Genome Engineering

7 October videos (review6 on vimeo lesson7 on vimeo) - John Glass (JCVI) and George Church (Harvard/MIT)

Email John Glass: jglass (AT) jcvi.org

• class slides here

Genome Design. Challenges of making multiple changes at once. Safety and containment considerations.

Assignment: Make a set of rules for redesigning a bacterial genome based on biological knowledge and transposon bombardment data. I have provided an Excel file that lists all the genes in Mycoplasma mycoides JCVI syn1.0, and tells you what transposon bombardment revealed about each gene. By that I mean whether it is essential (e), not-essential (n), or whether a disruption of that gene causes impaired growth (i). If one were to design an algorithm capable of designing a minimized cell capable of rapid growth, what are the rules one would use to program the algorithm.

Useful file for homework here: EMycoplasma mycoides JCVI syn1.0 transposon bombardment results

Krishnakumar R, Grose C, Haft DH, Zaveri J, Alperovich N, Gibson DG, Merryman C, Glass JI (2014) Simultaneous non-contiguous deletions using large synthetic DNA and site-specific recombinases. Nucleic Acids Res.

Karas BJ, Jablanovic J, Irvine E, Sun L, Ma L, Weyman PD, Gibson DG, Glass JI, Venter JC, Hutchison CA 3rd, Smith HO, Suzuki Y (2014). Nat Protoc. Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing.

Karas BJ, Diner RE, Lefebvre SC, McQuaid J, Phillips AP, Noddings CM, Brunson JK, Valas RE, Deerinck TJ, Jablanovic J, Gillard JT, Beeri K, Ellisman MH, Glass JI, Hutchison CA 3rd, Smith HO, Venter JC, Allen AE, Dupont CL, Weyman PD (2015) Designer diatom episomes delivered by bacterial conjugation. Nature Comm.

Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, Kuznetsov G, Norville JE, Gregg CJ, Stoddard BL, Church GM (2015) Biocontainment of genetically modified organisms by synthetic protein design. Nature