Unraveling Heterogeneity in Transcriptome and Its Regulation Through Single-Cell Multi-Omics Technologies

Abstract

Cellular heterogeneity plays a pivotal role in tissue homeostasis and the disease development of multicellular organisms. To deconstruct the heterogeneity, a multitude of single-cell toolkits measuring various cellular contents, including genome, transcriptome, epigenome, and proteome, have been developed. More recently, multi-omics single-cell techniques enable the capture of molecular footprints with a higher resolution by simultaneously profiling various cellular contents within an individual cell. Integrative analysis of multi-omics datasets unravels the relationships between cellular modalities, builds sophisticated regulatory networks, and provides a holistic view of the cell state. In this review, we summarize the major developments in the single-cell field and review the current state-of-the-art single-cell multi-omic techniques and the bioinformatic tools for integrative analysis.

Keywords: chromatin accessibility; integrative analysis; multimodal single-cell techniques; spatial transcriptome; transcriptome.

FIGURE 1

Principles and workflow of recently developed spatial transcriptomic techniques. Two spatial transcriptomic strategies with recent development can be broadly categorized as FISH-based and sequencing-based. FISH-based methods improve on its signal detection (branched MERFISH), diffraction limit (osmFISH and seqFISH+) and gene coverage (seqFISH+). In situ sequencing has been combined with tissue clearing technology and modified sequencing by ligation to improve deep tissue visibility and sequencing error in STARmap. Aside from that, many recent techniques are in favor of in situ indexing, either by utilizing immobilized (Visium Spatial, HDST, Slide-seq) or flowing (DBiT-seq) barcoded oligonucleotide, followed by in vitro sequencing.

FIGURE 2

Toolkits for chromatin accessibility and multimodal single-cell techniques. (A) Summary of techniques for chromatin accessibility, which have been adapted for single-cell applications. (B) Workflow of multimodal single-cell techniques for simultaneous measurement of transcriptome and chromatin accessibility.