Sequence composition dictates chromatin assembly, activity, folding and compartmentalization [CRAC-seq]

Genomic sequences co-evolve with chromatin-associated proteins to ensure that long DNA molecules are folded in the nucleus in an orderly and functional manner. In eukaryotes, this multiscale folding involves several molecular complexes and structures, ranging from nucleosomes to large cohesin-mediated DNA loops. To explore the causal relationships between the DNA sequence composition and the spontaneous loading and activity of these complexes, we circumvented the boundaries imposed by the evolved, fine-tuning of chromosome regulation by using yeast strains that carry artificial bacterial chromosomes that have diverged from eukaryotic sequences for over 1.5 billion years. By combining this chimeric? synthetic genomics approach with a deep learning-based in silico analysis, we show that sequence composition precisely dictates the whole spectrum of chromatin assembly, transcriptional activity, folding, and compartmentalization in a given cellular context. These results are a first step to understand the molecular events at stake during synthetic chromosome engineering as well as natural horizontal gene transfers. We explored whether PolII-associated RNA were detected along bacterial chromosomes integrated in a eukaryotic environment by performing CRAC-seq analysis of yeast strains containing linearized and telomerized bacterial chromosomes.