A three-dimensional model of the yeast genome

Abstract

Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes1-3. Interphase chromosomes are not positioned randomly within the nucleus but instead adopt preferred conformations4-7. Disparate DNA elements co-localize into functionally defined aggregates or “factories” for transcription8 and DNA replication9. In budding yeast, Drosophila and many other eukaryotes, chromosomes adopt a Rabl configuration, with arms extending from centromeres adjacent to the spindle pole body to telomeres that abut the nuclear envelope10-12. Nonetheless, the topologies and spatial relationships of chromosomes remain poorly understood. Here we developed a method to globally capture intra- and inter-chromosomal interactions, and applied it to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae. The map recapitulates known features of genome organization, thereby validating the method, and identifies new features. Extensive regional and higher order folding of individual chromosomes is observed. Chromosome XII exhibits a striking conformation that implicates the nucleolus as a formidable barrier to interaction between DNA sequences at either end. Inter-chromosomal contacts are anchored by centromeres and include interactions among tRNA genes, among origins of early DNA replication and among sites where chromosomal breakpoints occur. Finally, we constructed a three-dimensional model of the yeast genome. Our findings provide a glimpse of the interface between the form and function of a eukaryotic genome.

Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle

“…Hi‐C experiments have confirmed this Rabl organization, but the existence of sub‐megabase structures within yeast chromosomes similar to mammalian topological associated domains or their bacterial equivalent is still controversial (Duan et al , 2010; Hsieh et al , 2015; Eser et al , 2017). Importantly, genomic analysis of chromosome 3D architectures has usually been done using asynchronous populations, in which cells are found in various stages of the cell cycle.…”

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

“…The general protocol consists of the following steps: cross-linking of interacting DNA segments; digestion using a restriction enzyme such as HindIII; circularization by ligation-so that a large portion of the products include a ring with fragments from both ends of the cross-linked interacting DNA pair; and finally, reversal of the cross links. The next steps differ from method to method, and ultimately conclude with the sequencing and mapping of DNA fragments to their original positions on the chromosomes [10][11][12][13] . Specifically, such whole-genome contact maps have recently been published, including those of Homo sapiens (HS) 11 , Saccharomyces cerevisiae (SC) 12 , Schizosaccharomyces pombe (SP) 13 , Caulobacter crescentus 14 , Drosophila melanogaster 15 , Mus musculus (MM) 16 , Arabidopsis thaliana (AT) 17 and Plasmodium falciparum 18 .…”

Transcription factors in eukaryotic cells can functionally regulate gene expression by acting in oligomeric assemblies formed from an intrinsically disordered protein phase transition enabled by molecular crowding

“…The foci were also visible as hotspots using the green-red photoswitchable fluorescent protein mEos2 [60] excited by super-resolution stochastic optical reconstruction microscopy (STORM) (Figure 1(c)), with modeling using 3C structural data of the yeast chromosome [61] and sequence alignment analysis for the location of Mig1 target promoters supporting the hypothesis that the majority of Mig1 clusters were specifically binding to Mig1 target genes.…”