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Chick BY, Hargreaves DC. RNA polymerase II promoter-proximal pausing promotes BAF chromatin binding and remodeling. Nat Genet 2024; 56:19-20. [PMID: 38129539 DOI: 10.1038/s41588-023-01628-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Affiliation(s)
- Brent Y Chick
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of California at San Diego, La Jolla, CA, USA
| | - Diana C Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
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McDonald B, Chick BY, Hargreaves DC, Kaech SM. Early Chromatin Remodeling Events in Acutely Stimulated CD8 + T Cells. Yale J Biol Med 2023; 96:467-473. [PMID: 38161581 PMCID: PMC10751865 DOI: 10.59249/axgu7370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
T cells undergo extensive chromatin remodeling over several days following stimulation through the T cell receptor. However, the kinetics and gene loci targeted by early remodeling events within the first 24 hours of T cell priming to orchestrate effector differentiation have not been well described. We identified that chromatin accessibility is rapidly and extensively remodeled within 1 hour of stimulation of naïve CD8+ T cells, leading to increased global chromatin accessibility at many effector T cell-associated genes that are enriched for AP-1, early growth response (EGR), and nuclear factor of activated T cells (NFAT) binding sites, but this short duration of stimulation is insufficient for commitment to clonal expansion in vivo. Sustained 24-hour stimulation led to further chromatin remodeling and was sufficient to enable clonal expansion. These data suggest that the duration of antigen receptor signaling is intimately coupled to chromatin remodeling and activation of genes involved in effector cell differentiation and highlight a potential mechanism that helps CD8+ T cells discriminate between foreign- and self-antigens.
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Affiliation(s)
- Bryan McDonald
- NOMIS Center for Immunobiology and Microbial
Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of
California San Diego, La Jolla, CA, USA
| | - Brent Y. Chick
- Molecular and Cell Biology Laboratory, Salk Institute
for Biological Studies, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of
California at San Diego, La Jolla, California, USA
| | - Diana C. Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute
for Biological Studies, La Jolla, CA, USA
| | - Susan M. Kaech
- NOMIS Center for Immunobiology and Microbial
Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
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McDonald B, Chick BY, Ahmed NS, Burns M, Ma S, Casillas E, Chen D, Mann TH, O'Connor C, Hah N, Hargreaves DC, Kaech SM. Canonical BAF complex activity shapes the enhancer landscape that licenses CD8 + T cell effector and memory fates. Immunity 2023; 56:1303-1319.e5. [PMID: 37315534 PMCID: PMC10281564 DOI: 10.1016/j.immuni.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/08/2023] [Accepted: 05/10/2023] [Indexed: 06/16/2023]
Abstract
CD8+ T cells provide host protection against pathogens by differentiating into distinct effector and memory cell subsets, but how chromatin is site-specifically remodeled during their differentiation is unclear. Due to its critical role in regulating chromatin and enhancer accessibility through its nucleosome remodeling activities, we investigated the role of the canonical BAF (cBAF) chromatin remodeling complex in antiviral CD8+ T cells during infection. ARID1A, a subunit of cBAF, was recruited early after activation and established de novo open chromatin regions (OCRs) at enhancers. Arid1a deficiency impaired the opening of thousands of activation-induced enhancers, leading to loss of TF binding, dysregulated proliferation and gene expression, and failure to undergo terminal effector differentiation. Although Arid1a was dispensable for circulating memory cell formation, tissue-resident memory (Trm) formation was strongly impaired. Thus, cBAF governs the enhancer landscape of activated CD8+ T cells that orchestrates TF recruitment and activity and the acquisition of specific effector and memory differentiation states.
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Affiliation(s)
- Bryan McDonald
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Brent Y Chick
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Nasiha S Ahmed
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mannix Burns
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Shixin Ma
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Eduardo Casillas
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Dan Chen
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Thomas H Mann
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Carolyn O'Connor
- Flow Cytometry Core, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nasun Hah
- Chapman Charitable Foundations Genomic Sequencing Core, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Diana C Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Chick BY, Hargreaves DC. Switching under selection: how CoREST controls endocrine therapy resistance in ER + breast cancer. Nat Struct Mol Biol 2022; 29:1040-1042. [PMID: 36344845 DOI: 10.1038/s41594-022-00858-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Brent Y Chick
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.,Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Diana C Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
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