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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 (Hi-C)

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 | GSE210418 | GEO

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

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 (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 (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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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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Three-dimensional molecular architecture of mouse organogenesis

Project description:Mammalian embryos exhibits sophisticated cell organizations that are intricately orchestrated at both molecular and cellular level. It has recently become apparent that cells within the animal body display significant heterogeneity, both in terms of their cellular properties and their spatial distributions. However, current spatial transcriptomics profiling either lack three-dimensional representation or are limited in their ability to capture the complexity of embryonic tissues and organs. Here, we present a represented spatial transcriptome atlas of all major organs at embryonic day 13.5 (E13.5) in the mouse embryo, and provide a three- dimensional rendering of molecular regulation for embryonic patterning with stacked sections. By integrating this spatial transcriptome data with corresponding single-cell transcriptome data, we offer a detailed molecular annotation of the dynamic nature of organ development, spatial cellular interaction, embryonic axes and divergence of cell fates underlying mammalian development, which would pave the way for precise organ engineering and stem cell-based regenerative medicine.

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