2022
DOI: 10.1101/2022.08.23.504195
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A modular CRISPR screen identifies individual and combination pathways contributing to HIV-1 latency

Abstract: Transcriptional silencing of latent HIV-1 proviruses entails complex and overlapping mechanisms and are a major barrier to in vivo elimination of HIV-1. We developed a new latency CRISPR screening strategy, called Latency HIV-CRISPR, which uses the packaging of guideRNA-encoding lentiviral vector genomes into the supernatant of budding virions as a direct readout of factors involved in the maintenance of HIV-1 latency. We developed a custom guideRNA library targeting epigenetic regulatory genes and paired the … Show more

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“…We also added back the known dependency factors that fell below this threshold in the screen including CCR5 and PAPSS1 which are essential for CCR5-dependent strains. Because transcription and chromatin modification/ regulation were major categories of negatively enriched genes in the whole genome screen (Figure 1C), we also performed an additional targeted screen using a custom-designed Human Epigenome (HuEpi) library consisting of 838 human epigenome and epigenetic regulator genes (17) and included any gene with <10% false discovery rate (FDR) from the HuEpi screen that were not already included in the top TKOv3 gene list (Supplemental Figure S1A) as well as smaller number of negatively enriched genes in an ISG-related library (11) (Supplemental Figure S1B), resulting in an additional 131 genes. Finally, 11 genes previously called “non-essential” (18) that were neither depleted nor enriched in our genome-wide screen were included as negative control genes.…”
Section: Resultsmentioning
confidence: 99%
“…We also added back the known dependency factors that fell below this threshold in the screen including CCR5 and PAPSS1 which are essential for CCR5-dependent strains. Because transcription and chromatin modification/ regulation were major categories of negatively enriched genes in the whole genome screen (Figure 1C), we also performed an additional targeted screen using a custom-designed Human Epigenome (HuEpi) library consisting of 838 human epigenome and epigenetic regulator genes (17) and included any gene with <10% false discovery rate (FDR) from the HuEpi screen that were not already included in the top TKOv3 gene list (Supplemental Figure S1A) as well as smaller number of negatively enriched genes in an ISG-related library (11) (Supplemental Figure S1B), resulting in an additional 131 genes. Finally, 11 genes previously called “non-essential” (18) that were neither depleted nor enriched in our genome-wide screen were included as negative control genes.…”
Section: Resultsmentioning
confidence: 99%