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Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (ATAC-Seq)

ABSTRACT: We used ATAC-seq, RNA-seq, and HiC to create atlases of the regulatory elements to provide context to autoimmune disease associated variants from publically available Genome-wide association studies

ORGANISM(S): Homo sapiens

PROVIDER: GSE230343 | GEO | 2024/09/18

REPOSITORIES: GEO

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Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (HiC)

Project description:We used ATAC-seq, RNA-seq, and HiC to create atlases of the regulatory elements to provide context to autoimmune disease associated variants from publically available Genome-wide association studies

2024-09-18 | GSE230342 | GEO

Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (RNA-Seq)

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Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-C [Capture-C]

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Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-C [Hi-C]

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Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-C [RNA-Seq]

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Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-C [ATAC-Seq]

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Chromatin conformation dynamics during CD4+ T cell activation implicates 2 autoimmune disease-associated genes and regulatory elements

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

2024-09-18 | GSE230346 | GEO

Chromatin Conformation Capture in gg8tTAtetOP2 Olfactory Sensory Neurons

Project description:We performed HiC, Liquid HiC, and H3K27ac HiChIP in gg8tTA; tetOP2 OSNs sorted from the mouse main olfactory epithelium (MOE).

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New open conformation of SMYD3 implicates conformational selection and allostery.

Project description:SMYD3 plays a key role in cancer cell viability, adhesion, migration and invasion. SMYD3 promotes formation of inducible regulatory T cells and is involved in reducing autoimmunity. However, the nearly "closed" substrate-binding site and poor in vitro H3K4 methyltransferase activity have obscured further understanding of this oncogenically related protein. Here we reveal that SMYD3 can adopt an "open" conformation using molecular dynamics simulation and small-angle X-ray scattering. This ligand-binding-capable open state is related to the crystal structure-like closed state by a striking clamshell-like inter-lobe dynamics. The two states are characterized by many distinct structural and dynamical differences and the conformational transition pathway is mediated by a reversible twisting motion of the C-terminal domain (CTD). The spontaneous transition from the closed to open states suggests two possible, mutually non-exclusive models for SMYD3 functional regulation and the conformational selection mechanism and allostery may regulate the catalytic or ligand binding competence of SMYD3. This study provides an immediate clue to the puzzling role of SMYD3 in epigenetic gene regulation.

| S-EPMC5189988 | biostudies-literature

Ultrafine Mapping of Chromosome Conformation at hundred basepair resolution reveals regulatory genome architecture

Project description:The resolution limit of chromatin conformation capture methodologies (3Cs) has restrained their application in detection of fine-level chromatin structure mediated by cis-regulatory elements (CREs). Here we report two 3C-derived methods, Tri-4C and Tri-HiC, utilizing mult-restriction enzyme digestions capable of achieveing ultrafine genome digestion for targeted and global chromatin interaction mapping, respectively, at a one hundred basepair resolution. Tri-4C identified loops associated with CREs including those involving regulatory elements devoid of typical epigenomic marks, quantifatively revealing alterations in interaction networks underlying dynamic gene control. Tri-HiC successfully uncovers fine-gage enhancer:promoter (E:P) loops at genome-wide level, identifying > 20-fold more CRE loops than in situ HiC. In addition to refined loop detection, Tri-HiC also reveals interaction stripes and contact domain insulation from promoters and enhancers, revealing their loop extrusion behaviors resembling the topologically-associated domain (TAD) boundaries. Tri-4C and Tri-HiC provide robust approaches to achieve the high resolution interactome maps required for characterizing fine-gage regulatory chromatin interactions in analysis of development, homeostasis and disease.

2021-11-02 | GSE161014 | GEO

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