Host factors for retroviral integration site selection

Debyser, Zeger; Christ, Frauke; Rijck, Jan De; Gijsbers, Rik

doi:10.1016/j.tibs.2014.12.001

Cited by 83 publications

(72 citation statements)

References 81 publications

(202 reference statements)

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“…1D), which is similar to what we previously observed in wild-type cells (2). Therefore, even though LEDGF/ p75 is the main factor directing HIV-1 to specific gene-rich regions (9,11), it does not play a crucial role in the macrolocalization of HIV-1 viral complexes in the nucleus.…”

supporting

confidence: 87%

See 1 more Smart Citation

Comparative Analysis of HIV-1 and Murine Leukemia Virus Three-Dimensional Nuclear Distributions

Quercioli

Primio

Casini

et al. 2016

J Virol

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T o complete its replication cycle, HIV-1 has to reach the nucleus of the infected cell, where the viral cDNA integrates itself into the host chromatin (1). Although the integration reaction and the targeted chromatin regions have been well characterized, very little is known about the virus-cell interactions that take place within the nuclear compartment.The development of fluorescence imaging approaches to study HIV-1 early replication steps has significantly contributed to our knowledge of the HIV-1 life cycle. Indeed, fluorescence imaging techniques allow the observation at the single-particle level of HIV-1 interactions with target cell structures, preserving their main three-dimensional (3D) structural properties. Imaging techniques have revealed that HIV-1 particles (2-5) and integrated proviruses (6), preferentially localize in the nuclear periphery, which is consistent with the observation that peripheral chromatin, especially that near the nuclear pore complexes, is favored for HIV-1 integration (7,8).Here we further analyzed the 3D nuclear distribution of HIV-1 preintegration complexes (PICs) in relation to the expression of HIV-1 integrase (IN) cofactor LEDGF/p75 (for a recent review, see reference 9). We also developed a new tool for the detection of fluorescent murine leukemia virus (MLV) that allowed us to compare the 3D nuclear distributions of gammaretroviral and lentiviral particles.We set out to explore the role played by LEDGF/p75 in the 3D nuclear distribution of HIV-1 in the nucleus during the early phases of infection. Using a technique that allows us to produce and track fluorescent HIV-IN-enhanced green fluorescent protein (EGFP) PICs (2-4), we analyzed virus localization with respect to the levels of chromatin condensation as demarcated by the ectopic expression of histone H2B fused to red fluorescent protein (RFP) (2). Using the same procedures we previously established (2-4), we analyzed the localization of HIV-IN-EGFP PICs in HeLa-H2B-RFP cells stably silenced for LEDGF/p75 (10) (Fig. 1A). Figure 1B shows the preferential localization of HIV-IN-EGFP PICs toward less condensed euchromatic regions characterized by low H2B fluorescence. Statistical analysis using the nonparametric twotailed Kolmogorov-Smirnov test revealed no significant difference between the distributions of HIV-1 PICs in LEDGF/p75 knockdown and control cells (P ϭ 0.76; blue and pink curves). Conversely, the HIV-PIC distribution to euchromatin in both cell lines significantly differs from the random region of interest (ROI) distribution in the same cells (gray and black curves from control and LEDGF/p75 knockdown cells, respectively) (Fig. 1C). Analyses performed with a heterochromatin-specific marker (H3K9me3) confirmed the preferential localization of HIV-1 PICs in chromatin regions with low H3K9me3 signal intensity (Fig. 1D), which is similar to what we previously observed in wild-type cells (2). Therefore, even though LEDGF/ p75 is the main factor directing HIV-1 to specific gene-rich regions (9, 11), it does not ...

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confidence: 87%

“…Therefore, even though LEDGF/p75 knockdown generates a more random distribution of integrated proviruses (9,(15)(16)(17), in the absence of this IN cofactor, HIV-1 PICs preserve their localization toward subnuclear regions occupied by euchromatin.…”

mentioning

confidence: 99%

Comparative Analysis of HIV-1 and Murine Leukemia Virus Three-Dimensional Nuclear Distributions

Quercioli

Primio

Casini

et al. 2016

J Virol

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“…Previous research has shown that the distinct integration site preferences of retroviruses can be linked to interaction of the virally encoded IN protein with various host cell factors (8)(9)(10). Mechanistically, these host cell factors act largely as a bimodal tether to recruit the preintegration complex to the chromatin, thereby targeting proviral integrations (10).…”

Section: Fact Complex Promotes Alv Integrationmentioning

confidence: 99%

“…The lentivirus HIV-1 has been shown to exhibit strong integration site preferences within active gene units, whereas the gammaretrovirus MLV exhibits a strong preference for enhancers and transcription start sites (5-7). These biases have been attributed to interaction of IN in the context of the preintegration complex with their cognate host cell factors (8)(9)(10). For example, cellular chromatin-associated protein lens epithelial-derived growth factor (LEDGF/p75) interacts with HIV-1 IN and directs lentiviral integration into actively transcribed genes (11)(12)(13).…”

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confidence: 99%

The FACT Complex Promotes Avian Leukosis Virus DNA Integration

Winans

Larue

Abraham

et al. 2017

J Virol

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All retroviruses need to integrate a DNA copy of their genome into the host chromatin. Cellular proteins regulating and targeting lentiviral and gammaretroviral integration in infected cells have been discovered, but the factors that mediate alpharetroviral avian leukosis virus (ALV) integration are unknown. In this study, we have identified the FACT protein complex, which consists of SSRP1 and Spt16, as a principal cellular binding partner of ALV integrase (IN). Biochemical experiments with purified recombinant proteins show that SSRP1 and Spt16 are able to individually bind ALV IN, but only the FACT complex effectively stimulates ALV integration activity in vitro. Likewise, in infected cells, the FACT complex promotes ALV integration activity, with proviral integration frequency varying directly with cellular expression levels of the FACT complex. An increase in 2-long-terminal-repeat (2-LTR) circles in the depleted FACT complex cell line indicates that this complex regulates the ALV life cycle at the level of integration. This regulation is shown to be specific to ALV, as disruption of the FACT complex did not inhibit either lentiviral or gammaretroviral integration in infected cells. IMPORTANCEThe majority of human gene therapy approaches utilize HIV-1-or murine leukemia virus (MLV)-based vectors, which preferentially integrate near genes and regulatory regions; thus, insertional mutagenesis is a substantial risk. In contrast, ALV integrates more randomly throughout the genome, which decreases the risks of deleterious integration. Understanding how ALV integration is regulated could facilitate the development of ALV-based vectors for use in human gene therapy. Here we show that the FACT complex directly binds and regulates ALV integration efficiency in vitro and in infected cells.

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“…Recientemente se ha informado que, aunque la mayor parte del genoma hospedero es potencialmente accesible para la integración retroviral, la selección del sitio blanco para dicho proceso no se da totalmente al azar (Debyser, et al, 2015;Ambrosi, et al, 2008). En este sentido, la disponibilidad de la información sobre la secuencia completa del genoma humano ha permitido hacer estudios a gran escala para la identificación de sitios de inserción retroviral (Derse, et al, 2007;Bushman, et al, 2005).…”

Section: Introductionunclassified

Caracterización genómica de la integración simultánea del virus de la inmunodeficiencia humana 1 y el virus linfotrópico humano tipo1

Domínguez

Alzate

García-Vallejo

2015

Rev. Acad. Colomb. Cienc. Ex. Fis. Nat.

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ResumenLa selección de los sitios de integración del ADN retroviral en el genoma es crucial para moldear la dinámica de la infección. El objetivo de este estudio fue analizar la combinación específica de las características genómicas de la célula infectada que condicionarían la integración simultánea de ambos retrovirus. A partir de 203 secuencias de ADN humano vecinas a las repeticiones terminales largas (long terminal repeat, LTR) de ambos virus, depositadas en el GenBank, y mediante distintas herramientas computacionales, se hizo una simulación bioinformática para determinar la integración del VIH y el -HTLV-1 en una extensión de 100 kb, así como la localización cromosómica del provirus, el número de genes, su proceso molecular y función asociada, las islas CpG, las secuencias Alu y los elementos nucleares dispersos largos (long interspersed nuclear element, LINE), y su expresión en poblaciones de linfocitos de los genes blanco de la integración. El 47,3 % de las integraciones de ambos virus se localizó en regiones ricas en elementos repetidos. La integración en los genes de la clase II ocurrió en los intrones (p<0,05). Se observó una distribución cromosómica diferencial de ambos provirus en la que el HTLV-1 se localizó en regiones pericentroméricas y centroméricas, mientras que el VIH-1 lo hizo en zonas teloméricas y subteloméricas (p<0,001). El ambiente común para la integración de los linfocitos en el genoma estuvo conformado por genes codificantes de proteínas de unión a moléculas y de transducción de señales, así como por un elevado número de islas CpG y de repeticiones Alu. A partir de la simulación bioinformática de la integración entre el VIH-1 y el HTLV-1, se aportó evidencia que sustenta la hipótesis de que una combinación específica de variables genómicas condicionaría el proceso de integración diferencial simultánea de ambos retrovirus.Palabras clave: retrovirus, integración viral, linfocitos, islas de CpG, genes clase II, simulación por computador. Genomic characterization of human immunodeficiency virus 1 and human T-lymphotropic virus 1 simultaneous integration AbstractThe selection of retroviral cDNA integration sites in the human genome is a critical step to condition the dynamics of infection. The objective was to analyze the combination of genomic characteristics of infected cells that would condition the genomic profiles of HIV-1/HTLV-1 simultaneous integration. We carried out a computer simulation using 203 human genome sequences flanking 3´LTR of both retroviruses previously deposited in the GenBank, and applying several computational tools. The analyses were focused on determining the chromosomal integration, CpG islands, Alu sequences and the expression of integration target class II genes in lymphocytic populations in a 100 kb chromatin structure associated with simultaneous integration. We found 47.3% of simultaneous cDNA integrations localized in regions rich in repetitive elements. The rest of retroviral cDNA integrations occurred in class II gene introns (p<0.05). We determined a ...

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Host factors for retroviral integration site selection

Cited by 83 publications

References 81 publications

Comparative Analysis of HIV-1 and Murine Leukemia Virus Three-Dimensional Nuclear Distributions

Comparative Analysis of HIV-1 and Murine Leukemia Virus Three-Dimensional Nuclear Distributions

The FACT Complex Promotes Avian Leukosis Virus DNA Integration

Caracterización genómica de la integración simultánea del virus de la inmunodeficiencia humana 1 y el virus linfotrópico humano tipo1

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