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T-bet and Runx3 orchestrate effector CD8 T cell differentiation and lineage fidelity through cooperative and distinct chromatin regulatory mechanisms

ABSTRACT: T-bet and Runx3 orchestrate effector CD8 T cell differentiation and lineage fidelity through cooperative and distinct chromatin regulatory mechanisms

PROVIDER: PRJNA1291140 | ENA |

REPOSITORIES: ENA

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Integrative ATAC-seq and Cut&Run Profiling Reveals T-bet/Runx3 Epigenetic Regulation in Antiviral CD8+T Cells

Project description:Effector CD8? T cells must swiftly activate cytotoxic programs while preserving lineage identity and repressing alternative cell fates. T-bet and Runx3 serve as pivotal transcriptional regulators in this process, yet their integrated regulatory mechanisms have remained elusive owing to insufficient data on chromatin accessibility and binding dynamics. This study provides a systematic analysis of their cooperative and distinct roles in shaping the epigenetic landscape.

2025-07-19 | GSE302525 | GEO

T-bet and Runx3 orchestrate effector CD8 T cell differentiation and lineage fidelity through cooperative and distinct chromatin regulatory mechanisms

Project description:Effector CD8⁺T cells must rapidly acquire cytotoxic functions while maintaining lineage fidelity and suppressing alternative fates. T-bet and Runx3 are key transcription factors that drive this process, yet their integrated regulatory logic has remained unclear due to the lack of comprehensive binding and chromatin accessibility data. Here, we systematically dissect the cooperative and distinct roles of T-bet and Runx3 in shaping the transcriptional and epigenetic landscape of antiviral CD8⁺ T cells. Using CUT&RUN, ATAC-seq, RNA-seq and scRNA-seq across single and double knockout models, we reveal that T-bet and Runx3 coordinate effector differentiation through both chromatin remodeling–dependent and –independent mechanisms. T-bet preferentially binds promoters and restrains Th17-like programs, while Runx3 targets distal elements to suppress Tfh-associated genes and sustain cytotoxic identity. Our findings uncover a cis-regulatory logic wherein these factors act combinatorially to balance activation of effector programs with repression of alternative lineages, ensuring functional precision during antiviral responses. This work establishes a comprehensive framework for understanding lineage enforcement by transcription factors in effector T cells.

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T-bet and Runx3 orchestrate effector CD8 T cell differentiation and lineage fidelity through cooperative and distinct chromatin regulatory mechanisms [Multi-omics]

Project description:Effector CD8+ T cells must rapidly acquire cytotoxic functions while maintaining lineage fidelity and suppressing alternative fates. T-bet and Runx3 are key transcription factors that drive this process, yet their integrated regulatory logic has remained unclear due to the lack of comprehensive binding and chromatin accessibility data. Here, we systematically dissect the cooperative and distinct roles of T-bet and Runx3 in shaping the transcriptional and epigenetic landscape of antiviral CD8+ T cells. Using CUT&RUN, ATAC-seq, RNA-seq and scRNA-seq across single and double knockout models, we reveal that T-bet and Runx3 coordinate effector differentiation through both chromatin remodeling-dependent and -independent mechanisms. T-bet preferentially binds promoters and restrains Th17-like programs, while Runx3 targets distal elements to suppress Tfh-associated genes and sustain cytotoxic identity. Our findings uncover a cis-regulatory logic wherein these factors act combinatorially to balance activation of effector programs with repression of alternative lineages, ensuring functional precision during antiviral responses. This work establishes a comprehensive framework for understanding lineage enforcement by transcription factors in effector T cells. This SuperSeries is composed of the SubSeries listed below.

2026-08-04 | GSE342312 | GEO

Epigenetic Profiling of T-bet/Runx3 Double Knockout Models via ATAC-seq and Cut&Run in Antiviral CD8+T Cells

Project description:The rapid acquisition of cytotoxic functions while maintaining lineage fidelity in effector CD8? T cells relies on precise transcriptional control by T-bet and Runx3. Despite their critical role, the integrated regulatory logic of these factors remained unclear due to limited chromatin accessibility and binding data. This work clarifies their distinct and overlapping contributions through targeted genetic perturbations.

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Epigenetic Profiling of T-bet/Runx3 Double Knockout Models via ATAC-seq and Cut&Run in Antiviral CD8+T Cells

Project description:Epigenetic Profiling of T-bet/Runx3 Double Knockout Models via ATAC-seq and Cut&Run in Antiviral CD8+T Cells

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Project description:Effector CD8+ T cells require tight coordination of cytotoxic gene expression programs with lineage maintenance. T-bet and Runx3 are central to this process, but their combined transcriptional control mechanisms were poorly understood due to sparse transcriptional datasets. This study dissects their cooperative and distinct roles through systematic RNA-seq profiling of knockout models.

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Transcriptional Landscape Analysis of T-bet/Runx3 in Antiviral CD8+ T Cells via Single- and Double-Knockout RNA-seq

Project description:Transcriptional Landscape Analysis of T-bet/Runx3 in Antiviral CD8+ T Cells via Single- and Double-Knockout RNA-seq

| PRJNA1333555 | ENA

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Project description:To clarify the regulation of Zeb2 and T-bet in ABCs, we used flow cytometry to sort 50 million mouse age-associated B cells and perform Cut&RUN assay.

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Project description:Runx3 is an important transcription factor for the proper development of CD8+T cells. The number and functionality of CD8+T cells is severely affected in the absence of Runx3. To gain insight into the transcriptional program managed by Runx3 in CD8+T cells we conducted ChIP-seq on 50 million cells and CUT&RUN on 150,000 cells, using anti Runx3 antibodies. Both assays revealed similar results.

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Assembly of a spatial circuit of T-bet-expressing lymphocytes is required for antiviral humoral immunity

Project description:Effective antiviral immunity requires generation of T and B lymphocytes expressing transcription factor T-bet, a regulator of type 1 inflammatory responses. Using T-bet expression as an endogenous marker for cells participating in a type 1 response, we report coordinated interactions of T-bet-expressing T and B lymphocytes based on their dynamic co-localization at T cell zone and B follicle boundary (T-B boundary) and germinal centers (GC) within the draining lymph node during lung influenza infection. We demonstrate that the assembly of this circuit takes place in distinct anatomical niches, guided by CXCR3, which enables positioning of TH1 cells at the T-B boundary. The encounter of B and TH1 cells at T-B boundary enables IFN produced by the latter to induce IgG2c class switching. Within GCs, T-bet+ TFH cells represent a specialized stable sub-lineage required for GC growth, but dispensable for IgG2c class switching. Our studies show that during respiratory viral infection, T-bet-expressing T and B lymphocytes form a circuit assembled in a spatio-temporally controlled manner that acts as a functional unit enabling a robust and coherent humoral response tailored for optimal antiviral immunity.

2021-04-30 | GSE173605 | GEO

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