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Hierarchical interactions between chromatin remodeling transcription factors define the epigenetic landscape of antiviral T cells [scATAC]

ABSTRACT: Hierarchical interactions between chromatin remodeling transcription factors define the epigenetic landscape of antiviral T cells [scATAC]

PROVIDER: PRJNA762701 | ENA |

REPOSITORIES: ENA

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Hierarchical interactions between chromatin remodeling transcription factors define the epigenetic landscape of antiviral T cells [scATAC]

Project description:T cell activation induces rapid proliferative expansion and the acquisitions of specialized effector functions that enable protection against invading pathogens. While a multitude of transcription factors (TFs) have been implicated in the regulation of T cell activation, it remains largely unclear how their functions are organized and integrated at the genomic level. Here, we leveraged naturally occurring TF binding site polymorphisms in wild derived inbred mice to identify the most critical “heavy lifters” that shape the epigenetic landscape of naïve and activated antiviral CD4 and CD8 T cells. We found that representative members of Ets, Runx, and TCF/Lef families occupied the vast majority of accessible chromatin regions and that interactions between them were associated with distinct epigenetic responses to T cell activation. We define prevalent genomic functions of Ets1, Runx1, and TCF1 as “housekeeper”, “universal amplifier”, and “placeholder”, respectively. Interestingly, regulatory elements associated with some of the most strongly induced and well-characterized immune response genes showed a non-canonical pattern of TF recruitment.

2021-12-18 | GSE184006 | GEO

Hierarchical interactions between chromatin remodeling transcription factors define the epigenetic landscape of antiviral T cells

Project description:Hierarchical interactions between chromatin remodeling transcription factors define the epigenetic landscape of antiviral T cells

| PRJNA701671 | ENA

Hierarchical interactions between chromatin remodeling transcription factors define the epigenetic landscape of antiviral T cells

2021-12-13 | GSE166718 | GEO

scATAC-seq of mouse Plasmodium-specific CD4+ T cells

Project description:Plasmodium-specific CD4+ T cells from mice infected with Plasmodium chabaudi chabaudi AS parasites were recovered at Days 0, 4, 7, and 32 to undergo processing and to generate scATAC-seq dataset. At Day 7, CXCR5+ and CXCR6+ cells were recovered separately. At Day 32, mice were administered with either saline or artesunate (intermittent artesunate therapy - IAT). scATAC-seq dataset was analysed to investigate epigenomic landscapes of CD4+ T cells from effector to memory states.

2020-10-14 | E-MTAB-9402 | biostudies-arrayexpress

scATAC-seq of early brain organoid development from pluripotency

Project description:To study developmental trajectories in brain organoids, we conducted scRNA-seq and scATAC-seq in parallel on a dense timecourse of early development.

2022-08-18 | E-MTAB-11998 | biostudies-arrayexpress

Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis [scATAC-Seq]

Project description:Temporal profiling of chromatin accessibility during metastasis revealed dynamic changes in chromatin accessibility during osteosarcoma lung colonization. We sought to determine whether these changes were due to epigenomic reprogramming, or shifts in subclonal frequency. To do this we performed scATAC-seq on MG63.3-GFP cells grown in vitro.

2023-09-18 | GSE215758 | GEO

The antiviral protein IFIX is targeted for degradation during HSV-1 infection

Project description:IFIX has been shown to be an antiviral factor druing HSV-1 infection. Here we define a mechanism by which IFIX exerts it antiviral function and discover a means by which the virus target IFIX to inhibit this function.

2017-01-16 | PXD005152 | Pride

scATAC-seq of fetal thymus

Project description:scATAC-seq of fetal thymus

| PRJEB53030 | ENA

Single cell profiling of a Caki-1:HeLa cell mixture by scATAC-seq and scGET-seq

Project description:A mixture of Caki-1 and HeLa cells in known proportions (80:20) is profiled using 10x Chromium scATAC-seq or scGET-seq protocols.

2021-08-17 | E-MTAB-9650 | biostudies-arrayexpress

IL-1B signaling in dendritic cells induces antiviral interferon responses

Project description:Activation of interferon-stimulated gene (ISG) responses is critical for control of viral infection. We recently identified that stimulation of the NLRP3 inflammasome and mobilization of the inflammatory cytokine IL-1β act as critical host restrictive pathways against West Nile virus (WNV) in a mechanism dependent on the regulation of ISGs. In order to define the mechanism by which IL-1β regulates these antiviral immune programs, we utilized global transcriptome analysis in myeloid cells, known targets of WNV replication to define gene signatures required for IL-1β driven antiviral responses. Surprisingly, we found IL-1β dependent activation of interferon-beta (IFN-β) and ISGs at late times following IL-1β treatment. Expression of these antiviral innate immune genes was found to be dependent on activation of IRF3 and appears to reflect a general shift in IL-1β signaling from an inflammatory response early following treatment to an anti-inflammatory type-I IFN mediated response at later times post-treatment. These data demonstrate that inflammatory and antiviral signals integrate to control viral infection. Strategies to co-opt these cytokine activated antiviral signatures can act as novel targeted therapeutic strategies tailored specifically to individual pathogens.

2018-01-12 | GSE109069 | GEO

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