A Protein Guides HIV Integration Into Human Genome

Armen Hareyan's picture


A Mayo Clinic research collaboration has discovered that a human protein - LEDGF - plays a guiding role in where HIV inserts itself in the human genome. The findings appear in the current edition of Nature Medicine. Collaborating researchers are from the University of Pennsylvania and the Salk Institute.

Significance of the Research

As it infects a cell, HIV inserts or "integrates" a permanent DNA copy of itself somewhere into one of the cell's chromosomes, and production of new viruses starts. Scientists once thought that the integration sites were randomly distributed throughout the genome. Then they discovered that the virus prefers to integrate where the genes are. What determines this preference for genes over the vast regions of the human genome that do not contain genes has been unknown. "This finding is intriguing because it is the first example of a cellular protein that controls HIV integration site preferences," explains Mayo Clinic virologist Eric Poeschla, M.D., who co-led the research team.

The Mayo Collaboration's Approach

Earlier work by the University of Pennsylvania group had revealed the preferential integration into genes. The Mayo group and others had shown that LEDGF tightly tethers HIV's integration-catalyzing enzyme, integrase, to human cell DNA. The Mayo researchers had also shown that LEDGF protects HIV integrase from the cell's attempts to destroy it, and that LEDGF actually is found inside the virus as it is poised to integrate into the genome. Combining the two lines of inquiry resulted in exploring the possibility that LEDGF influences where HIV integrates. A method called RNA interference allowed the Mayo group to engineer target cells that were depleted of LEDGF.

The University of Pennsylvania and Salk investigators then determined exactly where thousands of different HIV DNA copies integrated in the genomes of these cells, and compared the pattern to that in cells still having LEDGF. Not only did depletion of LEDGF reduce the ability of HIV to land within genes, it also shifted the virus toward landing in DNA that differed in its basic letter makeup (DNA with more Gs and Cs as opposed to As and Ts). These data support the conclusion that LEDGF plays a guidance role in HIV integration.


Background Biology

To infect a cell, HIV must carry out two basic steps:

  • Its genetic material, or RNA, must be copied into DNA. *This DNA version, which is about 10,000 letters long, must then be inserted (integrated) into the DNA of the genome, between two of its approximately 3 billion letters. The integration step is carried out by an HIV protein called integrase.

Integration of HIV is permanent - which is why current antiviral drugs do not cure HIV infection. They only suppress it. When the drugs are stopped, the permanently archived HIV copies serve as launching pads to renew cycles of infection.

The Next Steps

The next steps are to determine if LEDGF can play additional roles for the virus, and to try to use this new knowledge to manipulate LEDGF and integrase to thwart HIV in its takeover of cells. "The presence of LEDGF in the integration-competent form of the virus, the ability of LEDGF to tether integrase to chromatin, its ability to protect it from the cell's protein-degrading machinery, and, as the current results show, to influence where the virus integrates, all add up to a very intriguing picture," says Dr. Poeschla. "After further research yields more knowledge about the detailed steps involved and clarifies the full role of LEDGF in the viral life cycle, it is conceivable that the knowledge gained could eventually be applied to the design of antiviral therapies." He adds that the findings may also help guide researchers to learn more about how gene therapy vehicles derived from HIV and other retroviruses sometimes cause leukemia and other cancers. A long-term goal would be to build on such knowledge to target the vectors to areas in the genome where they do not cause damage.

Collaboration and Support

The research team also included Mayo Clinic researcher Manuel Llano, M.D., Ph.D.; University of Pennsylvania researchers Angela Ciuffi, Ph.D., Christian Hoffman, Jeremy Leipzig, and Frederic Bushman, Ph.D.; and the Salk Institute researchers Paul Shinn and Joseph Ecker, Ph.D.

Their work was supported by the National Institutes of Health, the Tietze Foundation, the J.B. Pendleton Charitable Trust, the R. and F. Withington and the E.B. Burns Foundation and, in part, by the Swiss National Science Foundation.