Reverse transcriptase (RT) and integrase (IN) are retrovirus enzymes to convert virus genomic RNA into provirus DNA state in host cells. The RT and IN encoded tandemly in the pol gene, are translated as a fused form and incorporated into the virus particles. Recently, we discovered the potential role of HIV-1 IN to regulate the reverse transcription through the fused state with RT (RT-IN). On the other hand, analysis of HIV-1 transcripts have revealed the variations in number of guanine residue at the 5' end (5'G) due to fluctuations in the transcription initiation point within HIV-1 provirus DNA. Importantly, the number of 5'G dictates the packaging of HIV genome RNA into virus particles serving as a template for the reverse transcription reaction. In this review, we provide new insights into the mechanism of HIV genome replication based on our recent findings of the structural-functional correlation of HIV enzymes (RT and IN) and virus genomic RNA.