DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity.
Retroviral integrases (INs) catalyse the integration of the reverse transcribed viral DNA into the host cell genome. This process is selective, and chromatin has been proposed to be a major factor regulating this step in the viral life cycle. However, the precise underlying mechanisms are still unde...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2015-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4468133?pdf=render |
| _version_ | 1818480887274143744 |
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| author | Monica Naughtin Zofia Haftek-Terreau Johan Xavier Sam Meyer Maud Silvain Yan Jaszczyszyn Nicolas Levy Vincent Miele Mohamed Salah Benleulmi Marc Ruff Vincent Parissi Cédric Vaillant Marc Lavigne |
| author_facet | Monica Naughtin Zofia Haftek-Terreau Johan Xavier Sam Meyer Maud Silvain Yan Jaszczyszyn Nicolas Levy Vincent Miele Mohamed Salah Benleulmi Marc Ruff Vincent Parissi Cédric Vaillant Marc Lavigne |
| author_sort | Monica Naughtin |
| collection | DOAJ |
| description | Retroviral integrases (INs) catalyse the integration of the reverse transcribed viral DNA into the host cell genome. This process is selective, and chromatin has been proposed to be a major factor regulating this step in the viral life cycle. However, the precise underlying mechanisms are still under investigation. We have developed a new in vitro integration assay using physiologically-relevant, reconstituted genomic acceptor chromatin and high-throughput determination of nucleosome positions and integration sites, in parallel. A quantitative analysis of the resulting data reveals a chromatin-dependent redistribution of the integration sites and establishes a link between integration sites and nucleosome positions. The co-activator LEDGF/p75 enhanced integration but did not modify the integration sites under these conditions. We also conducted an in cellulo genome-wide comparative study of nucleosome positions and human immunodeficiency virus type-1 (HIV-1) integration sites identified experimentally in vivo. These studies confirm a preferential integration in nucleosome-covered regions. Using a DNA mechanical energy model, we show that the physical properties of DNA probed by IN binding are important in determining IN selectivity. These novel in vitro and in vivo approaches confirm that IN has a preference for integration into a nucleosome, and suggest the existence of two levels of IN selectivity. The first depends on the physical properties of the target DNA and notably, the energy required to fit DNA into the IN catalytic pocket. The second depends on the DNA deformation associated with DNA wrapping around a nucleosome. Taken together, these results indicate that HIV-1 IN is a shape-readout DNA binding protein. |
| first_indexed | 2024-12-10T11:28:10Z |
| format | Article |
| id | doaj.art-c7cf239038bd474bba473401f2b665c5 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T11:28:10Z |
| publishDate | 2015-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-c7cf239038bd474bba473401f2b665c52022-12-22T01:50:41ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-01106e012942710.1371/journal.pone.0129427DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity.Monica NaughtinZofia Haftek-TerreauJohan XavierSam MeyerMaud SilvainYan JaszczyszynNicolas LevyVincent MieleMohamed Salah BenleulmiMarc RuffVincent ParissiCédric VaillantMarc LavigneRetroviral integrases (INs) catalyse the integration of the reverse transcribed viral DNA into the host cell genome. This process is selective, and chromatin has been proposed to be a major factor regulating this step in the viral life cycle. However, the precise underlying mechanisms are still under investigation. We have developed a new in vitro integration assay using physiologically-relevant, reconstituted genomic acceptor chromatin and high-throughput determination of nucleosome positions and integration sites, in parallel. A quantitative analysis of the resulting data reveals a chromatin-dependent redistribution of the integration sites and establishes a link between integration sites and nucleosome positions. The co-activator LEDGF/p75 enhanced integration but did not modify the integration sites under these conditions. We also conducted an in cellulo genome-wide comparative study of nucleosome positions and human immunodeficiency virus type-1 (HIV-1) integration sites identified experimentally in vivo. These studies confirm a preferential integration in nucleosome-covered regions. Using a DNA mechanical energy model, we show that the physical properties of DNA probed by IN binding are important in determining IN selectivity. These novel in vitro and in vivo approaches confirm that IN has a preference for integration into a nucleosome, and suggest the existence of two levels of IN selectivity. The first depends on the physical properties of the target DNA and notably, the energy required to fit DNA into the IN catalytic pocket. The second depends on the DNA deformation associated with DNA wrapping around a nucleosome. Taken together, these results indicate that HIV-1 IN is a shape-readout DNA binding protein.http://europepmc.org/articles/PMC4468133?pdf=render |
| spellingShingle | Monica Naughtin Zofia Haftek-Terreau Johan Xavier Sam Meyer Maud Silvain Yan Jaszczyszyn Nicolas Levy Vincent Miele Mohamed Salah Benleulmi Marc Ruff Vincent Parissi Cédric Vaillant Marc Lavigne DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity. PLoS ONE |
| title | DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity. |
| title_full | DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity. |
| title_fullStr | DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity. |
| title_full_unstemmed | DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity. |
| title_short | DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity. |
| title_sort | dna physical properties and nucleosome positions are major determinants of hiv 1 integrase selectivity |
| url | http://europepmc.org/articles/PMC4468133?pdf=render |
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