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Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

ABSTRACT: Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

PROVIDER: PRJNA453780 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7071470_1.fastq.gz	Fastqsanger.gz
	SRR7071470_2.fastq.gz	Fastqsanger.gz
	SRR7071480_1.fastq.gz	Fastqsanger.gz
	SRR7071480_2.fastq.gz	Fastqsanger.gz
	SRR7071490_1.fastq.gz	Fastqsanger.gz

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Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells [ATAC-seq]

Project description:Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells [ATAC-seq]

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Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells [RNA-seq]

Project description:Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells [RNA-seq]

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Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells [RNA-seq]

Project description:Transcriptional regulatory networks (TRNs) provide insight into cellular behavior by describing interactions between transcription factors (TFs) and their gene targets. The Assay for Transposase Accessible Chromatin (ATAC)-seq, coupled with transcription-factor motif analysis, provides indirect evidence of chromatin binding for hundreds of TFs genome-wide. Here, we propose methods for TRN inference in a mammalian setting, using ATAC-seq data to influence gene expression modeling. We rigorously test our methods in the context of T Helper Cell Type 17 (Th17) differentiation, generating new ATAC-seq data to complement existing Th17 genomic resources (plentiful gene expression data, TF knock-outs and ChIP-seq experiments). In this resource-rich mammalian setting our extensive benchmarking provides quantitative, genome-scale evaluation of TRN inference combining ATAC-seq and RNA-seq data. We refine and extend our previous Th17 TRN, using our new TRN inference methods to integrate all Th17 data (gene expression, ATAC-seq, TF KO, ChIP-seq). We highlight new roles for individual TFs and groups of TFs (“TF-TF modules”) in Th17 gene regulation. Given the popularity of ATAC-seq (a widely adapted protocol with high resolution and low sample input requirements), we anticipate that application of our methods will improve TRN inference in new mammalian systems and be of particular use for rare, uncharacterized cell types.

2018-12-16 | GSE113720 | GEO

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells [ATAC-seq]

2018-12-16 | GSE113721 | GEO

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells.

Project description:Transcriptional regulatory networks (TRNs) provide insight into cellular behavior by describing interactions between transcription factors (TFs) and their gene targets. The assay for transposase-accessible chromatin (ATAC)-seq, coupled with TF motif analysis, provides indirect evidence of chromatin binding for hundreds of TFs genome-wide. Here, we propose methods for TRN inference in a mammalian setting, using ATAC-seq data to improve gene expression modeling. We test our methods in the context of T Helper Cell Type 17 (Th17) differentiation, generating new ATAC-seq data to complement existing Th17 genomic resources. In this resource-rich mammalian setting, our extensive benchmarking provides quantitative, genome-scale evaluation of TRN inference, combining ATAC-seq and RNA-seq data. We refine and extend our previous Th17 TRN, using our new TRN inference methods to integrate all Th17 data (gene expression, ATAC-seq, TF knockouts, and ChIP-seq). We highlight newly discovered roles for individual TFs and groups of TFs ("TF-TF modules") in Th17 gene regulation. Given the popularity of ATAC-seq, which provides high-resolution with low sample input requirements, we anticipate that our methods will improve TRN inference in new mammalian systems, especially in vivo, for cells directly from humans and animal models.

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Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

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

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Retinal pigment epithelial cells suppress interleukin-17-producing T-helper 17 cells

Project description:T cells that encounter cultured ocular pigment epithelial cells in vitro are inhibited from undergoing T cell receptor-triggered activation. Because retinal pigment epithelial (RPE) cells are able to suppress T-cell activation, we studied whether RPE cells could suppress cytokine production by activated T helper (Th) cells. In this study we showed that primary cultured RPE cells greatly suppressed activation of bystander CD4+ T cells in vitro, especially the cytokine production by the target T helper cells (Th1 cells, Th2 cells, Th17 cells, but not Th3 cells). Cultured RPE cells and RPE-supernatants significantly suppressed IL-17 producing CD4+ T cells, and RPE cells fully suppressed polarized Th17 cell lines that induced by recombinant proteins, IL-6 and TGFb2. Moreover, RPE cells failed to suppress IL-17 producing T cells in the presence of rIL-6. In addition, Th17 cells exposed to RPE were suppressed via TGFb, which produce RPE cells. These results indicate that retinal PE cells have immunosuppressive capacity in order to inhibit Th17-type effector T cells. Thus, ocular resident cells play a role in establishing immune regulation in the eye. Retinal pigment epithelium suppresses Th17 cells

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Project description:Important immune regulatory mechanisms mediated by CD4+ and CD8+ T-cells keep untoward CD4+ T-cell responses in check. CD4+ T-helper 17 (Th17) cells, characterized by IL-17 production, play critical roles in the body’s response to infections and cancer and in the pathogenesis of autoimmune diseases such as multiple sclerosis, psoriasis, arthritis, IBD, among others. Here we demonstrate that human CD4+ T-cells cells exposed to a Th17-differentiating milieu are highly resistant to immune suppression by CD8+ T-cells, compared to control Th0 cells. This resistance is mediated, in part, through the action of IL-17A, IL-17F and IL-17AF heterodimer through their receptors (IL-17RA and IL-17RC) on CD4+ T-cells themselves, but not through their action on CD8+ T-cells or APC. We further show that IL-17 can directly act on non-Th17 effector CD4+ T-cells to induce suppressive resistance and this resistance can be reversed by blockade of IL-1, IL-6 or STAT3. These studies reveal a novel function for IL-17 cytokines in a CD4-intrinsic mechanism of immune resistance. The pathways induced in this process may serve as a critical target for intensive investigation and therapeutic intervention.

2020-08-26 | GSE150805 | GEO

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Project description:Novel role for the T-helper 17 signature cytokine IL-17: CD4 resistance to immune suppression

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