ATAC-seq of SLTM knockdown in HIV infected Jurkats

In order to identify novel factors associated with regulation of HIV-1 transcription, we completed a genome-wide CRISPRi screen in a monogenic model of HIV-1. We identified SLTM mediated suppression of HIV-1 transcription. We hypothesized that SLTM would alter the chromatin acessibility at the site of HIV-1 integration. We conducted ATAC-seq of CRISPR ready cells encoding a single HIV-1 provirus in the SPECC1 gene transduced with a gRNA targetting SLTM and a Non-Targeting gRNA. We found that SLTM knockdown increased HIV-1 proviral acessibility across the provirus and host acessibility downstream of the site of HIV-1 integration. Overall design: We conducted ATAC-seq of a monogenic Jurkat line with HIV-1 integrated into SPECC1. This line stably expresses dCas9-KRAB and nontargetting and SLTM guide RNAs.