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| Status |
Public on Mar 24, 2024 |
| Title |
Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells [4C-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Cis-regulatory elements (CRE) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of adjacent T cell costimulatory genes CD28, CTLA4, and ICOS encoding regulators of cell-mediated immunity. Tiling CRISPR interference (CRISPRi) screens in primary human T cells – both Conventional and Regulatory subsets – uncovered gene-, cell subset- and stimulation-specific CREs. Integrating these data with CRISPR knockout (KO) screens and ATAC-seq characterization identified trans regulators influencing chromatin states at specific CRISPRi-responsive elements to control costimulatory gene expression. Lastly, we discovered and extensively validated a critical CTCF boundary that governs this locus, serving to reinforce CRE interaction with CTLA4 while also preventing promiscuous activation of CD28. By systematically mapping CREs and associated trans regulators directly in primary human T cell subsets, this work overcomes longstanding experimental limitations to decode context-dependent gene regulatory programs in a complex, multi-gene locus critical to immune homeostasis.
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| Overall design |
Primary human T cells were isolated, transduced with dCas9-ZIM3 and either control or CTCF-2 sgRNAs, and 4C-seq libraries prepared.
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| Contributor(s) |
Mowery C, Chen Z, Casaní-Galdón S, Bernstein BE, Marson A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Mar 11, 2024 |
| Last update date |
Mar 25, 2024 |
| Contact name |
Alexander Marson |
| Organization name |
Gladstone-UCSF Institute of Genomic Immunology
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| Street address |
1650 Owens Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE261332 |
Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells |
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| Relations |
| BioProject |
PRJNA1086506 |
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