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Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Dynamic changes of three-dimensional chromatin architecture during T cell differentiation.

ORGANISM(S): Mus musculus

PROVIDER: GSE210419 | GEO | 2023/07/02

REPOSITORIES: GEO

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Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation

Project description:Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation

| PRJNA865689 | ENA

Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation (ATAC-Seq)

Project description:Background: Activation of T cells results in widespread changes in transcriptional programs and multi-level remodeling of three-dimensional genome architecture. Although many efforts have been made in dissecting the epigenomic regulation during T cell activation and differentiation, it remains to be investigated in depth how alterations in the local and global chromatin structure coordinate gene expression in this process. Results: We characterize dynamic changes at different levels of chromatin organization during Naive CD4+ T (Naive) differentiation into T helper 17 (Th17) and T helper 1 (Th1) cells using Hi-C, RNA-Seq and ATAC-Seq assays. As a result of T cell activation, extensive changes occur at the transcriptome, chromatin accessibility and higher-order structure levels. We observe decreased short-range chromatin interactions and increased extra-long-range chromatin interactions upon activation. At compartment level, although A/B compartments have no apparent global switch, the intensity of compartmentalization markedly alters in activated T cells. At TAD level, a fraction of TADs is rearranged with increase TAD number upon activation. In addition, we identify promoter-enhancer (P-E) loops, many of which are associated with T cell activation or cell-type specificity, including Rorc encoding RORγt (retinoic-acid-receptor-related orphan receptor gamma t) that facilitates Th17 differentiation and Hif1a (hypoxia-inducible factor 1α) that responds to intracellular oxygen levels in Th1. Conclusion: T cell activation is conserved at multiple levels across T helper cells and species. From the 3D genome perspective, these results provide fresh insights into heterogeneity and plasticity of T helper cells during T cell activation based on chromatin reorganization.

2023-07-03 | GSE210417 | GEO

Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation (RNA-Seq)

2023-07-03 | GSE210416 | GEO

Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation (Hi-C)

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Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation (ATAC-Seq)

Project description:Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation (ATAC-Seq)

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Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation (RNA-Seq)

Project description:Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation (RNA-Seq)

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Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation (Hi-C)

Project description:Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation (Hi-C)

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