Related Experiment Video
Updated: Jun 28, 2026
09:32
Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
Published on: October 14, 2022
Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C)
1Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
Methods in Molecular Biology (Clifton, N.J.)
|October 28, 2008
Summary
Gene regulation involves long-range interactions between regulatory elements and target genes, forming chromatin loops. Chromosome conformation capture (3C) technology analyzes these spatial interactions to understand gene regulation and genome organization.
Area of Science:
- Molecular Biology
- Genomics
- Epigenetics
Background:
- Gene expression is regulated by elements potentially distant in linear genome sequence.
- Regulatory elements can influence genes located on different chromosomes (trans) or far away on the same chromosome (cis).
- These long-range interactions are mediated by physical proximity achieved through chromatin looping.
Purpose of the Study:
- To investigate the mechanisms of long-range gene regulation.
- To understand the spatial organization of chromosomes and genome architecture.
- To detail high-resolution protocols for analyzing cis- and trans- interactions using 3C technology.
Main Methods:
- Utilized chromosome conformation capture (3C) technology to study genome-wide interactions.
- Employed formaldehyde crosslinking to stabilize physical interactions between genomic loci.
- Involved chromatin digestion, intramolecular ligation, DNA purification, and quantitative PCR for interaction frequency analysis.
Main Results:
- Demonstrated that 3C technology can capture and quantify long-range cis- and trans- interactions.
- Provided insights into how genes and regulatory elements achieve spatial proximity.
- Established protocols applicable to both yeast (Saccharomyces cerevisiae) and mammalian cells.
Conclusions:
- 3C technology is a powerful tool for dissecting gene regulatory networks and chromosomal organization.
- Understanding spatial genome organization is crucial for comprehending gene expression control.
- The described protocols facilitate high-resolution analysis of chromatin interactions across different species.
Related Concept Videos
02:36Chromatin 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...
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...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...