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

Abstract

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 requires '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 organization in human cells. We focused on key histone modifications, and employed the 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. In line with a recent study demonstrating that minimal transcription is retained during mitosis, we show that RNA polymerase II does not fully disassociate from the genome, but rather maintains its genomic localization at reduced levels. Next, we followed up on previous studies demonstrating 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 in the vicinity of the NDR appear to both shift into the NDR during mitosis and undergo deacetylation. HDAC inhibition by the small molecule TSA reverts the deacetylation pattern of the shifted nucleosome. Taken together, our results demonstrate that the epigenomic landscape can serve as a major component of the mitotic bookmarking process, and provide evidence for a mitotic deposition and deacetylation of the nucleosomes surrounding the NDR.

Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3 and SIRT1

“…We have recently conducted a comprehensive study to assess the changes in histone modifications during mitosis (Javasky, Shamir et al, 2018). Our observations, together with other studies (Ginno, Burger et al, 2018, Hsiung, Morrissey et al, 2015, Kelly, Miranda et al, 2010, Kruhlak, Hendzel et al, 2001, Liang, Woodfin et al, 2015, McManus & Hendzel, 2006, Van Hooser, Goodrich et al, 1998 support the following notions: (i) the global epigenetic landscape is preserved during mitosis; (ii) the mitosis phase encompasses global reduction in histone acetylation; and (iii) there is a dramatic increase in histone phosphorylation.…”

“…To study the changes in histone acetylation during mitosis, we focused on H3K9ac, which is reduced approximately by 2.7-fold during mitosis in HeLa-S3 cells (Javasky et al, 2018). To better identify the mitotic stage in which deacetylation takes place, we enriched HeLa-S3 cells for mitotic cells by releasing the cells from a double thymidine block for 8.5 hours.…”

Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells

“…maintain sequence-specific binding throughout mitosis) may be higher in this hierarchy. Emerging genome-wide studies mapping histone marks during M-G1 transition, should help dissecting further the role of TFs during this period (Hsiung et al 2016;Javasky et al 2018;Kang et al 2020).…”

A changing paradigm of transcriptional memory propagation through mitosis

“…This observation suggests that antibody-based assays are not sensitive enough to demonstrate mitotic transcription events under normal conditions (BOX 1). A more recent study using Pol II ChIP–seq, coupled to the modelling of interphase contamination of their sample, confirmed that there are indeed low levels of Pol II bound to promoters in mitosis 39 . A knock-in of a functional HALO–Pol II further confirmed recruitment of Pol II to mitotic chromatin, although at much lower levels than in interphase 32 .…”

“…Globally, levels of histone methylation are retained and levels of histone acetylation decrease in mitosis 36-39 . More specifically, trimethylation of histone H3 at Lys27 (H3K27me3) and Lys9 (H3K9me3) as well as mono-methylation and dimethylation at Lys4 (H3K4me1 and H3K4me2) are largely retained in mitotic chromatin, whereas levels of histone H3 acetylation at Lys9 (H3K9ac) and Lys14 (H3K14ac) are reduced 32,36,37,40 (FIG.…”