HIRIS: HIV-1 Reservoirs Integration Sites “high-rise”

Proviral orientations of HIV-1

When using the data in HIRIS, it’s useful to have a clear, careful understanding of how reverse-transcribed HIV-1 integrates into human genomic DNA.

HIV-1 starts as single-stranded RNA diagramed like so:

 HIV-1  5ʹ R-U5~GAG~~~ENV~U3-R 3ʹ

The R, U5, and U3 regions form the building blocks of the two long terminal repeat (LTR) regions (composed of U3-R-U5) in the double-stranded DNA produced by reverse transcriptase:

 HIV-1  5ʹLTR~GAG~~~ENV~3ʹLTR
        5ʹLTR~GAG~~~ENV~3ʹLTR (complementary strand)

There are two orientations this double-stranded HIV-1 DNA may be integrated into genomic DNA as a provirus:

                    HIV-1
 Chr  1 ---- 5ʹLTR~GAG~~~ENV~3ʹLTR ---- N
      1 ---- 5ʹLTR~GAG~~~ENV~3ʹLTR ---- N
 
                    HIV-1
 Chr  1 ---- 3ʹLTR~ENV~~~GAG~5ʹLTR ---- N
      1 ---- 3ʹLTR~ENV~~~GAG~5ʹLTR ---- N

The following diagrams form a truth table of provirus orientation with respect to the chromosome crossed by provirus orientation with respect to the gene. Pay careful attention to the location of GAG and ENV.

Provirus is forward with respect to the chromosome…

…and forward with respect to the gene

         Gene is forward with
         respect to chromosome
         |——————→
 Chr  1 ---- 5ʹLTR~GAG~~~ENV~3ʹLTR ---- N
      1 ---- 5ʹLTR~GAG~~~ENV~3ʹLTR ---- N

…and reverse with respect to the gene

 Chr  1 ---- 5ʹLTR~GAG~~~ENV~3ʹLTR ---- N
      1 ---- 5ʹLTR~GAG~~~ENV~3ʹLTR ---- N
                             ←——————| Gene is reverse with
                                      respect to chromosome

Provirus is reverse with respect to the chromosome…

…and forward with respect to the gene

 Chr  1 ---- 3ʹLTR~ENV~~~GAG~5ʹLTR ---- N
      1 ---- 3ʹLTR~ENV~~~GAG~5ʹLTR ---- N
                             ←——————| Gene is reverse with
                                      respect to chromosome

…and reverse with respect to the gene

         Gene is forward with
         respect to chromosome
         |——————→
 Chr  1 ---- 3ʹLTR~ENV~~~GAG~5ʹLTR ---- N
      1 ---- 3ʹLTR~ENV~~~GAG~5ʹLTR ---- N

Orientation tuples of (chromosome, gene) which occur together

The above diagrams encompass all of the possible physical integrations. For any given gene, however, only one of two sets of orientation tuples can be true:

1. FF and RR — gene itself is forward with respect to the chromosome
2. FR and RF — gene itself is reverse with respect to the chromosome

Sets of tuples such as FF and FR aren’t possible because they imply conflicting orientations of the gene to the chromosome.¹ Such combinations most likely indicate that the data is bogus or was wrongly interpreted.