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This article mainly shows you "what is the use of Promoter Capture Hi-C tools", the content is easy to understand, clear, hope to help you solve your doubts, the following let the editor lead you to study and learn "what is the use of Promoter Capture Hi-C tools" this article.

The Hi-C library can obtain the interacting chromatin fragments in the whole genome at one time, and the spatial structure of chromatin can be studied from the perspective of the whole genome. In the Hi-C map, the chromatin interaction frequency is expressed by the number of junction reads between two bin. Similar to the concept of sequencing depth, the chromatin interaction information can be considered reliable only when a certain amount of sequencing depth is reached.

In general, the proportion of effective reads that can be used to build Hi-C maps is about 50%, and such a utilization requires more original sequencing than other genomics.

At the same time, it is said that there is a resolution for the Hi-C atlas, and different resolutions are used to analyze and identify different levels of chromatin structures. at present, a common saying is that only when the number of junction reads between 80% of bin is more than 1000, it shows that the data is applicable to the resolution corresponding to the length of bin.

At present, there is not a clear corresponding relationship between the sequencing depth and the resolution. According to the empirical value, when the sequencing depth is 100X, the resolution can get about 40kb, such a resolution can only meet the requirements of TAD analysis, and the 25kb and 5kb resolution requirements for the sequencing depth is even higher.

Due to the requirements of experimental efficiency and data resolution, the sequencing quantity of Hi-C library must be very large, so the cost of sequencing alone is very high.

If we only analyze the interaction between some chromatin fragments, the most classic thing is to study the interaction between promoter and other chromatin fragments, such as studying the interaction of enhancer-promoter. At this time, it is too expensive to use the whole genome Hi-C library, but the traditional 3CL4C can not meet the requirements. Based on such a demand-driven, Promoter Capture Hi-C technology application came into being.

Capture Hi-C technology is based on the traditional Hi-C library and adds a capture process to capture the target fragment for subsequent sequencing. The relationship between Hi-C and Capture Hi-C is like whole genome sequencing and whole exon sequencing. Hi-C can get more comprehensive information, but it is expensive, while Capture Hi-C only studies the target region, the same sequencing cost can achieve higher sequencing depth, and the information is more reliable and more economical.

The library construction of Promoter Capture Hi-C is as follows

The core is to capture promoter-related reads with a designed probe after the Hi-C library, and then sequence it. When the sequencing depth is enough, the reliable information of the interaction between promoter region and other chromatin fragments can be obtained directly.

If we only want to use Hi-C technology to study the interaction of promoters, Promoter Capture Hi-C is undoubtedly a better choice.

These are all the contents of this article entitled "what are Promoter Capture Hi-C tools for?" Thank you for reading! I believe we all have a certain understanding, hope to share the content to help you, if you want to learn more knowledge, welcome to follow the industry information channel!

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