Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq

• 成果类型: Article
• 署名作者: Liu, Zhiyuan; Chen, Yujie; Xia, Qimin; Liu, Menghan; Xu, Heming; Chi, Yi; Deng, Yujing; Xing, Dong
• 署名单位: Peking University; Peking University
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-13721
• DOI: 10.1126/science.adg3797
• 发表日期: 2023-06-08
• 页码: 1070-1076
• 关键词: dynamics

摘要

Much progress has been made recently in single-cell chromosome conformation capture technologies. However, a method that allows simultaneous profiling of chromatin architecture and gene expression has not been reported. Here, we developed an assay named Hi-C and RNA-seq employed simultaneously (HiRES) and performed it on thousands of single cells from developing mouse embryos. Single-cell three-dimensional genome structures, despite being heavily determined by the cell cycle and developmental stages, gradually diverged in a cell type-specific manner as development progressed. By comparing the pseudotemporal dynamics of chromatin interactions with gene expression, we found a widespread chromatin rewiring that occurred before transcription activation. Our results demonstrate that the establishment of specific chromatin interactions is tightly related to transcriptional control and cell functions during lineage specification.