{"doi":"10.1101/2020.05.01.072231","title":"An integrated genomics approach towards deciphering human genome codes shaping HIV-1 proviral transcription and fate","abstract":"ABSTRACT A large body of work has revealed fundamental principles of HIV-1 integration into the human genome. However, the effect of the integration site to proviral transcription activity has so far remained elusive. Here we combine open-source, large-scale datasets including epigenetics, transcriptome, and 3D genome architecture to interrogate the chromatin states, transcription activity landscape, and nuclear sub-compartments around HIV-1 integration sites in CD4 + T cells to decipher human genome codes shaping the transcription of proviral classes defined based on their position and orientation in the genome. Using a Hidden Markov Model, we describe the importance of specific chromatin states and genome architecture in the control of HIV-1 transcription activity. Additionally, implementation of a machine-learning logistic regression model reveals upstream chromatin accessibility, transcription activity, and categorical nuclear sub-compartments as optimal features predicting HIV-1 transcriptional outcomes. We finally demonstrate clinical relevance by interrogating the positions of intact proviruses persisting in patients under suppressive therapy and provide a compass compatible with clinical decision-making.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":124856,"datarank":0.18629390885778596,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0215020655575695,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.0215020655575695,"corpus_percentile":34.13785100951497,"corpus_rank":8515,"citation_count":2,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6675,"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":12401,"name":"Jeon Lee","orcid":"0000-0002-9071-7157","position":1,"is_corresponding":false},{"id":570096,"name":"Carlos Guzman","orcid":"0000-0003-2154-1765","position":2,"is_corresponding":false},{"id":22174,"name":"Venkat S. Malladi","orcid":"0000-0002-0144-0564","position":3,"is_corresponding":false},{"id":314068,"name":"Iván D’Orso","orcid":"0000-0002-1409-2351","position":4,"is_corresponding":false},{"id":570095,"name":"Holly Ruess","orcid":"0000-0001-9148-6672","position":0,"is_corresponding":true}],"reference_count":58,"raw_metadata":null,"created_at":"2026-07-18T23:15:11.632153Z","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":[]}