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.