Context-dependent neocentromere activity in synthetic yeast chromosome VIII

Stephanie Lauer; Jingchuan Luo; Luciana Lazar-Stefanita; Weimin Zhang; Laura H McCulloch; Viola Fanfani; Evgenii Lobzaev; Max A B Haase; Nicole Easo; Yu Zhao; Fangzhou Yu; Jitong Cai; Build-A-Genome Class; Joel S Bader; Giovanni Stracquadanio; Jef D Boeke

doi:10.1016/j.xgen.2023.100437

Context-dependent neocentromere activity in synthetic yeast chromosome VIII

Cell Genom. 2023 Nov 9;3(11):100437. doi: 10.1016/j.xgen.2023.100437. eCollection 2023 Nov 8.

Authors

Stephanie Lauer¹, Jingchuan Luo¹, Luciana Lazar-Stefanita¹, Weimin Zhang¹, Laura H McCulloch¹, Viola Fanfani², Evgenii Lobzaev^{2

3}, Max A B Haase¹, Nicole Easo¹, Yu Zhao¹, Fangzhou Yu¹, Jitong Cai⁴; Build-A-Genome Class; Joel S Bader⁴, Giovanni Stracquadanio², Jef D Boeke^{1

5}

Collaborators

Build-A-Genome Class:
Lajari Anne, James S Barger, Naz Belkaya, Kristin Boulier, Kirk Butler, Melanie Callaghan, Calvin Chang, Janice Chen, Xueni Jennifer Chen, In Young Cho, Elliot Choi, Woo Jin Choi, James Chuang, Ashley L Cook, Eric Cooper, Nicholas Timothy Culbertson, Jessilyn Dunn, Charlotte Floria, Breeana Grogan Anderson, Nathalie P Held, Emily Hsiao, Joseph-Kevin Igwe, Koeun Kang, Joana Karanxha, Marie Kelly, Arjun Khakhar, Chachrit Khunsriraksakul, John J Kim, Dong Kim, Jin Wan Kim, Alex Lamb, David Sung Han Lee, Yoon Kyung Lee, Jongseuk Lim, Steffi Liu, Jeremy Lopez, Zhen A Lu, Henry Ma, Jordan A Mandel, Jessica Mao, Jordan Matelsky, Jonathan Merran, Rishikesh Mohan, Christopher Montoya, Sindurathy Murugan, Lisa Ni, Won Chan Oh, Youngrok Park, Laura Paulsen, Nick Phillips, Sudarshan Pinglay, Vikram Aditya Rajan, Garrett Ransom, Erin Rhoads, Praneeth Sanna, Emily Scher, Jinesh Shah, Ashwyn Sharma, Maya C Shepardson, Joanne Song, Sainikhil Sontha, Venkatesh Srinivas, Scott Tan, Ang A Tu, Skyler Uhl, Wang Xiaoyue, Fangzhou Yu, Justine Yu, Amadeus Zhu

Affiliations

¹ Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
² School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
³ School of Informatics, The University of Edinburgh, Edinburgh, UK.
⁴ Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA.
⁵ Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA.

Abstract

Pioneering advances in genome engineering, and specifically in genome writing, have revolutionized the field of synthetic biology, propelling us toward the creation of synthetic genomes. The Sc2.0 project aims to build the first fully synthetic eukaryotic organism by assembling the genome of Saccharomyces cerevisiae. With the completion of synthetic chromosome VIII (synVIII) described here, this goal is within reach. In addition to writing the yeast genome, we sought to manipulate an essential functional element: the point centromere. By relocating the native centromere sequence to various positions along chromosome VIII, we discovered that the minimal 118-bp CEN8 sequence is insufficient for conferring chromosomal stability at ectopic locations. Expanding the transplanted sequence to include a small segment (∼500 bp) of the CDEIII-proximal pericentromere improved chromosome stability, demonstrating that minimal centromeres display context-dependent functionality.

Keywords: CRISPR; Saccharomyces cerevisiae; aneuploidy; centromere; chromosomal stability; genome engineering; genome rearrangements; pericentromere; synVIII.