Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

Abstract

Many biologically significant processes, such as cell differentiation and cell cycle progression, gene transcription and DNA replication, chromosome stability and epigenetic silencing etc. depend on the crucial interactions between cellular proteins and DNA. Chromatin immunoprecipitation (ChIP) is an important experimental technique for studying interactions between specific proteins and DNA in the cell and determining their localization on a specific genomic locus. In recent years, the combination of ChIP with second generation DNA-sequencing technology (ChIP-seq) allows precise genomic functional assay. This review addresses the important applications of ChIP-seq with an emphasis on its role in genome-wide mapping of transcription factor binding sites, the revelation of underlying molecular mechanisms of differential gene regulation that are governed by specific transcription factors, and the identification of epigenetic marks. Furthermore, we also describe the ChIP-seq data analysis workflow and a perspective for the exciting potential advancement of ChIP-seq technology in the future.

Keywords: AR; Burrows-Wheeler aligner; C. elegans; Caenorhabditis elegans; ChIP; ChIP sequencing; DNA; ChIP-seq processing pipeline; STAT; Model Organism ENCyclopedia Of DNA Elements; NF-κB; University of California Santa Cruz; UV; androgen receptor; BWA; c-Jun NH2-terminal kinase; K; chromatin; chromatin immunoprecipitation; CRs; chromatin regulators; ChIP-seq; deoxyribonuclease; EMSA; deoxyribonucleic acid; DNase; electrophoresis mobility shift assay; ENCODE; encyclopedia of DNA elements; FDR; false discovery rate; GR; glucocorticoid receptor; HDAC; haematopoietic stem progenitor cells; HM; high throughput; high throughput ChIP; IL-β; histone deacetylase; HEK; histone modification; HTChIP; human embryonic kidney; HSPCs; immunoprecipitation; interferon; JNK; interleukin β; IFN; lysine; MACS; model-based analysis of ChIP-seq; MEME; multiple Em for motif elicitation; modENCODE; nuclear factor κB; PCR; polymerase chain reaction; RNA; ribonucleic acid; R-ChIP; robotic ChIP; SNP; sequencing; short oligonucleotide alignment program; SPP; signal transducers and activators of transcription; SUMO; single nucleotide polymorphism; SOAP; small ubiquitin-like modifier; TFs; transcription factor binding sites; TSS; transcription factors; TFBS; transcription start site; UCSC; ultraviolet..

Figure 1.

Principle of ChIP assay. The protein-DNA complexes are crosslinked in the nucleus, so the protein of interest and its chromatin binding site can be fixed. After lysing the cells, the protein-DNA complexes are sonicated into 200-1000bp fragments, and immunoprecipitated by probing with specific antibody. The crosslinks of the protein-DNA complexes are then reversed, and DNA is further purified and subjected to further analysis.