학술논문
Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells
Document Type
Original Paper
Author
Mowery, Cody T.; Freimer, Jacob W.; Chen, Zeyu; Casaní-Galdón, Salvador; Umhoefer, Jennifer M.; Arce, Maya M.; Gjoni, Ketrin; Daniel, Bence; Sandor, Katalin; Gowen, Benjamin G.; Nguyen, Vinh; Simeonov, Dimitre R.; Garrido, Christian M.; Curie, Gemma L.; Schmidt, Ralf; Steinhart, Zachary; Satpathy, Ansuman T.; Pollard, Katherine S.; Corn, Jacob E.; Bernstein, Bradley E.; Ye, Chun Jimmie; Marson, Alexander
Source
Nature Genetics. 56(6):1156-1167
Subject
Language
English
ISSN
1061-4036
1546-1718
1546-1718
Abstract
Cis-regulatory elements (CREs) 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 the adjacent costimulatory genes CD28, CTLA4 and ICOS, encoding regulators of T 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. Integration with CRISPR knockout screens and assay for transposase-accessible chromatin with sequencing (ATAC-seq) profiling identified trans regulators influencing chromatin states at specific CRISPRi-responsive elements to control costimulatory gene expression. We then discovered a critical CCCTC-binding factor (CTCF) boundary that reinforces 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.
Functional characterization of the regulatory landscape of the adjacent costimulatory genes CD28, CTLA4 and ICOS in primary human T cell subsets identifies context-dependent programs controlling this locus critical for immune homeostasis.
Functional characterization of the regulatory landscape of the adjacent costimulatory genes CD28, CTLA4 and ICOS in primary human T cell subsets identifies context-dependent programs controlling this locus critical for immune homeostasis.