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Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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Updated: Feb 7, 2026

Analysis of the c-KIT Ligand Promoter Using Chromatin Immunoprecipitation
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Analysis of the c-KIT Ligand Promoter Using Chromatin Immunoprecipitation

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Chromatin Immunoprecipitation.

Julio C Ayala1,2, Jorge A Benitez1, Anisia J Silva3

  • 1Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, Atlanta, GA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|July 27, 2018
PubMed
Summary
This summary is machine-generated.

This study details a method for chromatin immunoprecipitation (ChIP) to identify Vibrio cholerae DNA bound by the histone-like nucleoid structuring protein (H-NS). The resulting DNA is suitable for next-generation sequencing and adaptable for other bacteria.

Keywords:
Chromatin immunoprecipitationDNA-binding proteinsImmunoprecipitationNext-generation sequencingTranscriptionVibrio cholerae

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Genomics

Background:

  • Chromatin immunoprecipitation (ChIP) is a technique used to study protein-DNA interactions within cells.
  • Combining ChIP with next-generation sequencing (NGS) allows for genome-wide identification of protein binding sites.
  • Understanding DNA-protein interactions is crucial for deciphering gene regulation and cellular processes.

Purpose of the Study:

  • To describe a protocol for immunoprecipitating Vibrio cholerae DNA bound to the Flag-tagged histone-like nucleoid structuring protein (H-NS).
  • To validate the suitability of the obtained DNA for downstream next-generation sequencing applications.
  • To present a adaptable method for studying other bacterial DNA-binding proteins.

Main Methods:

  • Flag-epitope tagging of the histone-like nucleoid structuring protein (H-NS) in Vibrio cholerae.
  • Chromatin immunoprecipitation (ChIP) to isolate DNA fragments bound by the tagged H-NS protein.
  • DNA purification and quality assessment for next-generation sequencing (NGS) compatibility.

Main Results:

  • Successful immunoprecipitation of Vibrio cholerae DNA associated with Flag-tagged H-NS.
  • The isolated DNA quality meets the requirements for next-generation sequencing.
  • Demonstration of a viable ChIP protocol for bacterial DNA-binding proteins.

Conclusions:

  • The described ChIP protocol effectively isolates bacterial DNA bound by specific proteins like H-NS.
  • This method provides high-quality DNA suitable for genome-wide analysis using next-generation sequencing.
  • The protocol is versatile and can be adapted for studying diverse DNA-binding proteins in various bacterial species.