Split decision: why it matters?

Cadmium affects mitotically inherited histone modification pathways in mouse embryonic stem cells

The fetal basis of adult disease (FeBAD) theorizes that embryonic challenges initiate pathologies in adult life through epigenetic modification of gene expression. In addition, inheritance of H3K27 methylation marks, especially in vitro, is still controversial. Metals, such as Cd, are known to affect differentiation, DNA repair and epigenetic status in mES cells. We tested the premise that Cd exerts differential toxicity in mouse embryonic stem (mES) cells by targeting total histone protein (THP) production early in stem cell development, while affecting H3K27-mono-methylation (H3K27me(1)) in latter stages of differentiation. The inability of mES cells to recover from Cd insult at concentrations greater than IC50 indicates that maximum cytotoxicity occurs during initial hours of exposure. Moreover, as a measure of chromatin stability, low dose acute Cd exposure lowers THP production. The heritable effects of Cd exposure on cell proliferation, chromatin stability and transcription observed through several cell population doublings were detected only during alternate passages on days 3, 7, and 11, presumably due to slower maturation of histone methylation marks. These findings demonstrate a selective disruption of chromatin structure following acute Cd exposure, an effect not seen in developmentally mature cells. Hence, we present that acute Cd toxicity is cumulative and disrupts DNA repair, while concurrently affecting cell cycle progression, chromatin stability and transcriptional state in mES cells.

Histone variants and epigenetic inheritance

Nucleosome particles, which are composed of core histones and DNA, are the basic unit of eukaryotic chromatin. Histone modifications and histone composition determine the structure and function of the chromatin; this genome packaging, often referred to as "epigenetic information", provides additional information beyond the underlying genomic sequence. The epigenetic information must be transmitted from mother cells to daughter cells during mitotic division to maintain the cell lineage identity and proper gene expression. However, the mechanisms responsible for mitotic epigenetic inheritance remain largely unknown. In this review, we focus on recent studies regarding histone variants and discuss the assembly pathways that may contribute to epigenetic inheritance. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly.

H3.3-H4 tetramer splitting events feature cell-type specific enhancers

Previously, we reported that little canonical (H3.1-H4)(2) tetramers split to form "hybrid" tetramers consisted of old and new H3.1-H(4) dimers, but approximately 10% of (H3.3-H4)2 tetramers split during each cell cycle. In this report, we mapped the H3.3 nucleosome occupancy, the H3.3 nucleosome turnover rate and H3.3 nucleosome splitting events at the genome-wide level. Interestingly, H3.3 nucleosome turnover rate at the transcription starting sites (TSS) of genes with different expression levels display a bimodal distribution rather than a linear correlation towards the transcriptional activity, suggesting genes are either active with high H3.3 nucleosome turnover or inactive with low H3.3 nucleosome turnover. H3.3 nucleosome splitting events are enriched at active genes, which are in fact better markers for active transcription than H3.3 nucleosome occupancy itself. Although both H3.3 nucleosome turnover and splitting events are enriched at active genes, these events only display a moderate positive correlation, suggesting H3.3 nucleosome splitting events are not the mere consequence of H3.3 nucleosome turnover. Surprisingly, H3.3 nucleosomes with high splitting index are remarkably enriched at enhancers in a cell-type specific manner. We propose that the H3.3 nucleosomes at enhancers may be split by an active mechanism to regulate cell-type specific transcription.

Epigenetic inheritance mediated by histone lysine methylation: maintaining transcriptional states without the precise restoration of marks?

'Epigenetics' has been defined as the study of 'mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence'. Chromatin modifications are major carriers of epigenetic information that both reflect and affect the transcriptional states of underlying genes. Several histone modifications are key players that are responsible for classical epigenetic phenomena. However, the mechanisms by which cells pass their histone modifications to daughter cells through mitotic division remain to be unveiled. Here, we review recent progress in the field and conclude that epigenetic modifications are not precisely maintained at a near-mononucleosome level of precision. We also suggest that transcription repression may be maintained by a buffer system that can tolerate a certain degree of fluctuation in repressive histone modification levels. This buffer system protects the repressed genes from potential improper derepression triggered by chromatin modification-level fluctuation resulting from cellular events, such as the cell-cycle-dependent dilution of the chromatin modifications and local responses to environmental cues.

Investigating the cell cycle-associated dynamics of histone modifications using quantitative mass spectrometry

In eukaryotic cells, posttranslational modifications (PTMs) on histones regulate chromatin structure and thus impact nearly all chromatin-templated events, including replication, transcription, and DNA repair. During S phase, newly synthesized histones are deposited onto DNA, leading to dilution of total chromatin-associated modifications. To maintain genome organization in daughter cells, histone PTMs must be reestablished in the subsequent cell cycle. Owing to their importance for determining cellular fate, the mechanisms that underlie the inheritance of epigenetic mark from parent cells by daughter cells are of great interest. In recent years, mass spectrometry (MS) has emerged as a powerful tool for identifying and quantifying histone modifications. This chapter describes strategies for investigating the reestablishment of histone PTMs during the mitotic cell cycle using quantitative MS approaches. By introducing these basic principles of experimental design and common protocols, we hope that this chapter will help readers to apply quantitative MS in their own research systems to study the biology of histone modifications.

A model for mitotic inheritance of histone lysine methylation

Histone lysine methylation has been implicated in epigenetic regulation of transcription. Using stable-isotope labelling and quantitative mass spectrometry, we analysed the dynamics of histone lysine methylation. Here we report that histone methylation levels are transiently reduced during S phase and are gradually re-established during subsequent cell cycle stages. However, despite the recovery of overall methylation levels before the next S phase, the methylation levels of parental and newly incorporated histones differ significantly. In addition, histone methylation levels are maintained at steady states by both restriction of methyltransferase activity and the active turnover of methyl groups in cells undergoing an extended G1/S phase arrest. Finally, we propose a 'buffer model' that unifies the imprecise inheritance of histone methylation and the faithful maintenance of underlying gene silencing.

Nucleolar protein Spindlin1 recognizes H3K4 methylation and stimulates the expression of rRNA genes

The tandem Tudor-like domain-containing protein Spindlin1 has been reported to be a meiotic spindle-associated protein. Here we report that Spindlin1 is not associated with the spindle in mouse embryonic fibroblast cells during mitotic divisions. In interphase cells, Spindlin1 specifically localizes to the nucleoli. Moreover, Spindlin1 is a histone methylation effector protein that specifically recognizes H3K4 methylation. Finally, Spindlin1 localizes to the active ribosomal DNA (rDNA) repeats, and Spindlin1 facilitates the expression of rRNA genes.