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| Status |
Public on Nov 25, 2022 |
| Title |
Single cell Hi-C deconvolutes proliferation and differentiation of chromosome conformation in embryonic mesoderm, ectoderm and blood |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Embryonic development involves massive proliferation and differentiation of cell lineages. This must be supported by chromosome replication and epigenetic reprogramming, but how proliferation and cell fate acquisition are balanced in this process is not well understood. Here we use single cell Hi-C to map chromosomal conformations in post-gastrulation mouse embryo cells and study their distributions and correlations with matching embryonic transcriptional atlases. We find that embryonic chromosomes show a remarkably strong cell cycle signature. Despite that, replication timing, chromosome compartment structure, topological associated domains (TADs) and promoter-enhancer loops are sufficiently heterogeneous to support de-novo clustering of single nuclei into distinct epigenetic states. About 10% of the nuclei are identified as primitive erythrocytes, showing exceptionally compact and organized compartment structure. The remaining cells are broadly associated with ectoderm and mesoderm identities, showing only mild differentiation of TADs and compartment structures, but more specific localized contacts in hundreds of ectoderm and mesoderm promoter-enhancer pairs. The data distinguish the chromosome folding of fully committed cells from those in plastic and continuously differentiating embryo cells, suggesting localized regulatory contacts in embryos are established prior to differentiation of compartment structure and TAD localization.
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| Overall design |
Hi-C: 10 plates analyzed overall. scRNA-seq: 15 plates analyzed overall.
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| Contributor(s) |
Rappoport N, Chomsky E, Nagano T, Seibert C, Lubling Y, Baran Y, Lifshitz A, Leung W, Mukamel Z, Shamir R, Fraser P, Tanay A |
| Citation(s) |
37386027 |
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| Submission date |
Apr 16, 2020 |
| Last update date |
Sep 11, 2023 |
| Contact name |
Nimrod Rappoport |
| Organization name |
Weizmann Institute of Science
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| Street address |
234 Herzl St.
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| City |
Rehovot |
| State/province |
Shfela |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA625734 |
| SRA |
SRP257959 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE148793_README.txt |
5.2 Kb |
(ftp)(http) |
TXT |
| GSE148793_UMI_counts.txt.gz |
10.8 Mb |
(ftp)(http) |
TXT |
| GSE148793_genomic_bin_a_score_per_cell.txt.gz |
458.8 Mb |
(ftp)(http) |
TXT |
| GSE148793_genomic_bin_a_score_per_cell_pery.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
| GSE148793_genomic_bin_coverage_per_cell.txt.gz |
291.9 Mb |
(ftp)(http) |
TXT |
| GSE148793_genomic_bin_coverage_per_cell_pery.txt.gz |
1016.4 Kb |
(ftp)(http) |
TXT |
| GSE148793_hic_embryo_all.map.gz |
73.0 Kb |
(ftp)(http) |
MAP |
| GSE148793_metacell_expression.txt.gz |
5.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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