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Compartment variegation in mammalian cell culture

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Valton, Anne-Laure | Ozadam, Hakan | Dekker, Job

Edité par CCSD -

International audience. In the interphase nucleus, the folding of the DNA varies at different genomic scales. At the mega base level chromatin folds into transcriptionally active A compartments and transcriptionally inactive B compartments. A and B compartments appear to be stable within a cell line. However, during cell differentiation, the compartment signature of the chromatin can change and compartment switches from A to B or B to A compartment occur between differentiation stages. Nevertheless, the molecular mechanism of compartment formation and how compartment boundaries are maintained across cell division remain elusive. To assess the stability of compartments through cell division, we cloned individual Human Fibroblast Foreskin (HFF) cells, grew them individually for several passages and determined their initial and final genome organization by Hi-C. We found that the majority of A- and B-compartments are stable. However, we found that a specific subset of A and B compartments are not stable across cell divisions. Loci in these compartments often switch compartment status as cells are passaged during standard culture maintenance or during the subcloning process. These locations with variegating compartment status are enriched in genes encoding cell surface proteins involved in cell adhesion and cell-cell communication. Moreover, cells coming from the same parental clone tend to have their compartment signal clustered together suggesting that the acquisition of compartment switches across cell division is gradually acquired. This study suggests that compartment switches at specific locations might allow plasticity for gene expression during cell culture. In addition, our results that specific parts of the genome display variegated compartment status highlight that interpretation of any compartment switches observed after CRISPR engineering and cloning of a pool of cells should be interpreted with caution.

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