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Series GSE213639 Query DataSets for GSE213639
Status Public on Dec 26, 2022
Title A modular CRISPR screen identifies individual and combination pathways contributing to HIV-1 latency
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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 screen with and without a latency reversal agent – AZD5582, an activator of the non-canonical NFkB pathway – to examine a combination of mechanisms controlling HIV-1 latency. A component of the Nucleosome Acetyltransferase of H4 histone acetylation (NuA4 HAT) complex, ING3, acts in concert with AZD5582 to activate proviruses in J-Lat cell lines and in a primary CD4+ T cell model of HIV-1 latency. We found that the knockout of ING3 reduces acetylation of the H4 histone tail and BRD4 occupancy on the HIV-1 LTR, and the combination of ING3 knockout with the activation of non-canonical NFkB via AZD5582 act together to dramatically increase initiation and elongation of RNA Polymerase II on the HIV-1 provirus in a manner that is nearly unique among all cellular promoters.
 
Overall design We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.
 
Contributor(s) Hsieh E, Janssens DH, Paddison PJ, Browne EP, OhAinle M, Henikoff S, Emerman M
Citation(s) 36706161
Submission date Sep 19, 2022
Last update date Mar 27, 2023
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platforms (1)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (89)
GSM6590598 JLat_Ing3_AZD_Brd4_R1_(220224_DJ_Hs_JLat_Ing3_Brd4_Epi_021622)
GSM6590599 JLat_Ing3_AZD_Brd4_R2_(220224_DJ_Hs_JLat_Ing3_Brd4_BT_021622)
GSM6590600 JLat_Ing3_AZD_Brd4_R3_(220401_DJ_Jl_Ing3_AZD_Brd4_R1_0322)
This SubSeries is part of SuperSeries:
GSE215430 A modular CRISPR screen identifies individual and combination pathways contributing to HIV-1 latency
Relations
BioProject PRJNA881982

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
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Supplementary file Size Download File type/resource
GSE213639_AutoCUTnTag_protocols_io.pdf 5.3 Mb (ftp)(http) PDF
GSE213639_RAW.tar 945.5 Mb (http)(custom) TAR (of BW)
GSE213639_hg38+HIV_masked.fasta.gz 905.2 Mb (ftp)(http) FASTA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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