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| 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
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| 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.
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| 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.
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| 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 |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 29, 2023 |
| Last update date |
Jan 03, 2024 |
| Contact name |
Xiaoyi Li |
| E-mail(s) |
xyli10@uw.edu
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| Organization name |
University of Washington
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| Department |
Department of Genome Sciences
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| Lab |
Jay Shendure
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| Street address |
3720 15th Ave NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL30173 |
NextSeq 2000 (Homo sapiens) |
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| Samples (27)
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| 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] |
| GSM7122384 |
RNA sequencing of K562 clone 5, CRISPRoff [K562-SC1-5-OFF-Ctrl-Rep1] |
| GSM7122385 |
RNA sequencing of K562 clone 5, CRISPRoff [K562-SC1-5-OFF-Ctrl-Rep2] |
| GSM7122386 |
RNA sequencing of K562 clone 5, CRISPRoff [K562-SC1-5-OFF-USP7-Rep1] |
| GSM7122387 |
RNA sequencing of K562 clone 5, CRISPRoff [K562-SC1-5-OFF-USP7-Rep2] |
| GSM7122388 |
RNA sequencing of K562 clone 5, CRISPRoff [K562-SC1-5-OFF-METTL2A-Rep1] |
| GSM7122389 |
RNA sequencing of K562 clone 5, CRISPRoff [K562-SC1-5-OFF-METTL2A-Rep2] |
| GSM7122390 |
RNA sequencing of K562 clone 5, CRISPRoff [K562-SC1-5-OFF-LRRC8C-Rep1] |
| GSM7122391 |
RNA sequencing of K562 clone 5, CRISPRoff [K562-SC1-5-OFF-LRRC8C-Rep2] |
| GSM8000245 |
ATAC seq library of K562 cells expressing control shRNA Rep1 |
| GSM8000246 |
ATAC seq library of K562 cells expressing control shRNA Rep2 |
| GSM8000247 |
RNA seq library of K562 cells expressing control shRNA Batch1 Rep1 |
| GSM8000248 |
RNA seq library of K562 cells expressing control shRNA Batch1 Rep2 |
| GSM8000249 |
RNA seq library of K562 cells expressing control shRNA Batch2 Rep1 |
| GSM8000250 |
RNA seq library of K562 cells expressing control shRNA Batch2 Rep2 |
| GSM8000251 |
RNA seq library of K562 cells expressing control shRNA Batch2 Rep3 |
| GSM8000252 |
ATAC seq library of K562 cells expressing shRNA(HLTF_6596_2367) targeting HLTF Rep1 |
| GSM8000253 |
ATAC seq library of K562 cells expressing shRNA(HLTF_6596_2367) targeting HLTF Rep2 |
| GSM8000254 |
RNA seq library of K562 cells expressing shRNA(HLTF_6596_2367) targeting HLTF Batch1 Rep1 |
| GSM8000255 |
RNA seq library of K562 cells expressing shRNA(HLTF_6596_2367) targeting HLTF Batch1 Rep2 |
| GSM8000256 |
ATAC seq library of K562 cells expressing shRNA(HLTF_6596_2623) targeting HLTF Rep1 |
| GSM8000257 |
ATAC seq library of K562 cells expressing shRNA(HLTF_6596_2623) targeting HLTF Rep2 |
| GSM8000258 |
RNA seq library of K562 cells expressing shRNA(HLTF_6596_2623) targeting HLTF Batch2 Rep1 |
| GSM8000259 |
RNA seq library of K562 cells expressing shRNA(HLTF_6596_2623) targeting HLTF Batch2 Rep2 |
| GSM8000260 |
RNA seq library of K562 cells expressing shRNA(HLTF_6596_2623) targeting HLTF Batch2 Rep3 |
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| This SubSeries is part of SuperSeries: |
| GSE228465 |
Chromatin context-dependent regulation and epigenetic modulation of prime editing |
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| Relations |
| BioProject |
PRJNA949972 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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