scCARE-seq – simultaneous profiling of chromatin architecture and transcription in single cells

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.

Researchers at Sun Yat-sen University have developed 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, the researchers observed 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, they found 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.

Overview of scCARE-seq

a, scCARE-seq workflow for measuring scHi-C and scRNA in the same single cell. mRNA reverse transcription, genome digestion and ligation are performed in intact nuclei. After flow cytometry sorting an individual cell into each well, single cells were lysed. Tn5 was then added to each well for tagmentation. Finally, following preamplification of each cell library, each well was divided into two halves for DNA and RNA library amplification, using a pair of common adapter primers and RNA index primers, respectively. b, Track view displaying both contact matrices, insulation score, CTCF ChIP signal and RNA signals from 33–36 Mb of chromosome 17 (Chr. 17).