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Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation

ABSTRACT: Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation

PROVIDER: PRJNA376468 | ENA |

REPOSITORIES: ENA

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Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation.

Project description:Dynamic changes in the expression of transcription factors (TFs) can influence the specification of distinct CD8+ T cell fates, but the observation of equivalent expression of TFs among differentially fated precursor cells suggests additional underlying mechanisms. Here we profiled the genome-wide histone modifications, open chromatin and gene expression of naive, terminal-effector, memory-precursor and memory CD8+ T cell populations induced during the in vivo response to bacterial infection. Integration of these data suggested that the expression and binding of TFs contributed to the establishment of subset-specific enhancers during differentiation. We developed a new bioinformatics method using the PageRank algorithm to reveal key TFs that influence the generation of effector and memory populations. The TFs YY1 and Nr3c1, both constitutively expressed during CD8+ T cell differentiation, regulated the formation of terminal-effector cell fates and memory-precursor cell fates, respectively. Our data define the epigenetic landscape of differentiation intermediates and facilitate the identification of TFs with previously unappreciated roles in CD8+ T cell differentiation.

| S-EPMC5395420 | biostudies-literature

Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-02-22 | GSE95238 | GEO

Epigenetic modifications induced by Blimp-1 regulate CD8+ T cell memory progression during acute virus infection

Project description:Blimp-1 regulates the overall accumulation of virus-specific CD8+ T cells during acute viral infections. Increased proliferation and survival of Blimp-1-deficient CD8+ T cells is promoted by persistent cytokine responsiveness, resulting from sustained expression of CD25 and CD27. Knockdown of these genes reduced the Blimp-1-deficient CD8+ T cell response. Genome-wide ChIP-sequencing analysis identified CD25 and CD27 genes as direct targets of Blimp-1. At the peak of the anti-viral response, but not earlier, Blimp-1 recruited the histone modifying enzymes G9a and HDAC2 to the Il2ra and Cd27 loci, thereby repressing expression of these genes. In the absence of Blimp-1, the Il2ra and Cd27 genes exhibited enhanced histone H3-acetylation and reduced histone H3K9-trimethylation. These data elucidate a central mechanism by which Blimp-1 acts as an epigenetic regulator, enhancing the numbers of short-lived effector cells while suppressing the development of memory precursor CD8+ T cells. NaM-CM-/ve CD8+ T cells from OT-I TCR transgenic Rag1-/- mice were stimulated with anti-CD3 and anti-CD28 for three days in vitro, in the presence of IL-2 to up-regulate Blimp-1 protein. Genome-wide mapping of Blimp-1 binding in mouse CD8+ T cells was conducted.

2013-10-10 | E-GEOD-48358 | biostudies-arrayexpress

CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA

Project description:CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA

| PRJNA490433 | ENA

Dynamic landscapes of protective influenza-specific CD8+ lung resident memory T cells revealed by intravital imaging

Project description:Lung tissue-resident memory CD8+ T-cells (Trm) are critical for heterosubtypic immunity against influenza virus-(IAV)-reinfection. How these cells surveil the lung, respond to infection and interact with other cells remains unresolved. Here, we used mouse models to identify and enrich lung Trm in combination with intravital and static imaging to assess spatiotemporal dynamics of IAV-induced lung TRM before and after recall-infection. CD69+CD103+ Trm localize to sites of prior influenza infection where they exhibit substantially slower movement properties than non-Trm that also surveil the lung. After rechallenge, lung Trm form tight clusters in an antigen-dependent manner. IAV-specific Trm express several factors that regulate myeloid cell biology and their protective immune responses are accompanied by activation and migration of dendritic cells to draining lymph nodes and recruitment of inflammatory monocytes. Overall, these data reveal the dynamic landscapes of lung Trm cells associated with early protective immunity against IAV infection.

2024-07-22 | GSE242558 | GEO

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

Project description:Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

| PRJNA267839 | ENA

CD8+ T cells regulate tumor ferroptosis during cancer immunotherapy

Project description:CD8+ T cells regulate tumor ferroptosis during cancer immunotherapy

| PRJNA527311 | ENA

Splicing and epigenetic factors jointly regulate epidermal differentiation

Project description:Splicing and epigenetic factors jointly regulate epidermal differentiation

| PRJNA471690 | ENA

CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [RNA-Seq]

Project description:CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [RNA-Seq]

| PRJNA490436 | ENA

CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [HumanMethylation850 BeadChip]

Project description:CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [HumanMethylation850 BeadChip]

| PRJNA490591 | ENA

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