Changes in the topology of gene expression networks by human immunodeficiency virus type 1 (HIV-1) integration in macrophages

Soto-Girón, Maria J.; García-Vallejo, Felipe

doi:10.1016/j.virusres.2011.08.015

Cited by 9 publications

(7 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The different transgenomic clones differ in their profiles. Viewed under the perspective of previously published investigations from our [5][6][7]16] and from other [11][12][13][14] laboratories, it is apparent that the insertion of foreign DNA into an established mammalian genome can lead to genome-wide destabilizations of cellular transcription and methylation patterns. We have not yet conducted a systematic investigation into the epigenetic trans effects of transgenome size, its From the sum total of all our previous investigations on this topic, we conclude that the integrations of Ad12, bacteriophage λ or plasmid DNA as well as the currently used pC1-5.6 plasmid have all led to alterations of methylation and transcriptional profiles in the recipient cells [5][6][7].…”

Section: Resultsmentioning

confidence: 99%

“…In Epstein-Barr virus (EBV)-transformed human lymphoblastoid cell lines, in EBV-infected cells [11,12] or in human macrophages carrying integrated HIV-1 proviral genomes [13], cellular DNA methylation and transcription patterns have been significantly altered. In induced pluripotent human stem cells with multiple integrated foreign genes, genome-wide alterations of CpG methylation profiles have been described [14].…”

mentioning

confidence: 99%

See 1 more Smart Citation

Destabilization of the Human Epigenome: Consequences of Foreign DNA Insertions

et al. 2015

View full text Add to dashboard Cite

Aim: We previously reported changes of DNA methylation and transcription patterns in mammalian cells that carry integrated foreign DNA. Experiments were now designed to assess the epigenetic consequences of inserting a 5.6 kbp plasmid into the human genome. Methods: Differential transcription and CpG methylation patterns were compared between transgenomic and nontransgenomic cell clones by using gene chip microarray systems. Results: In 4.7% of the 28.869 gene segments analyzed, transcriptional activities were up- or downregulated in the transgenomic cell clones. Genome-wide profiling revealed differential methylation in 3791 of > 480,000 CpG's examined in transgenomic versus nontransgenomic clones. Conclusion: The data document genome-wide effects of foreign DNA insertions on the epigenetic stability of human cells. Many fields in experimental biology and medicine employ transgenomic or otherwise genome-manipulated cells or organisms without considering the epigenetic consequences for the recipient genomes.

show abstract

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Destabilization of the Human Epigenome: Consequences of Foreign DNA Insertions

et al. 2015

View full text Add to dashboard Cite

show abstract

“…This integration event will have varying consequences depending on the genomic site of integration. These may involve direct modulation of host gene networks, controlling levels of viral transcription, and in some cases influence the outcome of active or latent infection 54,55 . Normally, A3 proteins play a major role in hindering reverse transcription of the HIV-1 RNA genome; however, HIV-1 Vif circumvents this restriction by reducing A3 protein levels.…”

Section: Discussionmentioning

confidence: 99%

Antiretroviral APOBEC3 Cytidine Deaminases Alter HIV-1 Provirus Integration Site Profiles

Ajoge

Renner

Kohio

et al. 2019

Preprint

View full text Add to dashboard Cite

APOBEC3 (A3) proteins are host-encoded deoxycytidine deaminases that provide an innate immune barrier to retroviral infection, notably against HIV-1. Low levels of deamination are believed to contribute to the rapid genetic evolution of HIV-1, while the catalytic activity of these proteins can induce catastrophic hypermutation in proviral DNA leading to near-total HIV-1 restriction. So far, little is known about how A3 cytosine deaminases might impact HIV-1 proviral DNA integrations into human chromosomal DNA. Using a deep sequencing approach, we analyzed the influence of catalytic active and inactive APOBEC3F and APOBEC3G on HIV-1 integration site selections. DNA editing was detected at the extremities of the long terminal repeat regions of the virus. Both catalytic active and non-catalytic A3 mutants decreased insertions into gene coding sequences and increased integration sites into SINE elements, oncogenes and transcriptionsilencing non-B DNA features. Our data implicates A3 as a host factor influencing HIV-1 integration site selection and promotes a more transcriptionally silent integration site profile. Ajoge et al., 2019 3 GRAPHICAL ABSTRACT Schematic depicting the influence of APOBEC3 (A3) proteins on HIV integration site targeting. Left, in the absence of A3, HIV has a strong preference for integrating into genes. Right, both catalytic active and non-catalytic A3 mutants decrease integration into genes and increase integration into SINE elements and in transcription-silencing non-B DNA features.

show abstract

“…Transcription levels were up or downregulated in 4.7% of the gene segments studied [5]. Several laboratories have shown virus infections to alter the methylation patterns of infected or transformed cells [6][7][8][9]. We have concluded that manipulations on a cell's genome can have far-reaching consequences including the generation of completely different cell types [1,18].…”

Section: Studies On the Epigenetic Impact Of Foreign Dna Entry Into Mammalian Cellsmentioning

confidence: 94%

Epigenetic Consequences of Genome Manipulations: Caveats for Human Germline Therapy and Genetically Modified Organisms

Doerfler

2019

Epigenomics

View full text Add to dashboard Cite

show abstract

Changes in the topology of gene expression networks by human immunodeficiency virus type 1 (HIV-1) integration in macrophages

Cited by 9 publications

References 45 publications

Destabilization of the Human Epigenome: Consequences of Foreign DNA Insertions

Destabilization of the Human Epigenome: Consequences of Foreign DNA Insertions

Antiretroviral APOBEC3 Cytidine Deaminases Alter HIV-1 Provirus Integration Site Profiles

Epigenetic Consequences of Genome Manipulations: Caveats for Human Germline Therapy and Genetically Modified Organisms

Contact Info

Product

Resources

About