All of the required signals for gene expression are found in the LTRs: Enhancer, promoter (can have both transcriptional enhancers or regulatory elements), transcription initiation (such as capping), transcription terminator and polyadenylation signal.
U3 and U5 has been further subdivided according to transcription factor sites and their impact on LTR activity and viral gene expression.
The multi-step process of reverse transcription results in the placement of two identical LTRs, each consisting of a U3, R, and U5 region, at either end of the proviral DNA.
The ends of the LTRs subsequently participate in integration of the provirus into the host genome.
Once the provirus has been integrated, the LTR on the 5′ end serves as the promoter for the entire retroviral genome, while the LTR at the 3′ end provides for nascent viral RNA polyadenylation and, in HIV-1, HIV-2, and SIV, encodes the accessory protein, Nef.
Long terminal repeats (LTRs) are identical sequences of DNA that repeat hundreds or thousands of times found at either end of retrotransposons or proviral DNA formed by reverse transcription of retroviral RNA The LTRs are partially transcribed into an RNA intermediate, followed by reverse transcription into complementary DNA (c DNA) and ultimately ds DNA (double-stranded DNA) with full LTRs. This method of dating is used by paleovirologists, though it fails to take into account confounding factors such as gene-conversion and homologous recombination.
The LTRs then mediate integration of the retroviral DNA via an LTR specific integrase into another region of the host chromosome. in length and, like other retroviral LTRs, is segmented into the U3, R, and U5 regions. As 5' and 3' LTRs are identical upon insertion, the difference between paired LTRs can be used to estimate the age of ancient retroviral insertions. Retroviruses such as Human Immunodeficiency Virus (HIV) use this basic mechanism.However, it has been suggested that the transcriptional activity of the 5' LTR is far greater than that of the 3' LTR, a situation that is very similar to that of other retroviruses.During transcription of the human immunodeficiency virus type 1 provirus, polyadenylation signals present in the 5' long terminal repeat (LTR) are disregarded while the identical polyadenylation signals present in the 3'LTR are utilized efficiently.It has been suggested that transcribed sequences present within the HIV-1 LTR U3 region act in cis to enhance polyadenylation within the 3' LTR.