Recent exponential advances in genome sequencing and engineering technologies have enabled an unprecedented level of interrogation into the impact of DNA variation (genotype) on cellular function (phenotype). Furthermore, these advances have also prompted realistic discussion of writing and radically re-writing complex genomes. In this Perspective, we detail the motivation for large-scale engineering, discuss the progress made from such projects in bacteria and yeast and describe how various genome-engineering technologies will contribute to this effort. Finally, we describe the features of an ideal platform and provide a roadmap to facilitate the efficient writing of large genomes.
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This work was supported by NIH grant RM1HG008525 “Center for Genomically Engineered Organs”.
G.M.C. is a co-founder of Editas Medicine and eGenesis Bio and serves advisory roles in several companies involved in genome editing and engineering. A detailed listing of G.M.C.'s Tech Transfer, Advisory Roles and Funding Sources can be obtained from http://arep.med.harvard.edu/gmc/tech.html. R.C. declares no competing interests.
- Homologous recombination
(HR). Exchange of sequence between two highly similar DNA molecules.
- Homology-directed repair
(HDR). The process by which double-strand breaks (DSBs) in DNA are repaired when in the presence of an additional DNA moiety that has homology to the DNA sequence surrounding the DSB.
- Protospacer adjacent motif
(PAM). A short, characteristic sequence (typically between 3 and 8 nucleotides in length) that the CRISPR-associated nuclease (such as Cas9 or Cpf1) recognizes before making its DNA break. Depending on the CRISPR system used, this sequence must either flank the 3′ end or 5′ end of the sequence of interest.
The use of massively parallel sequencing technologies to decipher nucleotide composition.
The use of either genome-editing tools and/or DNA synthesis to make desired changes in DNA sequence.
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Chari, R., Church, G. Beyond editing to writing large genomes. Nat Rev Genet 18, 749–760 (2017). https://doi.org/10.1038/nrg.2017.59
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