Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns

Mitosis encompasses key molecular changes including chromatin condensation, nuclear envelope breakdown, and reduced transcription levels. Immediately after mitosis, the interphase chromatin structure is reestablished and transcription resumes. The reestablishment of the interphase chromatin is probably achieved by bookmarking, i.e., the retention of at least partial information during mitosis. Yet, while recent studies demonstrate that chromatin accessibility is generally preserved during mitosis and is only locally modulated, the exact details of the bookmarking process and its components are still unclear. To gain a deeper understanding of the mitotic bookmarking process, we merged proteomics, immunofluorescence, and ChIP-seq approaches to study the mitotic and interphase genomic organization of human cells. We focused on key histone modifications and employed HeLa-S3 cells as a model system. Generally, we observed a global concordance between the genomic organization of histone modifications in interphase and mitosis, yet the abundance of the two types of modifications we investigated was different. Whereas histone methylation patterns remain highly similar, histone acetylation patterns show a general reduction while maintaining their genomic organization. These results demonstrate that the epigenomic landscape can serve as a major component of the mitotic bookmarking process. Next, to further investigate mitosis-associated chromatin changes, we followed up on previous studies that showed that nucleosome depleted regions (NDRs) become occupied by a nucleosome during mitosis. Surprisingly, we observed that the nucleosome introduced into the NDR during mitosis encompasses a distinctive set of histone modifications, differentiating it from the surrounding nucleosomes. We show that the nucleosomes near the NDR appear to both shift into the NDR during mitosis and adopt a unique modification pattern. HDAC inhibition by the small molecule TSA reverts this pattern. These results provide evidence for a mitotic deposition and change in the modifications of the nucleosomes surrounding the NDR. Altogether, by merging multiple approaches, our study provides evidence to support a model where mitotic bookmarking is achieved by histone modifications, and uncovers new insights into the deposition of nucleosomes during mitosis.