Difference Between Chia-Pet And Hi-C

Question

[rig]

Hi all,

To my understanding, in the ChiA-PET method we:

• Use formaldehyde to capture the cross-linking of the chromatin
• Digest the chromatin
• In general, ligate the chromatin strands to create pet samples

And in the Hi-C method we perform pretty much the same.

The end result of both should be information on chromatin interactions, so:

• What is the basic difference between the process of ChiA-PET and Hi-C methods?
• What is the difference in the result of the methods?

Thanks

Answer 1

[Devon Ryan]

I'm not an expert in either, but my understanding is that ChiA-PET is generally a more powerful method in that (1) it allows you to probe long-distance interactions relevant to some protein of interest, (2) it involves ligation of known adapters containing Mme1 cut-sites, which are exploited to get fragments with both sides of an interaction separated by known sequence, and (3) you can use multiple adapter sequences with ChiA-PET (divide the initial cross-linked and sonicated sample into multiple tubes) to gauge how frequently false-positives are found. In my mind, points 1 and 3 are big selling points, but there may be other big differences. There's a nice visual comparison of the two in figure 4 of this review article.

Answer 2

[Ben]

The key difference is that with ChIA-PET, you are looking for genome wide interactions brought about or associated with some protein-of-interest (like CTCF, for example), whereas Hi-C is just a genome-wide (probabilistic) assessment of proximity between all genomic regions.

[matted]

Yes, my (sort of bad) analogy would be that ChIA-PET is 2-D ChIP-seq and Hi-C is 2-D genome sequencing.

Answer 3

[caokai001]

this is a new paper discuss about ChIA-PET and Hi-C 2020-1 Methods by Ruan lab! Methods for comparative ChIA-PET and Hi-C data analysis https://www.sciencedirect.com/science/article/pii/S1046202319301008