CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration

ABSTRACT Lentiviral DNA integration favors transcriptionally active chromatin. We previously showed that the interaction of human immunodeficiency virus type 1 (HIV-1) capsid with cleavage and polyadenylation specificity factor 6 (CPSF6) localizes viral preintegration complexes (PICs) to nuclear spe...

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Autores principales:	Wen Li, Parmit K. Singh, Gregory A. Sowd, Gregory J. Bedwell, Sooin Jang, Vasudevan Achuthan, Amarachi V. Oleru, Doris Wong, Hind J. Fadel, KyeongEun Lee, Vineet N. KewalRamani, Eric M. Poeschla, Alon Herschhorn, Alan N. Engelman
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	CPSF6 integration LEDGF/p75 human immunodeficiency virus lentiviruses Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/7f4eaeb2c24147479988497d78e83da7
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spelling	oai:doaj.org-article:7f4eaeb2c24147479988497d78e83da72021-11-15T16:19:09ZCPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration10.1128/mBio.02254-202150-7511https://doaj.org/article/7f4eaeb2c24147479988497d78e83da72020-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02254-20https://doaj.org/toc/2150-7511ABSTRACT Lentiviral DNA integration favors transcriptionally active chromatin. We previously showed that the interaction of human immunodeficiency virus type 1 (HIV-1) capsid with cleavage and polyadenylation specificity factor 6 (CPSF6) localizes viral preintegration complexes (PICs) to nuclear speckles for integration into transcriptionally active speckle-associated domains (SPADs). In the absence of the capsid-CPSF6 interaction, PICs uncharacteristically accumulate at the nuclear periphery and target heterochromatic lamina-associated domains (LADs) for integration. The integrase-binding protein lens epithelium-derived growth factor (LEDGF)/p75 in contrast to CPSF6 predominantly functions to direct HIV-1 integration to interior regions of transcription units. Though CPSF6 and LEDGF/p75 can reportedly interact with the capsid and integrase proteins of both primate and nonprimate lentiviruses, the extents to which these different viruses target SPADs versus LADs, as well as their dependencies on CPSF6 and LEDGF/p75 for integration targeting, are largely unknown. Here, we mapped 5,489,157 primate and nonprimate lentiviral integration sites in HEK293T and Jurkat T cells as well as derivative cells that were knocked out or knocked down for host factor expression. Despite marked preferences of all lentiviruses to target genes for integration, nonprimate lentiviruses only marginally favored SPADs, with corresponding upticks in LAD-proximal integration. While LEDGF/p75 knockout disrupted the intragenic integration profiles of all lentiviruses similarly, CPSF6 depletion specifically counteracted SPAD integration targeting by primate lentiviruses. CPSF6 correspondingly failed to appreciably interact with nonprimate lentiviral capsids. We conclude that primate lentiviral capsid proteins evolved to interact with CPSF6 to optimize PIC localization for integration into transcriptionally active SPADs. IMPORTANCE Integration is the defining step of the retroviral life cycle and underlies the inability to cure HIV/AIDS through the use of intensified antiviral therapy. The reservoir of latent, replication-competent proviruses that forms early during HIV infection reseeds viremia when patients discontinue medication. HIV cure research is accordingly focused on the factors that guide provirus formation and associated chromatin environments that regulate transcriptional reactivation, and studies of orthologous infectious agents such as nonprimate lentiviruses can inform basic principles of HIV biology. HIV-1 utilizes the integrase-binding protein LEDGF/p75 and the capsid interactor CPSF6 to target speckle-associated domains (SPADs) for integration. However, the extent to which these two host proteins regulate integration of other lentiviruses is largely unknown. Here, we mapped millions of retroviral integration sites in cell lines that were depleted for LEDGF/p75 and/or CPSF6. Our results reveal that primate lentiviruses uniquely target SPADs for integration in a CPSF6-dependent manner.Wen LiParmit K. SinghGregory A. SowdGregory J. BedwellSooin JangVasudevan AchuthanAmarachi V. OleruDoris WongHind J. FadelKyeongEun LeeVineet N. KewalRamaniEric M. PoeschlaAlon HerschhornAlan N. EngelmanAmerican Society for MicrobiologyarticleCPSF6integrationLEDGF/p75human immunodeficiency viruslentivirusesMicrobiologyQR1-502ENmBio, Vol 11, Iss 5 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	CPSF6 integration LEDGF/p75 human immunodeficiency virus lentiviruses Microbiology QR1-502
spellingShingle	CPSF6 integration LEDGF/p75 human immunodeficiency virus lentiviruses Microbiology QR1-502 Wen Li Parmit K. Singh Gregory A. Sowd Gregory J. Bedwell Sooin Jang Vasudevan Achuthan Amarachi V. Oleru Doris Wong Hind J. Fadel KyeongEun Lee Vineet N. KewalRamani Eric M. Poeschla Alon Herschhorn Alan N. Engelman CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration
description	ABSTRACT Lentiviral DNA integration favors transcriptionally active chromatin. We previously showed that the interaction of human immunodeficiency virus type 1 (HIV-1) capsid with cleavage and polyadenylation specificity factor 6 (CPSF6) localizes viral preintegration complexes (PICs) to nuclear speckles for integration into transcriptionally active speckle-associated domains (SPADs). In the absence of the capsid-CPSF6 interaction, PICs uncharacteristically accumulate at the nuclear periphery and target heterochromatic lamina-associated domains (LADs) for integration. The integrase-binding protein lens epithelium-derived growth factor (LEDGF)/p75 in contrast to CPSF6 predominantly functions to direct HIV-1 integration to interior regions of transcription units. Though CPSF6 and LEDGF/p75 can reportedly interact with the capsid and integrase proteins of both primate and nonprimate lentiviruses, the extents to which these different viruses target SPADs versus LADs, as well as their dependencies on CPSF6 and LEDGF/p75 for integration targeting, are largely unknown. Here, we mapped 5,489,157 primate and nonprimate lentiviral integration sites in HEK293T and Jurkat T cells as well as derivative cells that were knocked out or knocked down for host factor expression. Despite marked preferences of all lentiviruses to target genes for integration, nonprimate lentiviruses only marginally favored SPADs, with corresponding upticks in LAD-proximal integration. While LEDGF/p75 knockout disrupted the intragenic integration profiles of all lentiviruses similarly, CPSF6 depletion specifically counteracted SPAD integration targeting by primate lentiviruses. CPSF6 correspondingly failed to appreciably interact with nonprimate lentiviral capsids. We conclude that primate lentiviral capsid proteins evolved to interact with CPSF6 to optimize PIC localization for integration into transcriptionally active SPADs. IMPORTANCE Integration is the defining step of the retroviral life cycle and underlies the inability to cure HIV/AIDS through the use of intensified antiviral therapy. The reservoir of latent, replication-competent proviruses that forms early during HIV infection reseeds viremia when patients discontinue medication. HIV cure research is accordingly focused on the factors that guide provirus formation and associated chromatin environments that regulate transcriptional reactivation, and studies of orthologous infectious agents such as nonprimate lentiviruses can inform basic principles of HIV biology. HIV-1 utilizes the integrase-binding protein LEDGF/p75 and the capsid interactor CPSF6 to target speckle-associated domains (SPADs) for integration. However, the extent to which these two host proteins regulate integration of other lentiviruses is largely unknown. Here, we mapped millions of retroviral integration sites in cell lines that were depleted for LEDGF/p75 and/or CPSF6. Our results reveal that primate lentiviruses uniquely target SPADs for integration in a CPSF6-dependent manner.
format	article
author	Wen Li Parmit K. Singh Gregory A. Sowd Gregory J. Bedwell Sooin Jang Vasudevan Achuthan Amarachi V. Oleru Doris Wong Hind J. Fadel KyeongEun Lee Vineet N. KewalRamani Eric M. Poeschla Alon Herschhorn Alan N. Engelman
author_facet	Wen Li Parmit K. Singh Gregory A. Sowd Gregory J. Bedwell Sooin Jang Vasudevan Achuthan Amarachi V. Oleru Doris Wong Hind J. Fadel KyeongEun Lee Vineet N. KewalRamani Eric M. Poeschla Alon Herschhorn Alan N. Engelman
author_sort	Wen Li
title	CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration
title_short	CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration
title_full	CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration
title_fullStr	CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration
title_full_unstemmed	CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration
title_sort	cpsf6-dependent targeting of speckle-associated domains distinguishes primate from nonprimate lentiviral integration
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/7f4eaeb2c24147479988497d78e83da7
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CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration

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