%0 Journal Article
%T Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells.
%A Mowery CT
%A Freimer JW
%A Chen Z
%A Casaní-Galdón S
%A Umhoefer JM
%A Arce MM
%A Gjoni K
%A Daniel B
%A Sandor K
%A Gowen BG
%A Nguyen V
%A Simeonov DR
%A Garrido CM
%A Curie GL
%A Schmidt R
%A Steinhart Z
%A Satpathy AT
%A Pollard KS
%A Corn JE
%A Bernstein BE
%A Ye CJ
%A Marson A
%J Nat Genet
%V 56
%N 6
%D 2024 Jun 29
%M 38811842
%F 41.307
%R 10.1038/s41588-024-01743-5
%X 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.