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| Status |
Public on Dec 09, 2020 |
| Title |
Genomic and epigenomic 1α,25(OH)2D3 responses in human colonic organoids |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Background & Aims: Active vitamin D, 1α,25(OH)2D3, is a nuclear hormone with roles in colonic homeostasis and carcinogenesis, yet mechanisms underlying these effects are incompletely understood. Human organoids are an ideal system to study genomic and epigenomic host-environment interactions. Here, we utilize human colonic organoids to measure 1α,25(OH)2D3 responses on genome-wide gene expression and chromatin accessibilityover time.
Methods: Human colonic organoids were cultured and treated in triplicate with either 100nM 1α,25(OH)2D3 or vehicle control for 4 and 18 hours (h) for chromatin accessibility, and 6 and 24hfor gene expression. DNA and RNA were extracted for ATAC- and RNA-sequencing, respectively. Differentially accessible peaks were analyzed using DiffBind and EdgeR; differentially expressed genes were analyzed using DESeq2. Motif enrichment was determined using HOMER.
Results: At 6h and 24h, 2870 and 2721 differentially expressed genes, respectively (FDR<5%) were identified with overall stronger responses with 1α,25(OH)2D3. Similarly, 1α,25(OH)2D3 treatment led to stronger chromatin accessibility especially at 4h. The vitamin D receptor (VDR) motif was strongly enriched among open chromatin peaks with 1α,25(OH)2D3 treatment accounting for 30.5% and 11% of target sequences at 4h and 18h, respectively (FDR<1%). A number of genes such as CYP24A1, FGF19, MYC, FOS and TGFBR2 showed significant transcriptional and chromatin accessibility responses to 1α,25(OH)2D3 treatment with open chromatin located distant from promoters for some gene regions.
Conclusions: Assessment of chromatin accessibility and transcriptional responses to 1α,25(OH)2D3 yielded new observations about vitamin D genome-wide effects in the colon facilitated by application of human colonic organoids. This framework can be applied to study host-environment interactions between individuals and populations in future.
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| Overall design |
Human colonic organoids from single indvidual treated with 100nM active vitamin D for 4 and 18 hours for ATAC-seq and 6 and 24 hours for RNA-seq
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| Contributor(s) |
Li J, Witonsky D, Sprague E, Alleyne D, Bielski M, Lawrence K, Kupfer SS |
| Citation(s) |
33900108 |
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| Submission date |
Dec 08, 2020 |
| Last update date |
May 03, 2021 |
| Contact name |
Sonia Kupfer |
| E-mail(s) |
[email protected]
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| Phone |
773-702-8076
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| Organization name |
University of Chicago
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| Department |
Department of Medicine
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| Street address |
900 East 57th Street, MB#9
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platforms (2) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA683597 |
| SRA |
SRP297073 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE162856_RAW.tar |
41.5 Mb |
(http)(custom) |
TAR (of NARROWPEAK, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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