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Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions.
Zhao, Yu; Coelho, Camila; Hughes, Amanda L; Lazar-Stefanita, Luciana; Yang, Sandy; Brooks, Aaron N; Walker, Roy S K; Zhang, Weimin; Lauer, Stephanie; Hernandez, Cindy; Cai, Jitong; Mitchell, Leslie A; Agmon, Neta; Shen, Yue; Sall, Joseph; Fanfani, Viola; Jalan, Anavi; Rivera, Jordan; Liang, Feng-Xia; Bader, Joel S; Stracquadanio, Giovanni; Steinmetz, Lars M; Cai, Yizhi; Boeke, Jef D.
Afiliação
  • Zhao Y; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
  • Coelho C; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
  • Hughes AL; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany.
  • Lazar-Stefanita L; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
  • Yang S; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
  • Brooks AN; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany.
  • Walker RSK; School of Engineering, Institute for Bioengineering, the University of Edinburgh, Edinburgh EH9 3BF.
  • Zhang W; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
  • Lauer S; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
  • Hernandez C; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
  • Cai J; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
  • Mitchell LA; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
  • Agmon N; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
  • Shen Y; BGI, Shenzhen, Beishan, Industrial Zone, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI, Shenzhen, Shenzhen 518120, China.
  • Sall J; Microscopy Laboratory, NYU Langone Health, New York, NY 10016, USA.
  • Fanfani V; School of Biological Sciences, the University of Edinburgh, Edinburgh EH9 3BF.
  • Jalan A; Department of Biology, New York University, New York, NY, USA.
  • Rivera J; Department of Biology, New York University, New York, NY, USA.
  • Liang FX; Microscopy Laboratory, NYU Langone Health, New York, NY 10016, USA.
  • Bader JS; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
  • Stracquadanio G; School of Biological Sciences, the University of Edinburgh, Edinburgh EH9 3BF.
  • Steinmetz LM; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Department of Genetics and Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA.
  • Cai Y; Manchester Institute of Biotechnology, the University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
  • Boeke JD; Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York, NY 11201, USA. Electronic address: jef.boeke@nyulangone.org.
Cell ; 186(24): 5220-5236.e16, 2023 11 22.
Article em En | MEDLINE | ID: mdl-37944511
ABSTRACT
The Sc2.0 project is building a eukaryotic synthetic genome from scratch. A major milestone has been achieved with all individual Sc2.0 chromosomes assembled. Here, we describe the consolidation of multiple synthetic chromosomes using advanced endoreduplication intercrossing with tRNA expression cassettes to generate a strain with 6.5 synthetic chromosomes. The 3D chromosome organization and transcript isoform profiles were evaluated using Hi-C and long-read direct RNA sequencing. We developed CRISPR Directed Biallelic URA3-assisted Genome Scan, or "CRISPR D-BUGS," to map phenotypic variants caused by specific designer modifications, known as "bugs." We first fine-mapped a bug in synthetic chromosome II (synII) and then discovered a combinatorial interaction associated with synIII and synX, revealing an unexpected genetic interaction that links transcriptional regulation, inositol metabolism, and tRNASerCGA abundance. Finally, to expedite consolidation, we employed chromosome substitution to incorporate the largest chromosome (synIV), thereby consolidating >50% of the Sc2.0 genome in one strain.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Saccharomyces cerevisiae / Genoma Fúngico / Cromossomos Artificiais de Levedura Idioma: En Revista: Cell Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Saccharomyces cerevisiae / Genoma Fúngico / Cromossomos Artificiais de Levedura Idioma: En Revista: Cell Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Estados Unidos