ATPase Chromatin Remodeling Complexes as Modulators of HIV-1 Latency and Therapeutic Targets

About This Grant

Abstract Significance: HIV persists in long-lived CD4⁺ T cell reservoirs despite suppressive ART, as integrated proviruses remain poised for reactivation. Chromatin remodeling is a central barrier to durable silencing, yet most studies have focused on SWI/SNF family members. The roles of non- SWI/SNF remodelers remain poorly defined, limiting our ability to rationally design host-directed “block-and-lock” cure strategies. Our unbiased shRNA screen of all 16 human remodeler ATPases identified EP400, CHD1, and CHD9 as repressors and INO80A, SMARCA5, and CHD2 as activators, establishing chromatin remodeling as a key determinant of HIV latency. Innovation: Our prior studies revealed that the p400 complex regulates HIV transcription through dual mechanisms: directly, by engaging Tat via the DMAP1 subunit to block Tat-TAR RNA interactions and restrict p-TEFb recruitment; and indirectly, by altering host transcriptional programs that control T cell activation states. Building on this mechanistic precedent and methodological platform, we now focus on INO80A, SMARCA5, CHD1, and CHD2, remodelers from distinct ATPase families that govern Tat-independent checkpoints at initiation, pause release, and elongation. Methodologically, we will apply TurboID-ChAP-MS (locus-specific proteomics), BEM-seq (single-nucleosome mapping), and degron-mediated acute depletion with ATPase-dead rescue to interrogate remodeler function with unprecedented resolution. Approach: Aim 1 will define the ATPase requirement and transcriptional checkpoints regulated by INO80A, SMARCA5, CHD1, and CHD2 using degron/CRISPR perturbations, ChIP-seq, nascent RNA profiling, and nucleosome mapping. Aim 2 will characterize remodeler-specific complexes and Tat dependence at the HIV promoter via TurboID proximity labeling integrated with chromatin affinity purification-mass spectrometry. Aim 3 will test combinatorial perturbations in Jurkat and primary CD4⁺ T cell latency models, including ART-suppressed donor cells, to identify synergistic “block-and-lock” strategies that enforce durable proviral silencing. Impact: By defining remodeler-specific mechanisms at discrete transcriptional checkpoints and leveraging their enzymatic, druggable activities, this work will establish chromatin remodeling as a therapeutic axis for durable HIV suppression and functional cure.