{"doi":"10.1101/2020.11.20.390765","title":"Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation","abstract":"Abstract 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.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":123110,"datarank":0.24141568686511508,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.0,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.55,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":29908,"name":"Vijay Ramani","orcid":"0000-0003-3345-5960","position":1,"is_corresponding":false},{"id":347248,"name":"Ritambhara Singh","orcid":"0000-0002-7523-160X","position":2,"is_corresponding":false},{"id":317048,"name":"He Fang","orcid":"0000-0001-9036-8092","position":3,"is_corresponding":false},{"id":565736,"name":"Dana L. Jackson","orcid":"0000-0002-6917-0580","position":4,"is_corresponding":false},{"id":36586,"name":"Sanjay Srivatsan","orcid":"0000-0001-7282-0487","position":5,"is_corresponding":false},{"id":279883,"name":"Ruolan Qiu","orcid":null,"position":6,"is_corresponding":false},{"id":94708,"name":"Choli Lee","orcid":"0000-0002-8901-1835","position":7,"is_corresponding":false},{"id":19437,"name":"Cole Trapnell","orcid":"0000-0002-8105-4347","position":8,"is_corresponding":false},{"id":36510,"name":"Jay Shendure","orcid":"0000-0002-1516-1865","position":9,"is_corresponding":false},{"id":565737,"name":"Zhijun Duan","orcid":"0000-0001-7976-4959","position":10,"is_corresponding":false},{"id":317050,"name":"Xinxian Deng","orcid":"0000-0002-5007-218X","position":11,"is_corresponding":false},{"id":4958,"name":"William Stafford Noble","orcid":"0000-0001-7283-4715","position":12,"is_corresponding":false},{"id":90408,"name":"Christine M. Distèche","orcid":"0000-0002-5433-495X","position":13,"is_corresponding":false},{"id":277584,"name":"Giancarlo Bonora","orcid":"0000-0001-7558-3798","position":0,"is_corresponding":true}],"reference_count":85,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T23:14:59.547352Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}