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Synthetic chromosome fusion: effects on genome structure and function

View ORCID ProfileJingchuan Luo, Guillaume Mercy, Luis A. Vale-Silva, Xiaoji Sun, Neta Agmon, Weimin Zhang, Kun Yang, Giovanni Stracquadanio, Agnès Thierry, Ju Young Ahn, Greg Adoff, Andrew D’Avino, Henri Berger, Yi Chen, Michael Chickering, Oren Fishman, Rebeca Vergara Greeno, Sangmin Kim, Sunghan Kim, Hong Seo Lim, Jay Im, Lauren Meyer, Allison Moyer, Surekha Mullangi, Natalie A. Murphy, Peter Natov, Maisa Nimer, Arthur Radley, Arushi Tripathy, Tony Wang, Nick Wilkerson, Tony Zheng, Vivian Zhou, David B. Kaback, Joel S. Bader, Leslie A. Mitchell, Julien Mozziconacci, Andreas Hochwagen, Romain Koszul, View ORCID ProfileJef D. Boeke
doi: https://doi.org/10.1101/381137
Jingchuan Luo
1Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
2Biochemistry, Cellular and Molecular Biology Graduate program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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  • ORCID record for Jingchuan Luo
Guillaume Mercy
3Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France
4UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France
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Luis A. Vale-Silva
5Department of Biology, New York University, New York, NY 10003, USA
12BioQuant Center, Heidelberg University, Heidelberg, Germany
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Xiaoji Sun
1Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
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Neta Agmon
1Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
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Weimin Zhang
1Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
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Kun Yang
6High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
7Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, JHU, Baltimore, MD 21218, USA.
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Giovanni Stracquadanio
6High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
7Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, JHU, Baltimore, MD 21218, USA.
8School of Computer Science and Electronic Engineering, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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Agnès Thierry
3Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France
4UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France
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Ju Young Ahn
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Greg Adoff
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Andrew D’Avino
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Henri Berger
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Yi Chen
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Michael Chickering
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Oren Fishman
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Rebeca Vergara Greeno
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Sangmin Kim
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Sunghan Kim
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Hong Seo Lim
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Jay Im
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Lauren Meyer
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Allison Moyer
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Surekha Mullangi
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Natalie A. Murphy
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Peter Natov
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Maisa Nimer
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Arthur Radley
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Arushi Tripathy
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Tony Wang
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Nick Wilkerson
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Tony Zheng
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Vivian Zhou
9Build A Genome Class, Krieger School of Arts and Sciences and Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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David B. Kaback
11Department of Microbiology and Molecular Genetics, UMDNJ, New Jersey Medical School, International Center for Public Health, Newark, New Jersey 07101-1709
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Joel S. Bader
6High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Leslie A. Mitchell
1Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
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Julien Mozziconacci
10Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR7600, Université Pierre et Marie Curie (Université Paris 6), Sorbonne Universités, Paris, France
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Andreas Hochwagen
5Department of Biology, New York University, New York, NY 10003, USA
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Romain Koszul
3Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France
4UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France
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Jef D. Boeke
1Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
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  • ORCID record for Jef D. Boeke
  • For correspondence: Jef.Boeke@nyumc.org
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SUMMARY

As part of the Synthetic Yeast 2.0 (Sc2.0) project, we designed and synthesized synthetic chromosome I. The total length of synI is ~21.4% shorter than wild-type chromosome I, the smallest chromosome in Saccharomyces cerevisiae. SynI was designed for attachment to another synthetic chromosome due to concerns of potential instability and karyotype imbalance. We used a variation of a previously developed, robust CRISPR-Cas9 method to fuse chromosome I to other chromosome arms of varying length: chrIXR (84 kb), chrIIIR (202 kb) and chrIVR (1 Mb). All fusion chromosome strains grew like wild-type so we decided to attach synI to synIII. Through the investigation of three-dimensional structures of fusion chromosome strains, unexpected loops and twisted structures were formed in chrIII-I and chrIX-III-I fusion chromosomes, which depend on silencing protein Sir3. These results suggest a previously unappreciated 3D interaction between HMR and the adjacent telomere. We used these fusion chromosomes to show that axial element Red1 binding in meiosis is not strictly chromosome size dependent even though Red1 binding is enriched on the three smallest chromosomes in wild-type yeast, and we discovered an unexpected role for centromeres in Red1 binding patterns.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted August 01, 2018.
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Synthetic chromosome fusion: effects on genome structure and function
Jingchuan Luo, Guillaume Mercy, Luis A. Vale-Silva, Xiaoji Sun, Neta Agmon, Weimin Zhang, Kun Yang, Giovanni Stracquadanio, Agnès Thierry, Ju Young Ahn, Greg Adoff, Andrew D’Avino, Henri Berger, Yi Chen, Michael Chickering, Oren Fishman, Rebeca Vergara Greeno, Sangmin Kim, Sunghan Kim, Hong Seo Lim, Jay Im, Lauren Meyer, Allison Moyer, Surekha Mullangi, Natalie A. Murphy, Peter Natov, Maisa Nimer, Arthur Radley, Arushi Tripathy, Tony Wang, Nick Wilkerson, Tony Zheng, Vivian Zhou, David B. Kaback, Joel S. Bader, Leslie A. Mitchell, Julien Mozziconacci, Andreas Hochwagen, Romain Koszul, Jef D. Boeke
bioRxiv 381137; doi: https://doi.org/10.1101/381137
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Synthetic chromosome fusion: effects on genome structure and function
Jingchuan Luo, Guillaume Mercy, Luis A. Vale-Silva, Xiaoji Sun, Neta Agmon, Weimin Zhang, Kun Yang, Giovanni Stracquadanio, Agnès Thierry, Ju Young Ahn, Greg Adoff, Andrew D’Avino, Henri Berger, Yi Chen, Michael Chickering, Oren Fishman, Rebeca Vergara Greeno, Sangmin Kim, Sunghan Kim, Hong Seo Lim, Jay Im, Lauren Meyer, Allison Moyer, Surekha Mullangi, Natalie A. Murphy, Peter Natov, Maisa Nimer, Arthur Radley, Arushi Tripathy, Tony Wang, Nick Wilkerson, Tony Zheng, Vivian Zhou, David B. Kaback, Joel S. Bader, Leslie A. Mitchell, Julien Mozziconacci, Andreas Hochwagen, Romain Koszul, Jef D. Boeke
bioRxiv 381137; doi: https://doi.org/10.1101/381137

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