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Related Concept Videos

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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.
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The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
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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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Related Experiment Video

Updated: Mar 25, 2026

Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation
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CCSI: a database providing chromatin-chromatin spatial interaction information.

Xiaowei Xie1, Wenbin Ma2, Zhou Songyang2

  • 1Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China xyyan@mail.sysu.edu.cn zhimdai@gmail.com.

Database : the Journal of Biological Databases and Curation
|February 13, 2016
PubMed
Summary

Researchers created the Chromatin-Chromatin Spatial Interaction (CCSI) database to map gene regulation. This resource links genetic variations (SNPs) to gene expression, aiding disease mechanism studies.

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Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology
  • Systems Biology

Background:

  • Distal regulatory elements control gene transcription via spatial chromatin interactions.
  • Single nucleotide polymorphisms (SNPs) in non-coding regions are linked to distal gene expression, explaining their role in disease pathogenesis.
  • Understanding chromatin interactions is crucial for elucidating transcriptional regulation mechanisms in diseases.

Purpose of the Study:

  • To construct and present the Chromatin-Chromatin Spatial Interaction (CCSI) database.
  • To integrate and annotate diverse chromatin interaction data for comprehensive analysis.
  • To provide a web interface for accessing and analyzing chromatin interaction data, including genes, enhancers, and SNPs.

Main Methods:

  • Integrated 91 sets of chromatin interaction data from literature and public databases (UCSC, NCBI GEO).
  • Utilized technologies such as 3C, 4C, 5C, ChIA-PET, and Hi-C to identify interactions.
  • Developed a web interface with search, download, and analysis pipeline functionalities for the CCSI database.

Main Results:

  • Constructed the CCSI database containing 3,017,962 pairwise chromatin interactions (FDR < 0.05) across human, mouse, and yeast.
  • The database links chromatin interactions with corresponding genes, enhancers, and SNPs.
  • A user-friendly web interface facilitates exploration and analysis of the integrated data.

Conclusions:

  • The CCSI database provides a valuable resource for studying transcriptional regulation.
  • It facilitates the exploration of disease pathogenesis mechanisms linked to spatial interactions between genes, regulatory regions, and SNPs.
  • CCSI will advance research into the functional impact of non-coding genetic variations on gene expression.