Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a bookkeeping mechanism. In differentiating embryonic stem cells, changes in contact decay profiles are detected in parallel on both the X chromosomes and autosomes, suggesting profound simultaneous reorganization.
More...Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a bookkeeping mechanism. In differentiating embryonic stem cells, changes in contact decay profiles are detected in parallel on both the X chromosomes and autosomes, suggesting profound simultaneous reorganization. The onset of the inactive X-specific structure in single cells is notably delayed relative to that of gene silencing, consistent with the idea that chromatin compaction is a late event of X inactivation. Novel computational approaches to effectively align single-cell gene expression, chromatin accessibility, and 3D chromosome structure reveal that long-range structural changes to chromosomes appear as discrete events, unlike progressive changes in gene expression and chromatin accessibility.
### Competing Interest Statement
The authors have declared no competing interest.
### This SuperSeries is composed of the SubSeries listed below.
Overall design: Refer to individual Series
Less...Accession | PRJNA765363; GEO: GSE184554 |
Type | Umbrella project |
Publications | Bonora G et al., "Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation.", Genome Biol, 2021 Sep 27;22(1):279 |
Submission | Registration date: 21-Sep-2021 4D Nucleome - Data Coordination and Integration Center |
Relevance | Superseries |
Project Data:
Resource Name | Number of Links |
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Sequence data |
SRA Experiments | 25 |
Publications |
PubMed | 1 |
PMC | 1 |
Other datasets |
BioSample | 16 |
GEO DataSets | 4 |
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation encompasses the following 3 sub-projects:
Project Type | Number of Projects |
Epigenomics | 1 |
BioProject accession | Organism | Title |
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PRJNA765361 | Mus musculus | 4DNESOUYRIO9 - sci-ATAC-seq on mESCs differentiated to embryoid body (4D Nucleome - Data Coordination...) |
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Other | 1 |
BioProject accession | Organism | Title |
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PRJNA770075 | Mus musculus | 4DNESB7XYI9V - sci-Hi-C on mESCs differentiated to embryoid body (4D Nucleome - Data Coordination...) |
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Transcriptome or Gene expression | 1 |
BioProject accession | Organism | Title |
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PRJNA765362 | Mus musculus | 4DNESCX7WHJ1 - sci-RNA-seq on mESCs differentiated to embryoid body (4D Nucleome - Data Coordination...) |
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