
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