4DNESOUYRIO9 - sci-ATAC-seq on mESCs differentiated to embryoid body

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. lab: Christine Disteche, UW award: 1U54DK107979-01 accession: 4DNESOUYRIO9 submitted_by: Giancarlo Bonora dataset_label: sci-ATAC-seq on mESCs differentiated to embryoid body contributing_labs: William Noble, UW, Zhijun Duan, UW, Jay Ashok Shendure, UW experiment_type: sci-ATAC-seq url: https://data.4dnucleome.org/experiment-sets/4DNESOUYRIO9/ number_of_experiments: 9 experiment: 4DNEXUTXVJNS; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEXOSQFCTM; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEXXXQ7SNN; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEXMJVA3ZW; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEXP788IVD; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEXOLF62PK; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEXOKNIX5B; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEXX4XDGPO; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEX55NM5L3; replicate_number: Biorep 1, Techrep 1 Series supplementary files: *************** genome_assembly: GRCm38 description: A tarball containing processed sci-ATAC-seq data. file name: 4DNFI3GQKK43.tar file_format: tar *************** file_type: readme description: A text file describing the contents and processing steps for the sci-ATAC-seq processed data in 4DNFI3GQKK43. file name: 4DNFIEIH3BBX.txt file_format: txt *************** file_type: directory tree description: A text file with a directory tree for the sci-ATAC-seq processed data in 4DNFI3GQKK43. file name: 4DNFIB8E2QM9.txt file_format: txt