protocol for pulldown of DNA breakpoints?

Question

Is there any method to do pulldown enrichment of DNA breakpoints from a cell? I have found this paper reporting a method to enrich for the DNA single-strand breakpoints from meiotic recombination events:
Khil PP, Smagulova F, Brick KM, Camerini-Otero RD, Petukhova GV. 2012. Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA. Genome research 22: 957–65.

I would like to know if there is something like that which will work on any status of the cell cycle, not only meiosis.

Answer 1

The paper you cite says that the break points are single stranded DNA which have specific proteins bound to them.

I'm not an expert here, but if thats the cause of meitotic break points there are some interesting possibilities for detecting them:

you could detect them with a tiling array. - that's an micro array which has an oligomer every 40 bp or so of the genome. The array could be used in a CHP experiment that detects the same proteins as in this paper.

Its possible that the array could possibly hybridize the single stranded DNA from the genome too if the conditions were right. This sounds noisy though.

On the cheap side it might be possible to use PCR to copy the single stranded DNA from a chromosomal DNA prep. if the oligos you use are labelled with streptavidin say, you could isolate it , re amplify it and sequence cheaply.

any of these sound like a good bit of work :)

Answer 2

The answer is yes, not only meiotic, but any DNA double-strand breaks will be detected as long as they are processed by homologous recombination. This method (SSDS) is based on the detection of resected ssDNA ends at DSBs. The only difference for the mitotic breaks will be that you cannot use anti-DMC1 for ChIP. Instead, you should use either anti-Rad51 or anti-RPA in ChIP.