How does the molecular machinery choose where to cut a chromosome for recombination?
In humans and mice anyway ,a lot of it boils down to the recognition of a specific sequence that marks recombination hotspots by PRDM9.
http://www.sciencemag.org/content/327/5967/836

Edit - I'm expanding in response to the comment below...

Meiotic recombination occurs at vastly greater frequencies in some locations in the genome than others and these are called Recombination Hotspots. For example, the figure here, sourced from http://www.sciencemag.org/content/327/5967/876/F1.large.jpg



shows the recombination rate at the hotspot and further away from it for Chimps and Humans.

These hotspots are recognised by the cutting machinery thanks to the binding of PRDM9, a zinc finger protein, to a DNA sequence that it specifically recognises and is present at hotspots. The DNA sequence varies from species to species (as does the sequence and the function of PRDM9) but in humans is a well-characterised motif 13 base pairs long and of the sequence CCNCCNTNNCCNC (where N is any one of the 4 bases in DNA) , and accounts for the activity of nearly 40% of known hotspots.

The first link I posted has evidence to suggest that variation in composition of PRDM9 is a determinant of which hotspots get used. PRDM9, it appears, stimulates the formation of a specific histone modification - H3k4me3 (DNA is wrapped around histones, there are five histones - H1, H2A, H2B, H3, H4, and each of them has a tail that can be chemically modified, and eight of these (2 of H2A, 2 of H2B, 2 of H3 and 2 of H4) form a nucleosome - in this case the fourth lysine residue of the tail of Histone H3 is trimethylated as regulated by PRDM9, and facilitates crossing over and recombination initiation.
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