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Exploring histone loading on HIV DNA reveals a dynamic nucleosome positioning between unintegrated and integrated viral genome

Authors :
David Depierre
Gaël Petitjean
Heng-Chang Chen
Olivier Cuvier
Monsef Benkirane
Cécile Doyen
Motoki Takaku
Shinichi Machida
Suzie Thenin-Houssier
Source :
Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences of the United States of America
Publication Year :
2020

Abstract

Significance The biology of HIV DNA, from its synthesis to its integration into the host genome, remains poorly understood. Here we show that in the nucleus, histones are rapidly loaded on newly synthesized unintegrated HIV DNA. Interestingly, the chromatin architecture around the HIV long terminal repeat (LTR) is different in unintegrated and integrated HIV DNA. Specifically, a nucleosome present only on the DNase hypersensitive site of unintegrated HIV DNA contributes to the transcriptional silencing of unintegrated HIV DNA by preventing RNAPII recruitment.<br />The aim of the present study was to understand the biology of unintegrated HIV-1 DNA and reveal the mechanisms involved in its transcriptional silencing. We found that histones are loaded on HIV-1 DNA after its nuclear import and before its integration in the host genome. Nucleosome positioning analysis along the unintegrated and integrated viral genomes revealed major differences in nucleosome density and position. Indeed, in addition to the well-known nucleosomes Nuc0, Nuc1, and Nuc2 loaded on integrated HIV-1 DNA, we also found NucDHS, a nucleosome that covers the DNase hypersensitive site, in unintegrated viral DNA. In addition, unintegrated viral DNA-associated Nuc0 and Nuc2 were positioned slightly more to the 5′ end relative to their position in integrated DNA. The presence of NucDHS in the proximal region of the long terminal repeat (LTR) promoter was associated with the absence of RNAPII and of the active histone marks H3K4me3 and H3ac at the LTR. Conversely, analysis of integrated HIV-1 DNA showed a loss of NucDHS, loading of RNAPII, and enrichment in active histone marks within the LTR. We propose that unintegrated HIV-1 DNA adopts a repressive chromatin structure that competes with the transcription machinery, leading to its silencing.

Details

ISSN :
00278424
Database :
OpenAIRE
Journal :
Proceedings of the National Academy of Sciences
Accession number :
edsair.doi.dedup.....a3e30a706757777a03166bb5becfc8a2
Full Text :
https://doi.org/10.1073/pnas.1913754117