Epigenetic diversity of Kaposi's sarcoma-associated herpesvirus.
Spontaneous lytic reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV) occurs at a low rate in latently infected cells in disease and culture. This suggests imperfect epigenetic maintenance of viral transcription programs, perhaps due to variability in chromatin structure at specific loci across the population of KSHV episomal genomes. To characterize this locus-specific chromatin structural diversity, we used MAPit single-molecule footprinting, which simultaneously maps endogenous CG methylation and accessibility to M.CviPI at GC sites. Diverse chromatin structures were detected at the LANA, RTA and vIL6 promoters. At each locus, chromatin ranged from fully closed to fully open across the population. This diversity has not previously been reported in a virus. Phorbol ester and RTA transgene induction were used to identify chromatin conformations associated with reactivation of lytic transcription, which only a fraction of episomes had. Moreover, certain chromatin conformations correlated with CG methylation patterns at the RTA and vIL6 promoters. This indicated that some of the diverse chromatin conformations at these loci were epigenetically distinct. Finally, by comparing chromatin structures from a cell line infected with constitutively latent virus, we identified products of lytic replication. Our findings show that epigenetic drift can restrict viral propagation by chromatin compaction at latent and lytic promoters.
Department of Biochemistry and Molecular Biology, 2033 Mowry Road, Box 103633, University of Florida College of Medicine, Gainesville, FL, 32610, USA.
Russell P
RP
Darst
Irina
I
Haecker
Carolina E
CE
Pardo
Rolf
R
Renne
Michael P
MP
Kladde
D001483:Base Sequence; D045744:Cell Line, Tumor; D002843:Chromatin / Q000235:genetics / Q000378:metabolism* / Q000821:virology; D042002:Chromatin Assembly and Disassembly; D002874:Chromosome Mapping; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D015967:Gene Expression Regulation, Viral; D056426:Genetic Loci; D019288:Herpesvirus 8, Human / Q000502:physiology*; D054884:Host-Pathogen Interactions; D006801:Humans; D017874:Immediate-Early Proteins / Q000096:biosynthesis / Q000235:genetics; D011401:Promoter Regions, Genetic; D015534:Trans-Activators / Q000096:biosynthesis / Q000235:genetics; D017735:Virus Latency
D002843:Chromatin; D017874:Immediate-Early Proteins; C417604:Rta protein, Human herpesvirus 8; D015534:Trans-Activators