ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells

Abstract

Joint profiling of chromatin accessibility and gene expression from the same single cell/nucleus provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms 1-7 . However, many methods are currently limited by low sensitivity, low throughput or complex workflow. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single nucleus. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from over 10,000 nuclei from the mouse cerebral cortex, we uncovered major and rare cell types and cell-type specific regulatory elements and identified heterogeneity at the chromatin level within established cell types defined by gene expression. Finally, we revealed distinct dynamics and relationships of gene expression and chromatin accessibility during an oligodendrocyte maturation trajectory. Main TextRecent technological development enables detailed characterization of various modalities at the single cell level, such as gene expression [8][9][10][11][12][13] , chromatin accessibility [14][15][16][17][18][19][20] and protein abundance 21,22 . Data from different modalities provide distinct and complementary information about cell types or states. Currently, most methods only assay one modality of the cell at a time. Though highly informative, only one molecular layer of the cell is profiled, .

Single-cell technologies for multimodal omics measurements

“…An alternative strategy is to simultaneously measure related molecular events, such as the "writing" and "erasing" of epigenetic modifications, to model the forward and reverse rates of cellular reprogramming and to reveal the underlying principles guiding cell state transition, especially during the initiation and progression of human diseases. Finally, future developments for the measurement of multiple molecular layers of single cells without compromising the cell's viability (Chen W. et al, 2022) could uncover the underlying molecular mechanisms of various cellular processes by linking the initial state of molecular networks with downstream responses.…”

“…Combining scATAC-seq with various single-cell indexing platforms, including combinatorial barcoding and microfluidics systems, high-throughput methods for joint analysis of chromosome accessibility and transcription were developed to reveal the associations between regulatory elements and putative targeted genes. These methods demonstrated their utilities in gaining a global view of the cellular composition and cell type-specific molecular programs in healthy tissues and diseases by the parallel generation of epigenome and transcriptome maps from a large number of single cells (Cao et al, 2018;Lake et al, 2018;Chen et al, 2019;Liu et al, 2019;Zhu et al, 2019;Ma et al, 2020;Xu et al, 2022). For example, sci-CAR and Paired-seq linked distal CREs to potential target genes with the covariance of chromatin accessibility and transcription across single cells (Cao et al, 2018;Zhu et al, 2019); SHARE-seq measures the chromatin potential of single cells and enables the finer dissection of closely related cellular states compared to scRNA-seq (Ma et al, 2020).…”

Methods and applications for single-cell and spatial multi-omics

“…3a,b ), which rely on combinatorial indexing; SNARE-seq 39 , 41 , ASTAR-seq 42 and the commercially available 10x Genomics Multiome technology, which rely on microfluidics for cell barcoding (Fig. 3c ); and ISSAAC-seq, which is amenable to both plate-based and microfluidics-based cell barcoding 43 , 44 . scGET-seq represents an unusual type of such methods, profiling both accessible and inaccessible chromatin but not the transcriptome 45 .…”

Into the multi-omics era: Progress of T cells profiling in the context of solid organ transplantation

“…10X Genomics Chromium platform has adopted this technique using hydrogel beads carrying divided oligonucleotides capturing the labeled genome and mRNA. Recently, based on the sequencing HEteRO RNA-DNA-hYbrid (SHERRY) ( 88 ) technique and a similar technique, in situ sequencing hetero RNA-DNA-hybrid after assay for transposase-accessible chromatin-sequencing (ISSAAC-seq) ( 89 ), as an optional approach for multi-omics sequencing of a single nucleus, tags the accessible chromatin at the first round followed by reverse transcription and tags DNA-RNA hybrids at the second round. For this approach, single nuclei are separated by microfluidic apparatus, and DNA and RNA libraries are built separately through the difference between two-step adaptor configurations.…”