美国卡内基梅隆大学Jian Ma等研究人员合作发现，GAGE-seq可同时剖析单细胞中的多尺度3D基因组组织和基因表达。相关论文于2024年5月14日在线发表在《自然—遗传学》杂志上。

研究人员表示，哺乳动物基因组的组织具有复杂、多尺度的3D结构，但由于能同时分析基因组组织和转录活动的单细胞技术有限，其功能意义仍然难以捉摸。

附：英文原文

Title: GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells

Author: Zhou, Tianming, Zhang, Ruochi, Jia, Deyong, Doty, Raymond T., Munday, Adam D., Gao, Daniel, Xin, Li, Abkowitz, Janis L., Duan, Zhijun, Ma, Jian

Issue&Volume: 2024-05-14

Abstract: The organization of mammalian genomes features a complex, multiscale three-dimensional (3D) architecture, whose functional significance remains elusive because of limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we introduce genome architecture and gene expression by sequencing (GAGE-seq), a scalable, robust single-cell co-assay measuring 3D genome structure and transcriptome simultaneously within the same cell. Applied to mouse brain cortex and human bone marrow CD34+ cells, GAGE-seq characterized the intricate relationships between 3D genome and gene expression, showing that multiscale 3D genome features inform cell-type-specific gene expression and link regulatory elements to target genes. Integration with spatial transcriptomic data revealed in situ 3D genome variations in mouse cortex. Observations in human hematopoiesis unveiled discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level. GAGE-seq provides a powerful, cost-effective approach for exploring genome structure and gene expression relationships at the single-cell level across diverse biological contexts.

DOI: 10.1038/s41588-024-01745-3

Source: https://www.nature.com/articles/s41588-024-01745-3