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Status |
Public on Feb 11, 2020 |
Title |
Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [ChIP-seq] |
Organism |
Mus musculus |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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Summary |
Despite overwhelming evidence supporting the role of genetics in susceptibility tocomplex diseases, such as autoimmune disorders, a fundamental unresolved questionis whether large numbers of sequence variants with small effect sizes can alter thespatial genome organization. Here, we provide the first report on the reconfiguration ofthe 3D genome due to nucleotide differences associated with type 1 diabetes, anautoimmune disorder. We show that the chromatin organization at T cell identity genesis identical between diabetes-susceptible and diabetes-resistant mouse strains despitethousands of sequence polymorphisms, suggesting that these loci are epigeneticallyresilient to genetic variation. However, molecular and optical mapping of genomefolding demonstrate that diabetes risk-conferring loci coalesce into close spatialproximity in T cells of diabetes-susceptible mice, forming regulatory cliques, andresulting in aberrant gene expression. Our data uncover 3D chromatin architecture asa new dimension in understanding complex diseases
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Overall design |
Cells were chemically cross-linked by 1% formaldehyde. Samples were sonicated and protein-DNA complexes were isolated with antibody.
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Contributor(s) |
Fasolino M, Goldman N, Wang W, Cattau B, Zhou Y, Petrovic J, Link VM, Cote A, Silverman M, Joyce EF, Little SC, Raj A, Henao-Mejia J, Faryabi RB, Vahedi G |
Citation(s) |
32049053 |
Submission date |
Dec 11, 2019 |
Last update date |
May 12, 2020 |
Contact name |
Naomi Goldman |
Organization name |
University of Pennsylvania
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Lab |
Golnaz Vahedi
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Street address |
324 BRB II/III, 421 Curie Blvd
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City |
Philadelphia |
State/province |
PA |
ZIP/Postal code |
19104 |
Country |
USA |
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Platforms (1) |
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Samples (16)
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This SubSeries is part of SuperSeries: |
GSE141853 |
Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells |
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Relations |
BioProject |
PRJNA594961 |
SRA |
SRP236884 |