A giant virus genome is densely packaged by stable nucleosomes

The doublet histones of Marseillevirus are distantly related to the four eukaryotic core histones and wrap DNA to form remarkably similar nucleosomes. By releasing Marseillevirus chromatin from virions into solution and performing genome-wide nuclease digestion and chemical cleavage assays, we find that the higher-order organization of Marseillevirus chromatin differs greatly from that of eukaryotes. Marseillevirus nucleosomes fully protect DNA within virions, without linker DNA or phasing along genes. Likewise, we observe that most nucleosomes reconstituted onto 3-copy tandem repeats of a nucleosome positioning sequence are tightly packed and fully wrapped. We also document repeat generation and instability during viral passage in amoeboid culture. Dense promiscuous packing of fully wrapped nucleosomes rather than “beads-on-a-string” with genic punctuation suggests a viral genome protection function for doublet histones. We used MNase-seq and MPE-seq, nucleosome mapping strategies in which either an endo/exonuclease or a small molecule DNA cleavage reagent removes accessible DNA, followed by end-polishing and ligation of sequencing adapters to produce libraries for paired-end DNA sequencing.