Suppression of CpG in HIV

The immune system has an inflammatory reaction to the DNA sequence "CG", as it uses this to detect foreign DNA. Interestingly, this sequence is very rare in HIV, appearing only where it is required for binding or because of overlapping reading frames. I suspect that this helps HIV evade the immune system. The following figure shows where CG shows up in the HIV genome; I had this published in the journal Trends in Microbiology.

Location of CpG dinucleotides in the HIV-1 genome. The location of each CpG in the HIV genome is indicated by a vertical line, with a histogram showing the numbers of CpGs in each region above. The majority of the CpGs is clustered near the 5' and 3' ends of the genome. Only 0.88% of the dinucleotides are CpG, compared with 6.25% expected, assuming random base usage (the HIVBRUCG sequence was analyzed). The profound CpG suppression in the HIV genome may help the retrovirus to avoid activating the CpG host-defense mechanism.

Reference:
A. Krieg, ``Lymphocyte activation by CpG dinucleotide motifs in prokaryotic DNA,'' Trends in Microbiology, 4(2), Feb. 1996, p. 75.

Ken Shirriff: shirriff@eng.sun.com