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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Systematic RNA-seq analysis of the early events of CD4+ T cell activation

ABSTRACT: RNA-seq was used to look at the transcriptome changes and the early events of T cell receptor stimulation in CD4+ T cells CD4+ T cells were stimulated with immobilised anti-CD3/CD28 antibodies for 4 hours and RNA was extracted and subjected to RNA-seq analysis.

ORGANISM(S): Mus musculus

SUBMITTER: Andrew Hutchins

PROVIDER: E-GEOD-34550 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells.

Hutchins Andrew Paul AP Poulain Stéphane S Fujii Hodaka H Miranda-Saavedra Diego D

Genomics 20120804 5

Despite the routine application of RNA-seq technology to profile cellular transcriptomes and report novel splice variants, the identification and validation of new transcripts remain underexplored. We prepared two RNA-seq libraries from resting and T cell receptor-stimulated mouse CD4(+) T cells. Transcripts unknown to Ensembl represent as much as 5% of the assembled transcripts and are robustly expressed but do not show the same degree of evolutionary conservation or exon distribution of known ...[more]

PMID: 22884873

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2015-01-20 | E-GEOD-59846 | biostudies-arrayexpress

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Project description:Signaling pathways are intimately involved in cellular differentiation, allowing cells to respond to their environment by regulating gene expression. While enhancers are recognized as key elements that regulate selective gene expression, the interplay between signaling pathways and actively used enhancer elements is not clear. Here, we use CD4+ T cells as a model of differentiation, mapping the acquisition of cell-type-specific enhancer elements in T-helper 1 (Th1) and Th2 cells. Our data establish that STAT proteins have a major impact on the acquisition of lineage-specific enhancers and the suppression of enhancers associated with alternative cell fates. Transcriptome analysis further supports a functional role for enhancers regulated by STATs. Importantly, expression of lineage-defining master regulators in STAT-deficient cells fails to fully recover the chromatin signature of STAT-dependent enhancers. Thus, these findings point to a critical role of STATs as environmental sensors in dynamically molding the specialized enhancer architecture of differentiating cells. Active enhancer elements were defined as p300-high/H3K4me1-high. Using ChIP-seq, we mapped active enhancer landscapes of two CD4+ T helper cells, Th1 and Th2. To investigate the effect of STAT proteins on this landscape, we profiled active enhancers in the absence of STATs. Overall, STATs deficiency had a major impact on recruitment of p300. In addition, ectopic expression of master regulators T-bet and GATA3 in STAT-deficient cells failed to recover most active enhancers.

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