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From 3C to Hi-C: How does this technology lead the genomics revolution?
As genomics continues to advance, researchers have been looking for more precise ways to understand the complex structures inside cells. The emergence of Hi-C technology has undoubtedly brought revolutionary changes to this field. Hi-C is a high-throughput genomic and epigenomic technology that comprehensively captures chromatin conformation and provides in-depth insights into gene interactions. This technology is considered to be a derivative of various chromosome configuration capture technologies, including the famous 3C, 4C and 5C technologies.
Hi-C comprehensively utilizes 3C and next-generation sequencing (NGS) technologies, marking a qualitative leap in C-type technology and the beginning of 3D genomics.
Unlike traditional 3C technology, Hi-C can perform "all-to-all" interactive analysis by labeling all fragmented chromatin. This process uses formaldehyde to cross-link chromatin, then solubilizes and fragments it, then rejoins the interacting genomic regions to create a library of chemically synthesized DNA molecules. By sequencing these rebound molecules, scientists can obtain data on how these chromatins interact in three dimensions. Hi-C technology not only reveals the overall structure of mammalian chromosomes, but also provides insights into the physical properties of chromatin and how long-distance contacts between genes and regulatory elements change over time when cells are exposed to external stimuli. Condition.
History of technological development
Hi-C technology was initially a low-resolution and high-noise technology that mainly mapped interaction regions of 1 million base pairs. Hi-C technology has gone through numerous revisions since 2012 as scientists continue to improve the technology, allowing it to address many of its early flaws and improve resolution. By adapting the sequencing depth or using more frequent cutting restriction enzymes, researchers were able to increase the resolution of Hi-C from the original lower standard to the kilobase pair (kb) level.
In addition to standard Hi-C, there are also various derivative technologies such as low Hi-C, SAFE Hi-C and Micro-C, which have different characteristics.
Traditional Hi-C workflow
In the traditional Hi-C workflow, cells are first cross-linked with formaldehyde and then digested with restriction enzymes to create overhangs at the 5' end of the DNA. Biotin labeling and ligation are then added to generate biotin-containing ligation products. These ligation products are then subjected to high-level sequencing, allowing for further analysis of pairwise interactions.
Improved Hi-C technology
At present, the progress and evolution of Hi-C have not only improved the resolution, but also changed its applicable cell number requirements. Standard Hi-C requires up to 20 to 25 million cells, while low Hi-C and Capture Hi-C can be used Perform efficient experiments with fewer cells. These improvements make Hi-C technology more widely used in biomedical research.
Variations of Hi-C technology include in situ Hi-C, which performs cross-linking within the nucleus, providing significantly improved resolution and requiring fewer cells.
The future of Hi-C technology
A series of changes related to Hi-C technology have not only promoted the understanding of protein and gene interactions in basic scientific research, but also demonstrated its potential in clinical applications. As technology continues to advance, it is expected to play a more important role in disease diagnosis, drug discovery and even gene therapy. Scientists anticipate that future technologies will allow for more rapid and efficient genomic analysis to support a deeper understanding of biological systems.
Reduced costs and improved data analysis capabilities have made Hi-C technology accessible to a wider range of research questions, prompting us to think about how future discoveries in this genomics revolution will change our understanding of life and How to deal with it?
