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Series GSE228464 Query DataSets for GSE228464
Status Public on Apr 12, 2023
Title Chromatin context-dependent regulation and modulation of prime editing [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Prime editing is a powerful means of introducing precise changes to specific locations in mammalian genomes. However, the widely varying efficiency of prime editing across target sites of interest has limited its adoption in the context of both basic research and clinical settings. Here, we set out to exhaustively characterize the impact of the cis-chromatin environment on prime editing efficiency. Utilizing a newly developed and highly sensitive method for mapping the genomic locations of a randomly integrated “sensor”, we identify specific epigenetic features that strongly correlate with the highly variable efficiency of prime editing across different genomic locations. Next, to assess the interaction of trans-acting factors with the cis-chromatin environment, we develop and apply a pooled genetic screening approach with which the impact of knocking down various DNA repair factors on prime editing efficiency can be stratified by cis-chromatin context. Finally, we demonstrate that we can dramatically modulate the efficiency of prime editing through epigenome editing, i.e. enhancing (or restricting) local chromatin accessibility in order to increase (or decrease) the efficiency of prime editing at a target site. Looking forward, we envision that the insights and tools described here will broaden the range of both basic research and therapeutic contexts in which prime editing is useful.
Overall design Bulk RNA sequencing of K562 cells (wild-type) and cells treated with CRISPRoff. For the CRISPRoff experiment, cells were transiently transfected with CRISPRoff-v2.1 and paired gRNA targeting gene promoters. After FACS sorting and expansion of the transfected cells, cells' total RNAs were extracted and used for bulk RNA sequencing. Differential gene expression analyses were performed between promoter-targeting gRNA (USP7, METTL2A, and LRRC8C) treated cells versus cells treated with non-targeting control gRNAs.
Contributor(s) Li X, Chen W, Martin BK, Calderon D, Lee C, Choi J, Chardon FM, McDiarmid T, Kim H, Lalanne J, Nathans JF, Shendure J
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Submission date Mar 29, 2023
Last update date Jan 03, 2024
Contact name Xiaoyi Li
Organization name University of Washington
Department Department of Genome Sciences
Lab Jay Shendure
Street address 3720 15th Ave NE
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (27)
GSM7122381 RNA sequencing of wild-type K562 cells [K562_DMSO_Rep1]
GSM7122382 RNA sequencing of wild-type K562 cells [K562_DMSO_Rep2]
GSM7122383 RNA sequencing of wild-type K562 cells [K562_DMSO_Rep3]
This SubSeries is part of SuperSeries:
GSE228465 Chromatin context-dependent regulation and epigenetic modulation of prime editing
BioProject PRJNA949972

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Supplementary file Size Download File type/resource
GSE228464_ATAC_HLTF.csv.gz 2.4 Mb (ftp)(http) CSV
GSE228464_CRISPRoff_RNAseq_count.csv.gz 623.3 Kb (ftp)(http) CSV
GSE228464_K562_WT_TPM.csv.gz 592.7 Kb (ftp)(http) CSV
GSE228464_RNAseq_HLTF_HLTF2367_vs_control.csv.gz 399.3 Kb (ftp)(http) CSV
GSE228464_RNAseq_HLTF_HLTF2623_vs_control.csv.gz 463.8 Kb (ftp)(http) CSV
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