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| Status |
Public on Nov 03, 2023 |
| Title |
Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
We have generated high-resolution Hi-C map of developing human retinal organoids to elucidate spatiotemporal dynamics of genomic architecture and its relationship with gene expression patterns. We demonstrate progressive and developmental stage-specific alterations in DNA topology and correlate these changes with transcription of cell type-restricted gene markers during retinal differentiation. Temporal Hi-C reveals a shift towards A compartment for protein-coding genes and B compartment for non-coding RNAs, displaying high and low expression respectively. Notably, retina-enriched genes are clustered near lost boundaries of topologically associated domains (TADs), and higher-order assemblages of TADs (i.e., TAD cliques) tend to localize in the active chromatin regions with binding sites for eye-field transcription factors. These genes show a gain of chromatin contacts at their transcription start site as organoid differentiation proceeds. Our study provides a global view of chromatin architecture dynamics associated with diversification of cell types during retinal development and serves as a foundational resource for in-depth functional investigations of retinal developmental traits.
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| Overall design |
High resolution Hi-C at five time points in retinal organoid development (D60, D70, D90, D120, D200).
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| Contributor(s) |
Qu Z, Batz Z, Singh N, Marchal C, Swaroop A |
| Citation(s) |
38048222 |
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| Submission date |
Apr 13, 2023 |
| Last update date |
Jan 29, 2024 |
| Contact name |
Zachary A Batz |
| Organization name |
NIH
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| Department |
NEI
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| Lab |
NNRL
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| Street address |
6 Center Dr Bldg 6, Rm 303
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (5)
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| This SubSeries is part of SuperSeries: |
| GSE229683 |
Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids |
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| Relations |
| BioProject |
PRJNA955280 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE229681_Domain_scores.tsv.gz |
75.9 Kb |
(ftp)(http) |
TSV |
| GSE229681_Loop_comparison_5kb_gaps.csv.gz |
623.7 Kb |
(ftp)(http) |
CSV |
| GSE229681_Loop_comparison_5kb_gaps_with_counts.csv.gz |
749.5 Kb |
(ftp)(http) |
CSV |
| GSE229681_RAW.tar |
17.0 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, BEDPE, HIC, MCOOL, TXT) |
| GSE229681_loops_community_coord.bedpe.gz |
155.9 Kb |
(ftp)(http) |
BEDPE |
| GSE229681_loops_hubs_with_loop_feet_counts.txt.gz |
18.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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