Exogenous chromosomes reveal how sequence composition drives chromatin assembly, activity, folding and compartmentalization

Abstract

Genomic sequences co-evolve with DNA-associated proteins to ensure the orderly folding of long DNA molecules into functional chromosomes. In eukaryotes, this multiscale folding involves several molecular complexes and structures, ranging from nucleosomes to large cohesin-mediated DNA loops. To directly explore the causal relationships between the DNA sequence composition and the spontaneous loading and activity of these complexes in the absence of co-evolution, we used and characterized yeast strains carrying exogenous bacterial chromosomes that diverged from eukaryotic sequences over 1.5 billion years ago. By combining this synthetic approach with deep learning-based in silico analysis, we show that sequence composition drives chromatin assembly, transcriptional activity, folding, and compartmentalization in this cellular context. These results are also a step forward in understanding the molecular events at play following natural horizontal gene transfers, and could also be considered in synthetic genomic engineering projects.

Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal

“…To further support the relationship between chromatin inactivity and 2μ contacts, we explored the plasmid behavior in presence of a Mb-long exogenous sequence. The plasmid positioning in strains carrying the linearized sequence of the Mycoplasma mycoides (Mmyco) chromosome as supernumerary, artificial chromosome, was investigated using Hi-C (Chapard et al, 2023) (Lartigue et al, 2009) ( Fig. 2h ).…”

“…It is chromatinized by well-formed nucleosomes, imposes little fitness cost to the yeast, and segregates properly. Mmyco AT-rich sequence is devoid of transcription and shows no enrichment in RNA Pol II (Chapard et al, 2023). Strikingly, contacts between the 2µ sequence and the entire length of Mmyco’s inactive 1.2Mb sequence were 6 fold higher than the average value on wild-type chromosomes.…”

“…Strikingly, contacts between the 2µ sequence and the entire length of Mmyco’s inactive 1.2Mb sequence were 6 fold higher than the average value on wild-type chromosomes. Our past work demonstrated that the Mmyco chromosome adopts a globular shape at the nuclear periphery (Chapard et al, 2023). In absence of Mmyco, the plasmid appears as several foci distributed in the nucleoplasm as previously reported (Heun et al, 2001; Velmurugan et al, 1998).…”

ProA and ProB repeat sequences shape genome organization, and enhancers open domains

“…Therefore, %GC is a good predictor of A/B partitioning (30). Strikingly, high %AT appears to promote the spreading of the recently described heterochromatin in prokaryotes (31), and there is evidence suggesting that this may also be true in eukaryotes (32)(33)(34). Thus, one reason for the presence of high %AT, and hence low %GC, in the B compartment might be because it may promote the binding of structural heterochromatin proteins to DNA or nucleosomes by mechanisms which await characterization.…”

“…Notably, the GF-GO.slim "development, differentiation" includes terms related to morphogenesis. GF.GO slim were grouped into four clades: I (01-04): Crosscutting principles; II (05-16): Typical housekeeping functions, such as metabolism and intracellular transport, also including cell cycle, apoptosis, autophagy; III (17)(18)(19)(20)(21): Housekeeping functions associated with a specific cellular substructure, possibly associated with a cell differentiated phenotype; IV (22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34): Cell communication with its environment (23,24), chromatin and transcription (25), development and differentiation, and differentiated cell functions, in particular related to Immunity (34). Clade IV thus encompasses what may be called "evolutionarily specialized function", as opposed to housekeeping functions, which are represented par excellence in clade II and to some extent also in clade III.…”