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

Rasika Mundade, Hatice Gulcin Ozer, Han Wei, Lakshmi Prabhu, Tao Lu

Research output: Contribution to journalArticle

42 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)2847-2852
Number of pages6
JournalCell Cycle
Volume13
Issue number18
DOIs
StatePublished - Sep 15 2014

Fingerprint

Chromatin Immunoprecipitation
Epigenomics
Transcription Factors
Binding Sites
Genes
Technology
cdc Genes
Chromosomal Instability
Workflow
Chromosome Mapping
DNA
DNA Replication
DNA Sequence Analysis
Cell Differentiation
Proteins

Keywords

  • Chromatin
  • High throughput
  • Immunoprecipitation
  • Sequencing

ASJC Scopus subject areas

  • Cell Biology
  • Molecular Biology
  • Developmental Biology

Cite this

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond. / Mundade, Rasika; Ozer, Hatice Gulcin; Wei, Han; Prabhu, Lakshmi; Lu, Tao.

In: Cell Cycle, Vol. 13, No. 18, 15.09.2014, p. 2847-2852.

Research output: Contribution to journalArticle

Mundade, Rasika ; Ozer, Hatice Gulcin ; Wei, Han ; Prabhu, Lakshmi ; Lu, Tao. / Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond. In: Cell Cycle. 2014 ; Vol. 13, No. 18. pp. 2847-2852.
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