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Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
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Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method.

Nele Gheldof1, Marion Leleu, Daan Noordermeer

  • 1Center for Integrative Genomics, University of Lausanne, Le Génopode, Quartier UNIL-Sorge, Lausanne, Switzerland. Nele.Gheldof@unil.ch

Methods in Molecular Biology (Clifton, N.J.)
|September 23, 2011
PubMed
Summary

Chromosome conformation capture sequencing (4C-seq) offers a high-throughput method to study gene regulation. This technique maps long-range interactions, revealing how distant regulatory elements influence gene activity through chromatin looping.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Eukaryotic transcription is regulated by distant transcriptional regulatory elements.
  • Chromatin loops bring these distant elements into proximity with target genes.
  • The 3C technique captures these long-range interactions.

Purpose of the Study:

  • To describe chromosome conformation capture sequencing (4C-seq), a high-throughput method.
  • To combine the 4C protocol with next-generation Illumina sequencing.
  • To provide a method for studying chromatin interactions in mammalian systems.

Main Methods:

  • Adaptation of the chromosome conformation capture (3C) technique.
  • Integration of the 3C-on-chip (4C) protocol with Illumina sequencing.
  • Formaldehyde fixation, DNA digestion, and ligation to capture interacting elements.

Main Results:

  • Development of 4C-seq, a high-throughput approach for analyzing 3D genome organization.
  • Demonstration of the method's applicability in mammalian cell lines.
  • Potential for adaptation to mammalian tissues and other eukaryotic genomes.

Conclusions:

  • 4C-seq significantly enhances the scale and throughput of chromatin interaction analysis.
  • This method provides a powerful tool for understanding the role of 3D genome structure in transcriptional regulation.
  • The adaptability of 4C-seq broadens its utility across diverse biological systems.