Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein
Edited by Thomas Shenk, Princeton University, Princeton, NJ, and approved June 27, 2013 (received for review March 25, 2013)
Abstract
Human CMV (hCMV) establishes lifelong infections in most of us, causing developmental defects in human embryos and life-threatening disease in immunocompromised individuals. During productive infection, the viral >230,000-bp dsDNA genome is expressed widely and in a temporal cascade. The hCMV genome does not carry histones when encapsidated but has been proposed to form nucleosomes after release into the host cell nucleus. Here, we present hCMV genome-wide nucleosome occupancy and nascent transcript maps during infection of permissive human primary cells. We show that nucleosomes occupy nuclear viral DNA in a nonrandom and highly predictable fashion. At early times of infection, nucleosomes associate with the hCMV genome largely according to their intrinsic DNA sequence preferences, indicating that initial nucleosome formation is genetically encoded in the virus. However, as infection proceeds to the late phase, nucleosomes redistribute extensively to establish patterns mostly determined by nongenetic factors. We propose that these factors include key regulators of viral gene expression encoded at the hCMV major immediate-early (IE) locus. Indeed, mutant virus genomes deficient for IE1 expression exhibit globally increased nucleosome loads and reduced nucleosome dynamics compared with WT genomes. The temporal nucleosome occupancy differences between IE1-deficient and WT viruses correlate inversely with changes in the pattern of viral nascent and total transcript accumulation. These results provide a framework of spatial and temporal nucleosome organization across the genome of a major human pathogen and suggest that an hCMV major IE protein governs overall viral chromatin structure and function.
Data Availability
Data deposition: The data reported in this paper are available at http://genie.weizmann.ac.il/pubs/hcmv2013.
Acknowledgments
We thank C. Sinzger for TB40-BAC4, K. Tischer and K. Osterrieder for pLAY2 and GS1783, and H. Zhu for T-BACwt as well as K. Bernhardt and M. Zenger for experimental help. This work was supported by Human Frontier Science Program Grant RGY0071/2008 (to F.G., E.S., and M.N.) and Deutsche Forschungsgemeinschaft Grant NE791/2-2 (to M.N.).
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Data Availability
Data deposition: The data reported in this paper are available at http://genie.weizmann.ac.il/pubs/hcmv2013.
Submission history
Published online: July 22, 2013
Published in issue: August 6, 2013
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Acknowledgments
We thank C. Sinzger for TB40-BAC4, K. Tischer and K. Osterrieder for pLAY2 and GS1783, and H. Zhu for T-BACwt as well as K. Bernhardt and M. Zenger for experimental help. This work was supported by Human Frontier Science Program Grant RGY0071/2008 (to F.G., E.S., and M.N.) and Deutsche Forschungsgemeinschaft Grant NE791/2-2 (to M.N.).
Notes
*This Direct Submission article had a prearranged editor.
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The authors declare no conflict of interest.
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Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein, Proc. Natl. Acad. Sci. U.S.A.
110 (32) 13126-13131,
https://doi.org/10.1073/pnas.1305548110
(2013).
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