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

Chemical Biology and Biological Chemistry

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
Pages (from-to)	100418
Journal	Cell genomics
Volume	3
Issue number	11
DOIs	https://doi.org/10.1016/j.xgen.2023.100418
Publication status	Published - 8 Nov 2023

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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), 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.",

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

note = "{\textcopyright} 2023 The Author(s).",

year = "2023",

month = nov,

day = "8",

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

language = "English",

volume = "3",

pages = "100418",

journal = "Cell genomics",

issn = "2666-979X",

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Blount, BA, Lu, X, Driessen, MRM, Jovicevic, D, Sanchez, MI, Ciurkot, K, Zhao, Y, Lauer, S, McKiernan, RM, Gowers, G-OF, 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, pp. 100418. https://doi.org/10.1016/j.xgen.2023.100418

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

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.

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 -

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

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