The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis-Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation

• Published in: Immunity (Cambridge, Mass.) Mass.), 2018-04, Vol.48 (4), p.659-674.e6
• Main Authors: Wang, Dapeng, Diao, Huitian, Getzler, Adam J., Rogal, Walter, Frederick, Megan A., Milner, Justin, Yu, Bingfei, Crotty, Shane, Goldrath, Ananda W., Pipkin, Matthew E.
• Format: Article
• Language: English
• Subjects: Accessibility; Animals; Antigens; Binding Sites - immunology; CD8 antigen; Cell Differentiation - immunology; Cell division; Cell Line; Cell Proliferation; Chlorocebus aethiops; Chromatin; Chromatin - metabolism; chromatin accessibility; Core Binding Factor Alpha 3 Subunit - metabolism; Cricetinae; Cytotoxicity; Differentiation; Effector cells; Enzyme Activation - immunology; epigenetic reprogramming; Experiments; Female; Gene expression; Genomics; Humans; Immunologic Memory - immunology; Infections; Interferon regulatory factor 4; Interferon Regulatory Factors - biosynthesis; Lymphocytes; Lymphocytes T; Male; Memory cells; memory CTL differentiation; Mice; Mice, Inbred C57BL; Mice, Knockout; pioneer transcription factor; Positive Regulatory Domain I-Binding Factor 1 - biosynthesis; Receptors, Antigen, T-Cell - immunology; Regulatory sequences; Runx-family transcription factor; Runx3 protein; Stimulation; T cell receptors; T-Lymphocytes, Cytotoxic - cytology; T-Lymphocytes, Cytotoxic - immunology; Transcription factors; Vero Cells
• ISSN: 1074-7613; 1097-4180
• DOI: 10.1016/j.immuni.2018.03.028

T cell receptor (TCR) stimulation of naive CD8+ T cells initiates reprogramming of cis-regulatory landscapes that specify effector and memory cytotoxic T lymphocyte (CTL) differentiation. We mapped regions of hyper-accessible chromatin in naive cells during TCR stimulation and discovered that the transcription factor (TF) Runx3 promoted accessibility to memory CTL-specific cis-regulatory regions before the first cell division and was essential for memory CTL differentiation. Runx3 was specifically required for accessibility to regions highly enriched with IRF, bZIP and PRDM1-like TF motifs, upregulation of TFs IRF4 and Blimp1, and activation of fundamental CTL attributes in early effector and memory precursor cells. Runx3 ensured that nascent CTLs differentiated into memory CTLs by preventing high expression of the TF T-bet, slowing effector cell proliferation, and repressing terminal CTL differentiation. Runx3 overexpression enhanced memory CTL differentiation during iterative infections. Thus, Runx3 governs chromatin accessibility during TCR stimulation and enforces the memory CTL developmental program. [Display omitted] •TCR signals and Runx3 initiate accessibility to the memory CTL cis-regulatory landscape•Runx3 promotes accessibility of cis-regions enriched with IRF, bZIP, and PRDM1 motifs•Runx3-deficiency impairs MP CTL transcription, differentiation, and memory CTL formation•Increased Runx3 dosage enhances differentiation of MP CTLs and memory CTLs Chromatin accessibility in naive CD8+ T cells is globally reprogrammed during infection. Wang et al. show that the transcription factor Runx3 programs chromatin accessibility during stimulation of naive CD8+ T cells, which establishes early transcriptional circuits that drive differentiation of nascent cytotoxic T lymphocytes (CTLs), and also represses terminal differentiation to ensure the development of long-lived memory CTLs.