Karyotype engineering reveals spatio-temporal control of replication firing and gene contacts

Luciana Lazar-Stefanita, Jingchuan Luo, Remi Montagne, Agnes Thierry, Xiaoji Sun, Guillaume Mercy, Julien Mozziconacci, Romain Koszul, Jef D. Boeke

Research output: Contribution to journalArticlepeer-review


Eukaryotic genomes vary in terms of size, chromosome number, and genetic complexity. Their temporal organization is complex, reflecting coordination between DNA folding and function. Here, we used fused karyotypes of budding yeast to characterize the effects of chromosome length on nuclear architecture. We found that size-matched megachromosomes expand to occupy a larger fraction of the enlarged nucleus. Hi-C maps reveal changes in the three-dimensional structure corresponding to inactivated centromeres and telomeres. De-clustering of inactive centromeres results in their loss of early replication, highlighting a functional correlation between genome organization and replication timing. Repositioning of former telomere-proximal regions on chromosome arms exposed a subset of contacts between flocculin genes. Chromatin reorganization of megachromosomes during cell division remained unperturbed, and it revealed that centromere-rDNA contacts in anaphase, extending over 0.3 Mb on wild-type chromosome, cannot exceed ∼1.7 Mb. Our results highlight the relevance of engineered karyotypes to unveiling relationships between genome organization and function.

Original languageEnglish (US)
Article number100163
JournalCell Genomics
Issue number8
StatePublished - Aug 10 2022


  • FLO genes
  • Hi-C
  • karyotype engineering
  • nuclear and chromosome architecture
  • replication origin
  • spatiotemporal DNA replication

ASJC Scopus subject areas

  • Genetics
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)


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