Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq

Abstract

Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) have enabled us to dissect the pan-genomic regulatory landscape of cells and tissues in both time and space dimensions by detecting specific chromatin state and its corresponding transcription factors. Pioneered by the advancement of chromatin immunoprecipitation-chip (ChIP-chip) technology, abundant epigenome profiling technologies have become available such as ChIP-seq, DNase I hypersensitive site sequencing (DNase-seq), ATAC-seq and so on. The advent of single-cell sequencing has revolutionized the next-generation sequencing, applications in single-cell epigenetics are enriched rapidly. Epigenome sequencing technologies have evolved from low-throughput to high-throughput and from bulk sample to the single-cell scope, which unprecedentedly benefits scientists to interpret life from different angles. In this review, after briefly introducing the background knowledge of epigenome biology, we discuss the development of epigenome sequencing technologies, especially ChIP-seq & ATAC-seq and their current applications in scientific research. Finally, we provide insights into future applications and challenges.

Keywords: Chromatin regulatory landscape; Developmental biology; Epigenome sequencing; Single cell.

Fig. 1

Workflows of ChIP-seq and ATAC-seq. a In ChIP-seq, chromatin is crosslinked using formaldehyde and sonicated to obtain DNA fragments of 200–600 base pairs. Then the DNA-protein complex of interest can be immunoprecipitated by the antibody. Library preparation steps: end repair, A-tailing and adapters ligation, library sequencing. b ATAC-seq identifies regions of open chromatin using a hyperactive Tn5 transposase, which preferentially inserts into accessible chromatin and tags the sites with sequencing adaptors

Fig. 2

Workflows of single-cell ChIP-seq. a Workflow of Drop-ChIP. b Workflow of sc-itChIP-seq. FACS: fluorescence-activated cell sorting. NGS: next-generation sequencing. c Workflow of coBatch. PAT: the fusion of the N-terminal of Tn5 transposase with protein A (pA-Tn5 [PAT])

Fig. 3

Development of ATAC-seq and analysis tools

Fig. 4

Workflows of single-cell ATAC-seq. a The combinatorial indexing method of sci-ATAC-seq. The first barcodes are introduced by Tn5 transposase and the second indexing is introduced by amplification using primers containing a second barcode. b scATAC-seq based on the integrated fluidic circuit (IFC). In scATAC-seq using a microfluidics platform (Fluidigm), after transposition and PCR on the IFC, libraries were collected and PCR amplified with cell-identifying barcoded primers. Single-cell libraries were then pooled and sequenced on a high-throughput sequencing instrument. c Workflow of droplet-based scATAC-seq (10 × ATAC-seq) implemented on the Chromium platform (10 × Genomics). GEM: gel bead in emulsion

Fig. 5

Future applications of single-cell epigenomics. a Long-range interaction of regulatory elements. b Chromatin dynamics in rare cell types (e.g., early embryos). c Cell lineage tracking. d Deconvolution of intercellular heterogeneity