{Reference Type}: Journal Article
{Title}: Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells.
{Author}: Mowery CT;Freimer JW;Chen Z;Casaní-Galdón S;Umhoefer JM;Arce MM;Gjoni K;Daniel B;Sandor K;Gowen BG;Nguyen V;Simeonov DR;Garrido CM;Curie GL;Schmidt R;Steinhart Z;Satpathy AT;Pollard KS;Corn JE;Bernstein BE;Ye CJ;Marson A;
{Journal}: Nat Genet
{Volume}: 56
{Issue}: 6
{Year}: 2024 Jun 29
{Factor}: 41.307
{DOI}: 10.1038/s41588-024-01743-5
{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.