Cell Genomics
Volume 2, Issue 8, 10 August 2022, 100163
Journal home page for Cell Genomics

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

https://doi.org/10.1016/j.xgen.2022.100163Get rights and content
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Highlights

  • Nuclear size is influenced by chromosome size and their relative length

  • Chromosome-core repositioning of subtelomeres unveils specific gene contacts in 3D

  • Centromere inactivation delays replication firing in their vicinity

  • The rDNA-centromere bridge of contacts expands over 1.5 Mb linear genomic distance

Summary

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.

Keywords

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

Data and code availability

Cited by (0)

5

These authors contributed equally

6

Present address: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA

7

Present address: Institute Curie, 26 rue d'Ulm, 75005 Paris France

8

Present address: Cellarity, Cambridge, MA, USA

9

Present address: Fondation Hospitalière de France, 1 bis Rue Cabanis, 75014 Paris, France

10

Lead contact