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*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

We describe construction of the synthetic yeast chromosomeXI (synXI) and reveal the effects of redesign at non-coding DNA elements. The660-kb synthetic yeast genome project (Sc2.0) chromosome was assembled fromsynthesized DNA fragments before CRISPR-based methods were used in a process ofbug discovery, redesign, and chromosome repair, including precise compaction of200 kb of repeat sequence. Repaired defects were related to poor centromerefunction and mitochondrial health and were associated with modifications tonon-coding regions. As part of the Sc2.0 design, loxPsym sequences forCre-mediated recombination are inserted between most genes. Using the GAP1locus from chromosome XI, we show that these sites can facilitate inducedextrachromosomal circular DNA (eccDNA) formation, allowing direct study of theeffects and propagation of these important molecules. Construction andcharacterization of synXI contributes to our understanding of non-coding DNAelements, provides a useful tool for eccDNA study, and will inform futuresynthetic genome design. 

Original languageEnglish
Article number100418
Number of pages29
JournalCell Genomics
Volume3
Issue number11
DOIs
Publication statusPublished - 8 Nov 2023

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