Chromosome Conformation Capture
Chromosome Conformation Capture - Related Videos
10:15
Capturing Chromosome Conformation Across Length Scales
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Cited by 1 •
2023
Hi-C 3.0 is an improved Hi-C protocol that combines formaldehyde and disuccinimidyl glutarate crosslinkers with a cocktail of DpnII and DdeI restriction enzymes to increase the signal-to-noise ratio and the resolution of chromatin interaction detection.
09:13
Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates
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2023
Here, we present an adaption of the chromosome conformation capture (3C) technique in detail with an emphasis on undergraduate involvement and learning.
10:02
Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)
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Cited by 1 •
2020
We report the application of quantitative chromosome conformation capture followed by high-throughput sequencing in embryoid bodies generated from embryonic stem cells. This technique allows to identify and quantitate the contacts between putative enhancers and promoter regions of a given gene during embryonic stem cell differentiation.
01:51
Lampbrush Chromosomes
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2020
In 1882, Flemming observed lampbrush chromosomes (LBC) in salamander eggs. Later in 1892, Rückert observed LBCs in shark egg cells and coined the term "lampbrush chromosomes" because they looked like brushes used to clean kerosene lamps. LBCs are made up of two pairs of conjugating homologous chromatids. Each chromatid consists of alternatively positioned regions of condensed-inactive chromatin and loosely placed-active side loops, which can be contracted and extended. The loops resemble the...
09:06
High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
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Cited by 5 •
2018
The identification of physical interactions between genes and regulatory elements is challenging but has been facilitated by chromosome conformation capture methods. This modification to the 4C-seq protocol mitigates PCR bias by minimizing over-amplification of PCR templates and maximizes the mappability of reads by incorporating an addition restriction enzyme digest step.
FAQs
Chemical cross-linking stabilizes DNA segments that are nearby inside the nucleus before the chromatin is processed. This preserves physical associations that could otherwise be disrupted during digestion and ligation. Because the captured relationships originate from the cellular three-dimensional arrangement, the resulting DNA products retain information about contacts between genomic regions and can be analyzed afterward.
Restriction enzymes cut chromatin into defined DNA fragments, creating ends that can participate in the next step. Ligation then joins ends from fragments that were adjacent in the nucleus after cross-linking and digestion. The resulting junctions provide molecular evidence of those preserved contacts, which can subsequently be measured with targeted PCR or sequencing.
Contact frequency indicates how often selected genomic fragments were captured together across the analyzed cell population. Measuring this frequency helps identify physical associations such as enhancer-promoter interactions and chromatin loops. Comparing contact frequencies among genomic regions therefore connects local DNA proximity with broader questions about how three-dimensional genome organization relates to gene regulation.
These related approaches differ in the scale and breadth of contact information they provide. The overview identifies 3C as a method for measuring selected contacts, while 4C, 5C, and Hi-C extend the strategy to broader interaction analyses. Together, they support investigation of specific interactions as well as larger features such as domain structure.
A typical workflow begins by chemically cross-linking cells to preserve nearby DNA segments. Researchers then digest the chromatin with restriction enzymes and ligate DNA ends from fragments that were adjacent in the nucleus. Finally, they quantify the resulting contact products using targeted PCR or sequencing, producing measurements that can be related to genome architecture.
The source material identifies targeted PCR and sequencing as alternative ways to measure contact frequency after ligation. Targeted PCR is suited to examining selected genomic relationships, whereas sequencing can support analysis across the contact products generated by the assay. The choice therefore depends on whether the investigation focuses on particular regions or broader interaction patterns.
Contact data can link three-dimensional genome organization to gene regulation by revealing relationships such as enhancer-promoter interactions and chromatin looping. Researchers also use related capture approaches to study domain structure. In biology, these measurements provide context for understanding how genome architecture contributes to development, disease, and the maintenance of cellular identity.