Manipulating the 3D organization of the largest synthetic yeast chromosome.

Autor:	Zhang W; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Lazar-Stefanita L; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Yamashita H; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan., Shen MJ; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Mitchell LA; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Kurasawa H; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan., Lobzaev E; School of Biological Sciences, The University of Edinburgh, Edinburgh, UK., Fanfani V; School of Biological Sciences, The University of Edinburgh, Edinburgh, UK., Haase MAB; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Sun X; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Jiang Q; CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China., Goldberg GW; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Ichikawa DM; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Lauer SL; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., McCulloch LH; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Easo N; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Lin SJ; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Camellato BR; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Zhu Y; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Cai J; Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA., Xu Z; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Zhao Y; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Sacasa M; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Noyes MB; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA., Bader JS; Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA., Deutsch S; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Stracquadanio G; School of Biological Sciences, The University of Edinburgh, Edinburgh, UK., Aizawa Y; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan; Kanagawa Institute of Industrial Science and Technology (KISTEC), Ebina, Kanagawa 243-0435, Japan. Electronic address: yaizawa@bio.titech.ac.jp., Dai J; CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. Electronic address: junbiao.dai@siat.ac.cn., Boeke JD; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York, NY, USA. Electronic address: jef.boeke@nyulangone.org.
Jazyk:	angličtina
Zdroj:	Molecular cell [Mol Cell] 2023 Dec 07; Vol. 83 (23), pp. 4424-4437.e5. Date of Electronic Publication: 2023 Nov 08.
DOI:	10.1016/j.molcel.2023.10.015
Abstrakt:	Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field. Here, we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp yeast chromosome resulting from extensive genome streamlining and modification. We developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction. Besides the drastic sequence changes, we further manipulated the 3D structure of synIV to explore spatial gene regulation. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tethered synIV to the inner nuclear membrane via its hundreds of loxPsym sites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of synIV sheds light on higher-order architectural design of the synthetic genomes. Competing Interests: Declaration of interests J.D.B. is a founder and director of CDI Labs, Inc.; a founder of and consultant to Neochromosome, Inc; and a founder, Scientific Advisory Board (SAB) member of, and consultant to ReOpen Diagnostics, LLC. J.D.B. also serves or served on the SABs of the following: Logomix, Inc.; Sangamo, Inc.; Modern Meadow, Inc.; Rome Therapeutics, Inc.; Sample6, Inc.; Tessera Therapeutics, Inc.; and the Wyss Institute. Y.A. is a Founder and CSO of Logomix, Inc. (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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