Chemical Fixation Alters Chromosome Contacts at Short Scales.

Chemical fixation is often used in the early steps of molecular biology protocols to freeze macro-molecular complexes in cells, so that their composition and structural organization can be investigated through a broad range of techniques. However, the influence of this step on the experimental results remains an open question. Due to the labile structure of chromatin, the field of genome organization often rely on this stabilizing step. We used here chromosome conformation capture (Hi-C), a technique that quantifies contacts between all regions within (and between) chromosome(s), to investigate the potential deformations induced by the sequential formation of irreversible cross-links. The analysis of Hi-C data unveils two different responses at short and long genomic distances. The long-distance behavior reflects the in vivo structure of the chromosomes and can be interpreted in terms of classical equilibrium polymer models. On the other hand, the short distance behavior reflects the combination of the fixative concentration and exposure time, and cannot be interpreted by an equilibrium dynamics. Modeling the dynamics of the polymer irreversible collapse we show that chemical fixation induces the formation of dense pearls of cross-linked monomers altering the native structure. These results have important implications for the interpretation of patterns observed in Hi-C genome-wide contact maps, and more generally of any experiment involving a cross-linking step.