Next-Generation Technologies for Multiomics Approaches Including Interactome Sequencing

Table 2

Types and features of next-generation sequencing technologies.

Type of analysis	Type of sequencing	Feature
Genome	Whole-genome sequencing	Used to detect somatic mutations by sequencing the whole genome
	Whole-exome sequencing	Used to detect somatic mutations by sequencing the whole exon region
Epigenome	Bisulfite sequencing	Used for analyzing methylation by sequencing genome exhaustively
	ChIP-seq	Used to detect the targets of transcription factors or analysis of histone modifications
	DNase-seq	Used for analysis of chromatin architecture
	FAIRE-seq
	Hi-C
	ChIA-PET	Used to characterize chromatin interactions that are mediated by nuclear protein of interest
Transcriptome	RNA sequencing	Used for analysis of gene expression or detection of fusion genes and splice variants
Interactome	IVV-HiTSeq	Used to detect reliable protein (domain) interactome without cloning including interactions of protein-protein/DNA/RNA/metabolic compounds/small molecules/drugs and so forth, suitable for high-throughput application, acquisition of high-reliability datasets, and analysis of cytotoxic proteins
	Y2H-seq	Used to detect interacting proteins or protein-domain pairs, but mating and the following diploid culture become the rate-limiting steps when applied in high-throughput technologies

ChIP-seq: chromatin immunoprecipitation sequencing; FAIRE-seq: formaldehyde-assisted isolation of regulatory elements sequencing; ChIA-PET: chromatin interaction analysis by means of paired-end tag sequencing; IVV-HiTSeq: IVV high-throughput sequencing; Y2H-seq: yeast two-hybrid interaction screening approach involving short-read second-generation sequencing.