A modular CRISPR screen identifies individual and combination pathways contributing to HIV-1 latency

The goal of this CRISPR-based screen (Latency HIV-CRISPR) is to identify HIV-1 latency factors by evaluating multiple pathways simultaneously. Here are Illumina sequencing data and counts files from a Latency HIV-CRISPR screen using a custom guide RNA library targeting human epigenome genes (HuEpi). The Latency HIV-CRISPR screens described here were performed in clonal ZAP knockout J-Lat 10.6 (PMID: 12682019) or J-Lat 5A8 (PMID: 24204950) cells lines as ZAP inhibition of the HIV-CRISPR vector has been previously described (PMID: 30520725). The screens were performed in the presence or absence of AZD5582, a SMAC mimetic and latency reversal agent, in order to identify factors that are dependent and independent of this transcriptional activator. Overall design: Latency HIV-CRISPR is performed by generating a pool of ZAP-knockout J-Lat 10.6 and 5A8 cells that are each knocked out for human epigenome genes using the HuEpi guide RNA library. Each knockout pool is then treated with or without a low-activating dosage (10 nM) of AZD5582 for 24 hours. Each screen is performed in two biological replicates. Afterwards, for each condition, the cell pellets were harvested, genomic DNA (gDNA) was extracted, and sequencing was performed to evaluate the single guide RNA (sgRNA) representation of the library. Simultaneously, the viral supernatant was harvested, viral RNA (vRNA) was extracted, and sequencing was performed. By comparing the sgRNA representation of the viral RNA to the library representation of the genomic DNA, the sgRNAs that are enriched and depleted in the viral population are associated with potential HIV-1 latency factors. The plasmid library of the HIV-CRISPR HuEpi guide RNA library was also sequenced.