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

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

PROVIDER: PRJNA865700 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20789666_1.fastq.gz	Fastqsanger.gz
	SRR20789666_2.fastq.gz	Fastqsanger.gz
	SRR20789667_1.fastq.gz	Fastqsanger.gz
	SRR20789667_2.fastq.gz	Fastqsanger.gz
	SRR20789668_1.fastq.gz	Fastqsanger.gz

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

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

2023-07-02 | GSE210419 | GEO

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

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

| PRJNA865689 | ENA

Transcription profiling of human lymphoblastoid cell line GM06690 in conjunction with Hi-C to determine the three-dimensional architecture of the genome

Project description:We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes. These expression data are used in the paper to show that there are marked differences in mRNA expression between loci in the open and closed chromatin compartments. Experiment Overall Design: Affy Expression array for GM06690 cells

2009-10-10 | E-GEOD-18350 | biostudies-arrayexpress

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)

| PRJNA865702 | ENA

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)

| PRJNA865701 | ENA

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

Three-dimensional molecular architecture of mouse organogenesis

Project description:Three-dimensional molecular architecture of mouse organogenesis

| PRJNA994551 | ENA

Three-dimensional chromatin re-organization during muscle stem cell aging [Hi-C]

Project description:Age-related skeletal muscle atrophy or sarcopenia is a significant societal problem that is becoming amplified as the world’s population continues to increase. A critical contributor to sarcopenia is the loss in the number and function of muscle stem cells, which maintain tissue homeostasis and regenerate damage. The molecular mechanisms that govern muscle stem cell aging encompass changes across multiple regulatory layers and are integrated by the three-dimensional organization of the genome. To quantitatively understand how hierarchical chromatin architecture changes during muscle stem cell aging, we generated 3D chromatin conformation maps (Hi-C) and integrated these datasets with multi-omic (chromatin accessibility and transcriptome) profiles from bulk populations and single cells. We observed that muscle stem cells display static behavior at global scales of chromatin organization during aging and extensive rewiring of local contacts at finer scales that were associated with variations in transcription factor binding and aberrant gene expression. These data provide insights into genome topology as a regulator of molecular function in stem cell aging.

2023-02-02 | GSE214045 | GEO

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