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Status |
Public on Jun 26, 2019 |
Title |
Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [HiC-seq] |
Organism |
Mus musculus |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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Summary |
In mammals, chromosomes are partitioned into megabase-sized topologically associating domains (TADs). TADs can be in either A (active) or B (inactive) subnuclear compartments, which correspond to early (E) and late (L) replicating timing (RT) domains, respectively. Here, we show that RT changes are tightly correlated with A/B compartment changes during mouse embryonic stem cell (mESC) differentiation. A/B compartments changed mostly by a “boundary shift,” frequently causing compartment switching of single TADs, which coincided with or preceded RT changes. Upon differentiation, mESCs acquired an A/B compartment organization that closely resembled EpiSCs (epiblast-derived stem cells), suggesting that accumulation of compartment boundary repositioning eventually led to naïve-to-primed pluripotency transition in A/B compartment organization. We propose that large-scale reorganization of A/B compartments, which is reflected in RT domain reorganization, represents major cell fate changes. Collectively, our data provides valuable insights into the regulatory principles of 3-dimensional (3D) genome organization during early embryonic stages.
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Overall design |
Hi-C: 10 cell types, with a total of 22 individual replicates (in duplicates or triplicates).
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Contributor(s) |
Miura H, Takahashi S, Poonperm R, Tanigawa A, Takebayashi S, Hiratani I |
Citation(s) |
31406346 |
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Submission date |
May 02, 2018 |
Last update date |
Sep 25, 2019 |
Contact name |
Ichiro Hiratani |
E-mail(s) |
ichiro.hiratani@riken.jp
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Phone |
+81-78-306-3179
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Organization name |
RIKEN
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Department |
Center for Developmental Biology
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Lab |
Laboratory for Developmental Epigenetics
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Street address |
2-2-3 Minatojima-minamimachi, Chuo-ku
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City |
Kobe |
State/province |
Hyogo |
ZIP/Postal code |
650-0047 |
Country |
Japan |
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Platforms (1) |
GPL18480 |
Illumina HiSeq 1500 (Mus musculus) |
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Samples (22)
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This SubSeries is part of SuperSeries: |
GSE113985 |
Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization |
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Relations |
BioProject |
PRJNA454725 |
SRA |
SRP144391 |