Characterization of Transcriptome and Chromatin Interactome in Accessible Regions at Single-cell Resolution by scAIR

The increasing prevalence of single-cell technologies has brought significant advancements in the study of cellular heterogeneity. However, there is a lack of techniques that can simultaneously capture both the transcriptome and chromatin interactions. In this study, we introduce a novel approach called scAIR, which utilizes the 10x Genomics platform to perform single-cell RNA-seq and ATAC-seq analysis on pre-proximity-ligated nuclei. By leveraging this technology, we were able to obtain comprehensive data that offers a deeper understanding of transcriptional regulation and chromatin dynamics at the single-cell level. This innovative methodology holds great promise in unraveling the complex intricacies of cellular processes and their underlying regulatory mechanisms. Overall design: To perform scAIR (single-cell Assay for Integration of scATAC-seq, chromatin interactome, and RNA-seq data) on Drosophila embryo nuclei, we first targeted chromatin using a restriction enzyme. This allowed us to label specific chromatin regions of interest. Next, we performed proximity ligation to capture the interactions between these targeted chromatin regions. The proximity-ligated nuclei were then loaded onto the 10x Genomics platform, enabling us to perform scRNA-seq and scATAC-seq simultaneously. After library construction, the samples were sequenced using Illumina Nova-seq6000 with a paired-end sequencing approach. By integrating the scRNA-seq and ATAC-seq data, we were able to identify the accessible regions of the chromatin and the interactions within, providing valuable insights into the cell-specific transcriptome and chromatin landscape on Drosophila embryo nuclei.