BackgroundThe persistence of the latent HIV-1 reservoir is a major obstacle to curing HIV-1 infection. HIV-1 integrates into the cellular genome and some targeted genomic loci are frequently detected in clonally expanded latently HIV-1 infected cells, for instance, the geneBTB domain and CNC homology 2 (BACH2).MethodsWe investigated HIV-1 promoter activity after integration into specific sites inBACH2in Jurkat T-cells. The HIV-1-based vector LTatCL[M] contains two fluorophores: (1) Cerulean, which reports the activity of the HIV-1 promoter and (2) mCherry driven by a constitutive promotor and flanked by genetic insulators. This vector was inserted into introns 2 and 5 ofBACH2of Jurkat T-cells via CRISPR/Cas9 technology in the same and convergent transcriptional orientation ofBACH2, and into the genomic safe harbour AAVS1. Single cell clones representing active (Cerulean⁺/mCherry⁺) and inactive (Cerulean^–/mCherry⁺) HIV-1 promoters were characterised.ResultsUpon targeted integration of the 5.3 kb vector LTatCL[M] intoBACH2, the HIV-1 promoter was gradually silenced as reflected by the decrease in Cerulean expression over a period of 162 days. Silenced HIV-1 promoters could be reactivated by TNF-α and Romidepsin. This observation was independent of the targeted intron and the transcriptional orientation.BACH2mRNA and protein expression was not impaired by mono-allelic integration of LTatCL[M].ConclusionSuccessful targeted integration of the HIV-1-based vector LTatCL[M] allows longitudinal analyses of HIV-1 promoter activity.