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.
Overall design: lab: Christine Disteche, UW
award: 1U54DK107979-01
accession: 4DNESCX7WHJ1
submitted_by: Giancarlo Bonora
dataset_label: sci-RNA-seq on mESCs differentiated to embryoid body
contributing_labs: William Noble, UW, Zhijun Duan, UW, Jay Ashok Shendure, UW
experiment_type: sci-RNA-seq
url: https://data.4dnucleome.org/experiment-sets/4DNESCX7WHJ1/
number_of_experiments: 10
experiment: 4DNEXAY3ALVE; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEX2VTS1YZ; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXXCVEEE2; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXCWGVH6G; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEX7A9NPK2; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXPGR1CVZ; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXYO7LG9X; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXT7D5EOI; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXA8OVCDB; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXNPCRAKI; replicate_number: Biorep 1, Techrep 1
Series supplementary files:
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genome_assembly: GRCm38
description: A tarball containing processed sci-RNA-seq data.
file name: 4DNFISJGP9HU.tar
file_format: tar
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file_type: readme
description: A text file describing the contents and processing steps for the sci-RNA-seq processed data in 4DNFISJGP9HU.
file name: 4DNFIMO8WA45.txt
file_format: txt
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file_type: directory tree
description: A text file with a directory tree for the sci-RNA-seq processed data in 4DNFISJGP9HU.
file name: 4DNFIWL392QV.txt
file_format: txt
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