HiC: method of identifying interactions between genomic loci
The disclosed Hi-C protocol can identify genomic loci that are spatially co-located in vivo. These spatial co-locations may include, but are not limited to, intrachromosomal interactions and/or interchromosomal interactions. Hi-C techniques may be applied to many different scales of interest. For example, on a large scale, Hi-C techniques can be used to identify long-range interactions between distant genomic loci.
1. A method for identifying an interaction frequency, comprising;
a) providing;
i) a cell comprising at least one chromosome, wherein said at least one chromosome comprises a first region and a second region; and
ii) a junction marker;
b) extracting said at least one chromosome from said cell;
c) incorporating said junction marker into said extracted chromosome; and
d) identifying an interaction frequency between said first region and said second region.
2. The method of claim 1 , wherein said method further comprises fragmenting said at least one chromosome into fragments.
3. The method of claim 1 , wherein said junction marker comprises biotin.
4. The method of claim 1 , wherein said first and second regions are located on the same chromosome.
5. The method of claim 1 , wherein said first and second regions are located on different chromosomes.
6. The method of claim 1 , wherein said interaction frequency identifies a long range interaction.
7. The method of claim 1 , wherein said interaction frequency identifies a short range interaction.
8. The method of claim 1 , wherein said interaction frequency identifies a close neighbor interaction.
9. The method of claim 1 , wherein said at least one chromosome comprises a human chromosome.
10. The method of claim 1 , wherein said at least one chromosome comprises a yeast chromosome.
11. The method of claim 2 , further comprising digesting said chromosome fragments with a restriction endonuclease wherein a first region fragment comprising a first sticky end and a second region fragment comprising a second sticky end are created.
12. The method of claim 11 , further comprising filling in said first sticky end and said second sticky end to create a first blunt end and a second blunt end; and ligating said first and second blunt ends, wherein said first region and said second region are joined.
13. The method of claim 2 , further comprising digesting said chromosome fragments with an exonuclease.