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Simultaneous profiling of chromatin architecture and transcription in single cells
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Simultaneous profiling of chromatin architecture and transcription in single cells
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Journal Article
Simultaneous profiling of chromatin architecture and transcription in single cells
2023
Overview
The three-dimensional structure of chromatin plays a crucial role in development and disease, both of which are associated with transcriptional changes. However, given the heterogeneity in single-cell chromatin architecture and transcription, the regulatory relationship between the three-dimensional chromatin structure and gene expression is difficult to explain based on bulk cell populations. Here we develop a single-cell, multimodal, omics method allowing the simultaneous detection of chromatin architecture and messenger RNA expression by sequencing (single-cell transcriptome sequencing (scCARE-seq)). Applying scCARE-seq to examine chromatin architecture and transcription from 2i to serum single mouse embryonic stem cells, we observe improved separation of cell clusters compared with single-cell chromatin conformation capture. In addition, after defining the cell-cycle phase of each cell through chromatin architecture extracted by scCARE-seq, we find that periodic changes in chromatin architecture occur in parallel with transcription during the cell cycle. These findings highlight the potential of scCARE-seq to facilitate comprehensive analyses that may boost our understanding of chromatin architecture and transcription in the same single cell.
Here the authors develop a single-cell multiomics sequencing method (scCARE-seq), which allows the simultaneous probing of 3D chromatin architecture and transcription for single cells. Using scCARE-seq they explore the relationship between the 3D genome and transcriptome in cell fate transitions and the cell cycle.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
