Can chromatin be preserved after cross-linking?

Chromatin can be preserved after crosslinking. Chromatin conformation capture techniques (3C and Hi-C) and their derivatives (DNase Hi-C and Micro-C) search and analyze the folded forms of chromosomes at different levels and resolutions. The existing chromatin conformation capture technology relies on formaldehyde to cross-link protein and DNA, cut DNA by restriction endonuclease or DNase and Mnase, and then reconnect spatially adjacent DNA. The reconnected DNA library was passed through high-throughput sequencing, and its sources were analyzed and compared, and the chromatin interaction map was drawn. Through this crossplot, many structures formed by chromosome folding were found, including chromatin ring 1, chromatin structural bands, chromatin domains, topological structural domains 2 and active and inactive compartments 3. However, the reaction of cross-linked DNA and protein with formaldehyde is reversible, and the cross-linked products are unstable. In addition, protein cross-linked with DNA may prevent restriction endonucleases from recognizing DNA in space, resulting in incomplete restriction of DNA. Therefore, in different cells, the connection sites will be different, which greatly increases the heterogeneity, thus increasing the "background" on the chromatin cross graph and affecting the correct analysis of chromatin structure. In addition, compared with restriction endonucleases, DNase and MNase can cut DNA into smaller fragments, so DNase Hi-C and Micro-C based on DNASE and MNase can greatly improve the resolution of chromatin cross-map. However, since DNA and protein are still cross-linked by formaldehyde, DNase and MNase will be more inclined to cut the chromatin region. Therefore, the observed chromosome structure will also be biased.