A point mutation in HIV-1 integrase redirects proviral integration into centromeric repeats
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Abstract
Retroviruses utilize the viral integrase (IN) protein to integrate a DNA copy of their genome into the host chromosomal DNA. HIV-1 integration sites are highly biased towards actively transcribed genes, likely mediated by binding of the IN protein to specific host factors, particularly LEDGF, located at these gene regions. We here report a dramatic redirection of integration site distribution induced by a single point mutation in HIV-1 IN. Viruses carrying the K258R IN mutation exhibit more than a 25-fold increase in integrations into centromeric alpha satellite repeat sequences, as assessed by both deep sequencing and qPCR assays. Immunoprecipitation studies identified host factors that uniquely bind to the mutant IN protein and thus may account for the novel bias for integration into centromeres. Centromeric integration events are known to be enriched in the latent reservoir of infected memory T cells, as well as in patients who control viral replication without intervention (so-called elite controllers). The K258R point mutation in HIV-1 IN reported in this study has also been found in databases of latent proviruses found in patients. The altered integration site preference induced by this mutation has uncovered a hidden feature of the establishment of viral latency and control of viral replication.
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This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/4546551.
Here, the authors seek to better understand the mechanism of Human Immunodeficiency Virus 1 (HIV-1) viral Integrase (IN). They hypothesize that four major sites on the C-terminal domain (CTD) are responsible for directing the viral integration site. They accomplish this by generating IN mutants at each of the four sites and generated different viruses carrying these mutations to assay for changes in viral transduction, proviral transcription, and viral integration sites. They found that viruses carrying the K258R mutation exhibited a 25-fold increase change in integration site preference to centromeric sites. They also identified unique host factors that bound to this mutant. Together, the …
This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/4546551.
Here, the authors seek to better understand the mechanism of Human Immunodeficiency Virus 1 (HIV-1) viral Integrase (IN). They hypothesize that four major sites on the C-terminal domain (CTD) are responsible for directing the viral integration site. They accomplish this by generating IN mutants at each of the four sites and generated different viruses carrying these mutations to assay for changes in viral transduction, proviral transcription, and viral integration sites. They found that viruses carrying the K258R mutation exhibited a 25-fold increase change in integration site preference to centromeric sites. They also identified unique host factors that bound to this mutant. Together, the data try to offer a better explain to the mechanism of HIV-1 IN and the establishment of viral latency.
Overall, the manuscript seeks to obtain a clearer understanding of the mechanism behind HIV-1 IN function, which remains largely unclear. The field has been able to clearly identify hotspots of viral integration as well as factors such as LEDGF that are critical for viral integration; however, there remain many questions beyond that. It is still unclear why certain sites of integration are preferred and what factors guide this. The manuscript helps the fields' understanding of this by showing that IN mutations can lead to changes in integration site as well as changes in host factors. The data contribute significantly in that they expand the current understanding of these concepts as well as begin to help make it clearer why certain individuals are able to control HIV infection and establish latent reservoirs.
As a whole, the manuscript itself is strong in its current state. The authors successfully test the hypothesis they set out to investigate and do so in a manner that produces further questions to investigate.
Major Comments/Essential Revisions:
· Figure 3 displays IN biases toward centromeres is significantly different in the K258R mutant, however, this mutant seems to potentially have a dramatic outlier. This could potentially be helped with more data points.
· Figure 4 contains a very similar issue to the previous figure where there seems to be a potential outlier that could be skewing the data.
Minor Comments:
· Figure 1. clearly shows effects of the point mutation on viral replication, however, MOI is not included.
· In figure 5., the labeling scheme used for the graphs quantifying centromeric integration are difficult to compare across chromosomes. Normalizing the Y-axis across all quantifications could be useful for the reader.
· Visually representing the gene ontology analysis in table 4 could help make the data stronger. The importance of these findings seem to get lost in the current tabular format.
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