{"doi":"10.1101/2020.03.30.011395","title":"HIV-1 promoter is gradually silenced when integrated into <i>BACH2</i>","abstract":"Abstract The persistence of the latent HIV-1 reservoir is a major obstacle to cure 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 gene BTB domain and CNC homology 2 (BACH2) . We investigated HIV-1 promoter activity after integration into specific sites in BACH2 . 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 of BACH2 of Jurkat T-cells via CRISPR/Cas9 technology in the same and convergent transcriptional orientation of BACH2 , and into the genomic safe harbour AAVS1. Single cell clones representing active (Cerulean + /mCherry + ) and inactive (Cerulean − /mCherry + ) HIV-1 promoters were characterized. Upon targeted integration of the 5.3 kb vector LTatCL[M] into BACH2 , active HIV-1 promoters were gradually silenced as reflected by decrease in Cerulean expression over a period of 162 days in culture. Silenced HIV-1 promoters could be reactivated by TNF-α and Romidepsin. This observation was independent of the targeted intron and the transcriptional orientation. BACH2 mRNA and protein expression was not impaired by mono-allelic integration of LTatCL[M]. Our results show that the HIV-1 promoter is silenced when integrated into BACH2 without impairing BACH2 mRNA and protein expression. This might contribute to HIV-1 persistence, enabling infected T-cells to complete differentiation into a memory phenotype, persist, and clonally expand over time.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":123557,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9625,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":438497,"name":"Yik Lim Kok","orcid":null,"position":1,"is_corresponding":false},{"id":437379,"name":"Lisa Jörimann","orcid":"0009-0006-3076-2999","position":2,"is_corresponding":false},{"id":438498,"name":"Audrey Kelley","orcid":null,"position":3,"is_corresponding":false},{"id":437380,"name":"Kathrin Neumann","orcid":"0000-0001-5034-6999","position":4,"is_corresponding":false},{"id":437381,"name":"Daniel Heinzer","orcid":"0000-0002-3282-4042","position":5,"is_corresponding":false},{"id":17192,"name":"Toni Cathomen","orcid":"0000-0002-7757-4630","position":6,"is_corresponding":false},{"id":437382,"name":"Karin J. Metzner","orcid":"0000-0003-4862-1503","position":7,"is_corresponding":false},{"id":437378,"name":"Anne Inderbitzin","orcid":"0000-0003-4742-5201","position":0,"is_corresponding":true}],"reference_count":44,"raw_metadata":null,"created_at":"2026-07-18T23:15:03.403566Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}