It has been shown for some time now that the way the genome is arranged in 3D is important to the regulations of genome functions. Particularly, the spatio-temporal arrangements of a given DNA locus relative to other loci; the prime example being enhancers and promoters. These sequences, although sometimes situated many hundreds of bases away from each other, are able to come together in 3D.
Methods of manipulation of DNA interactions in situ do exist:
- Making DNA-DNA looping (eg: CrisprCas + dimerization domain)
- Tethering DNA-Protein (eg: LacO Tethers to anchor single loci to lamina)
Change the epigenetic environment of the target
However, there is no current tool for physical separation of two target sequences independent of context… in eukaryotes.
Prokaryotes do have at their disposal a variety of protein complexes which ensure the non-random segregation of very large low-copy-number plasmids (of which there may only be 1-2 copies per cell).
This complex is the segrosome, generally found as a polycistronic operon encoded in these plasmids. The best studied segrosome is the one from E. coli plasmid R1 and is comprised of:
- A mitotic-like-spindle protein. (parM, yellow)
- A centromere-like sequence (parC, grey)
- A plasmid specific adaptor protein (parR)
Salje and Löwe. The EMBO Journal (2008)
This project attempts to harness the properties of the segrosome to interfere with the spatial contacts of target sequences in the mammalian genome, allowing us to literally take apart a locus, gaining understanding of the fundamental requirements in contact frequencies and lengths that give rise to proper genome function.
This is an ambitions goal, not without some risks and failures…