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Programmed chromosome fission

Programmed chromosome fission

A technique for splitting apart chromosomes and large genome fragments in Escherichia coli that utilizes CRISPR-Cas9.

Programmed chromosome fission and fusion are techniques described in a 2019 Science article by a research group at the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK which enables the manipulation of large chunks of chromosomes in Escherichia coli. 



The programmed chromosome fission technique adapts CRISPR-Cas9 to excise long stretches without leaving unwanted errors of “genetic scars”. After a segment of DNA is excised, the programmed chromosome fusion technique uses an altered version of lambda red recombinase to join the ends of both the original chromosome and the excised piece to form two circular DNA molecules that are protected form endonucleases. The smaller DNA segments will be easier to make changes to and they can later be combined back together. 



The 2019 Science paper by Wang et al. demonstrates the splitting of an E. coli genome without prior modification into pairs of synthetic chromosomes. Together, their method of chromosome fission and fusion provide a pathway towards assembling new genomes through convergent assembling of large genomic fragments from distinct strains. 



The technique introduces Cas9 with appropriate spacers, lambda-red recombination machinery and a fission bacterial artificial chromosome (BAC). Two Cas-directed cut were made to the genome and four to the fission BAC, creating genomic fragment 1 and 2 and the release of linker sequences 1 and 2 from the fission BAC. Lambda-red-mediated recombination joined genomic fragment 1 and linker sequence 1 using 50-base pair regions of homology to create synthetic Chromosome 1 of 3.43. Mb. Synthetic Chromosome 2, of 0.56 Mb, was similarly formed from the other genomic fragment and linker. Splitting of the genome at different sites were tested, showing the technique could be applied generally. Constraints were on the choice of fission sites, in that they contained a protospacer adjacent motif (PAM) for Cas9 more than 30 bp outside any gene. 



The researchers used fusion to regenerate the original genome by replacing its linker sequence 1 with a fusion sequence for chromosome 2 and used Cas9 for cutting and lambda-red-mediated recombination. Wang et al. (2019) went on to demonstrate the fission and then fusion of genomic regions from two different strains of bacteria. Precise and scarless genomic translocations and inversions were demonstrated. 

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