Chromosomal breakpoints and Hi-C data

Question

[shiningstarbzu]

Hi, How can we find the breakpoint regions and more stable regions of the chromosome by using the Hi-C data?

Answer 1

[Anton Goloborodko]

I don't think there is any published method to find breakpoint regions with Hi-C (personally, I doubt it is even possible).

You can, however, detect possible chromosomal rearrangements in your sample, at least for mammalian cells. The method is based on the fact that, in mammalian cells, we still have not observed any validated stable trans interactions. Therefore, all outstanding interactions observed in trans Hi-C maps are most likely due to chromosomal rearrangements, which effectively assign truly cis interactions to the trans part of the map. Thus, with a properly designed null hypothesis on the frequency distribution of trans contacts, you can find candidate chromosomal rearrangements as regions in the trans map that significantly deviate from the null hypothesis. A recent review of Hi-C data analysis from Job Dekker's lab had a chapter dedicated to detection of chromosomal rearrangements. This paper from Jay Shendure's lab and this paper from Lieberman-Aiden's lab have nice examples of detected chromosomal translocations. Obviously, these are just a few examples and there are many more papers on this subject.

[shiningstarbzu]

Thanks Sir for your nice and valuable suggestions. You are absolutely right sir, but I take this idea from the literature where it was written that "regions around breakpoints will have lower Hi-C interaction frequency" specifically with the reference of translocations. So, I assumed that maybe we can find breakpoint regions and more stable regions of the chromosome by using the Hi-C data. Respected Sir, Can you please explain to me that if not possible then what's its reason? Thanks

[Anton Goloborodko]

Hi! I'm not entirely sure, which paper you mean by this?