TY - JOUR
T1 - Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics
AU - Blount, Benjamin A
AU - Lu, Xinyu
AU - Driessen, Maureen R M
AU - Jovicevic, Dejana
AU - Sanchez, Mateo I
AU - Ciurkot, Klaudia
AU - Zhao, Yu
AU - Lauer, Stephanie
AU - McKiernan, Robert M
AU - Gowers, Glen-Oliver F
AU - Sweeney, Fiachra
AU - Fanfani, Viola
AU - Lobzaev, Evgenii
AU - Palacios-Flores, Kim
AU - Walker, Roy S K
AU - Hesketh, Andy
AU - Cai, Jitong
AU - Oliver, Stephen G
AU - Cai, Yizhi
AU - Stracquadanio, Giovanni
AU - Mitchell, Leslie A
AU - Bader, Joel S
AU - Boeke, Jef D
AU - Ellis, Tom
N1 - © 2023 The Author(s).
PY - 2023/11/8
Y1 - 2023/11/8
N2 - We describe construction of the synthetic yeast chromosome XI (synXI) and reveal the effects of redesign at non-coding DNA elements. The 660-kb synthetic yeast genome project (Sc2.0) chromosome was assembled from synthesized DNA fragments before CRISPR-based methods were used in a process of bug discovery, redesign, and chromosome repair, including precise compaction of 200 kb of repeat sequence. Repaired defects were related to poor centromere function and mitochondrial health and were associated with modifications to non-coding regions. As part of the Sc2.0 design, loxPsym sequences for Cre-mediated recombination are inserted between most genes. Using the GAP1 locus from chromosome XI, we show that these sites can facilitate induced extrachromosomal circular DNA (eccDNA) formation, allowing direct study of the effects and propagation of these important molecules. Construction and characterization of synXI contributes to our understanding of non-coding DNA elements, provides a useful tool for eccDNA study, and will inform future synthetic genome design.
AB - We describe construction of the synthetic yeast chromosome XI (synXI) and reveal the effects of redesign at non-coding DNA elements. The 660-kb synthetic yeast genome project (Sc2.0) chromosome was assembled from synthesized DNA fragments before CRISPR-based methods were used in a process of bug discovery, redesign, and chromosome repair, including precise compaction of 200 kb of repeat sequence. Repaired defects were related to poor centromere function and mitochondrial health and were associated with modifications to non-coding regions. As part of the Sc2.0 design, loxPsym sequences for Cre-mediated recombination are inserted between most genes. Using the GAP1 locus from chromosome XI, we show that these sites can facilitate induced extrachromosomal circular DNA (eccDNA) formation, allowing direct study of the effects and propagation of these important molecules. Construction and characterization of synXI contributes to our understanding of non-coding DNA elements, provides a useful tool for eccDNA study, and will inform future synthetic genome design.
UR - https://www.scopus.com/pages/publications/85175653913
U2 - 10.1016/j.xgen.2023.100418
DO - 10.1016/j.xgen.2023.100418
M3 - Article
C2 - 38020971
SN - 2666-979X
VL - 3
SP - 100418
JO - Cell genomics
JF - Cell genomics
IS - 11
ER -