@article{9807e45b68334c68aa1957f22abb071d,
title = "Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond",
abstract = "We describe design, rapid assembly, and characterization of synthetic yeast Sc2.0 chromosome VI (synVI). A mitochondrial defect in the synVI strain mapped to synonymous coding changes within PRE4 (YFR050C), encoding an essential proteasome subunit; Sc2.0 coding changes reduced Pre4 protein accumulation by half. Completing Sc2.0 specifies consolidation of 16 synthetic chromosomes into a single strain. We investigated phenotypic, transcriptional, and proteomewide consequences of Sc2.0 chromosome consolidation in poly-synthetic strains. Another {"}bug{"} was discovered through proteomic analysis, associated with alteration of the HIS2 transcription start due to transfer RNA deletion and loxPsym site insertion. Despite extensive genetic alterations across 6% of the genome, no major global changes were detected in the poly-synthetic strain {"}omics{"} analyses. This work sets the stage for completion of a designer, synthetic eukaryotic genome.",
author = "Mitchell, {Leslie A.} and Ann Wang and Giovanni Stracquadanio and Zheng Kuang and Xuya Wang and Kun Yang and Sarah Richardson and Martin, {J. Andrew} and Yu Zhao and Roy Walker and Yisha Luo and Hongjiu Dai and Kang Dong and Zuojian Tang and Yanling Yang and Yizhi Cai and Adriana Heguy and Beatrix Ueberheide and David Feny{\"o} and Junbiao Dai and Bader, {Joel S.} and Boeke, {Jef D.}",
note = "Funding Information: This work was supported in part by U.S. NSF grants MCB-1026068 and MCB-1158201 to J.D.B. L.A.M. was funded by a postdoctoral fellowship from the Natural Sciences and Engineering Research Council of Canada. GenScript funded the synthesis of 150 kb of synVI DNA chunks with corporate funds. We thank P. Meluh for thoughtful discussions and K. Palacios for analysis of genome sequence data. The New York University Langone Medical Center (NYULMC) Genome Technology Center is partially supported by the Cancer Center Support Grant (P30CA016087) at the Laura and Isaac Perlmutter Cancer Center. Work in the United Kingdom was funded by a Chancellor's Fellowship from the University of Edinburgh, a start-up fund from Scottish Universities Life Sciences Alliance, and UK Biotechnology and Biological Sciences Research Council grants (BB/M005690/1, BB/M025640/1, and BB/M00029X/1) to Y.C. J.D.B. and J.S.B. are founders and directors of Neochromosome Inc. J.D.B. serves as a scientific adviser to Recombinetics Inc. and Sample6 Inc. These arrangements are reviewed and managed by the committees on conflict of interest at NYULMC (J.D.B.) and Johns Hopkins University (J.S.B.). S.R. and J.D.B. designed synVI. H.D. and K.D. are employees of GenScript, who constructed most of the synVI synthetic DNA chunks. L.A.M., Y.Z., and J.A.M. (in the lab of J.D.B.), together with A.W. (in the labs of J.D.B. and J.D.) and R.W. and Y.L. (in the lab of Y.C.), performed experiments. A.H. oversaw all RNA and DNA sequencing efforts. Y.Y. (in the lab of B.U.) performed tandem mass tag proteomic experiments and analysis. G.S. and K.Y. (in the lab of J.S.B.), Z.K. (in the lab of J.D.B.), and Z.T. and X.W. (in the lab of D.F.) performed computational analyses. L.A.M. and J.D.B. wrote the manuscript, and all authors contributed to its editing. All genomic data for this paper are available under the Sc2.0 umbrella BioProject accession number PRJNA351844. Proteomic data are available through MassIVE with reference number MSV000080584. Additional information related to synVI [design diagram, PCRTag sequences, feature summary table (WT VI, designed VI, physical strain yLM953; yeast-chr6-9-03), variants in physical strain (yeast-chr6-3-09), chunks used for assembly, and an extended yeast strain table] can be accessed on the Sc2.0 website. Publisher Copyright: {\textcopyright} 2017, American Association for the Advancement of Science. All rights reserved.",
year = "2017",
month = mar,
day = "10",
doi = "10.1126/science.aaf4831",
language = "English (US)",
volume = "355",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "6329",
}