Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics

Benjamin A. Blount; Xinyu Lu; Maureen R.M. Driessen; Dejana Jovicevic; Mateo I. Sanchez; Klaudia Ciurkot; Yu Zhao; Stephanie Lauer; Robert M. McKiernan; Glen Oliver F. Gowers; Fiachra Sweeney; Viola Fanfani; Evgenii Lobzaev; Kim Palacios-Flores; Roy S.K. Walker; Andy Hesketh; Jitong Cai; Stephen G. Oliver; Yizhi Cai; Giovanni Stracquadanio; Leslie A. Mitchell; Joel S. Bader; Jef D. Boeke; Tom Ellis

doi:10.1016/j.xgen.2023.100418

Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics

Benjamin A. Blount, Xinyu Lu, Maureen R.M. Driessen, Dejana Jovicevic, Mateo I. Sanchez, Klaudia Ciurkot, Yu Zhao, Stephanie Lauer, Robert M. McKiernan, Glen Oliver F. Gowers, Fiachra Sweeney, Viola Fanfani, Evgenii Lobzaev, Kim Palacios-Flores, Roy S.K. Walker, Andy Hesketh, Jitong Cai, Stephen G. Oliver, Yizhi Cai, Giovanni StracquadanioLeslie A. Mitchell, Joel S. Bader, Jef D. Boeke, Tom Ellis

Biomedical Engineering

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English (US)
Article number	100418
Journal	Cell Genomics
Volume	3
Issue number	11
DOIs	https://doi.org/10.1016/j.xgen.2023.100418
State	Published - Nov 8 2023

Keywords

Sc2.0
Yeast 2.0
eccDNA
extrachromosomal circular DNA
genome editing
stress adaptation
synthetic biology
synthetic genomics

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology (miscellaneous)
Genetics

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10.1016/j.xgen.2023.100418

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Blount, B. A., Lu, X., Driessen, M. R. M., Jovicevic, D., Sanchez, M. I., Ciurkot, K., Zhao, Y., Lauer, S., McKiernan, R. M., Gowers, G. O. F., Sweeney, F., Fanfani, V., Lobzaev, E., Palacios-Flores, K., Walker, R. S. K., Hesketh, A., Cai, J., Oliver, S. G., Cai, Y., ... Ellis, T. (2023). Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics. Cell Genomics, 3(11), Article 100418. https://doi.org/10.1016/j.xgen.2023.100418

Blount, BA, Lu, X, Driessen, MRM, Jovicevic, D, Sanchez, MI, Ciurkot, K, Zhao, Y, Lauer, S, McKiernan, RM, Gowers, GOF, Sweeney, F, Fanfani, V, Lobzaev, E, Palacios-Flores, K, Walker, RSK, Hesketh, A, Cai, J, Oliver, SG, Cai, Y, Stracquadanio, G, Mitchell, LA, Bader, JS, Boeke, JD & Ellis, T 2023, 'Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics', Cell Genomics, vol. 3, no. 11, 100418. https://doi.org/10.1016/j.xgen.2023.100418

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title = "Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics",

abstract = "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.",

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doi = "10.1016/j.xgen.2023.100418",

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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

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.

KW - Sc2.0

KW - Yeast 2.0

KW - eccDNA

KW - extrachromosomal circular DNA

KW - genome editing

KW - stress adaptation

KW - synthetic biology

KW - synthetic genomics

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JF - Cell Genomics

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M1 - 100418

ER -

Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics

Abstract

Keywords

ASJC Scopus subject areas

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