A novel histone molecular timer reveals minute-resolution nucleosome turnover

The pattern of histone modification along DNA encodes epigenetic information. Extensive studies have defined enzymes that dynamically deposit epigenetic marks. Histone turnover – the dissociation and binding of histones at a given locus – is key in shaping this landscape. Nevertheless, histone-turnover remains poorly understood, primarily due to drawbacks of current pulse-chase methodologies, which significantly limit the detection of rapid turnover dynamics. Clearly, histone turnover rates are expected to be on par with minute-scale processes like transcriptional activation.

Here, we present a method to measure rapid single-nucleosome dynamics genomewide using an unperturbed yeast culture. We genetically label a histone subunit of choice with a ‘molecular timer’ tag that undergoes proteolytic cleavage only in nucleosomes bound to DNA for a long enough duration. The relative abundance of cleaved versus noncleaved histone measures nucleosome dynamics. Notably, this method can be applied in animal models previously unreachable.

We verify increased H3/H4 turnover in high-expressing promoters. We find turnover is predominantly at the (-1) TSS nucleosome, and prominent in inducible promoters not actively transcribing. Conversely, H2A/B turnover occurs mostly in ORFs, and is transcription-dependent. By subjecting cells to stress, we detect minute-scale histone dynamics in target-gene promoters.

Finally, we probe the relationships between histone-modifications and turnover, and experimentally demonstrate that H3K56-acetylation increases turnover. During prolonged replication, cells actively maintain turnover at newly replicated loci via H3K56-acetylation. We propose this delays the accumulation of transcription-promoting histone marks, thus attenuating expression from genes already replicated, with double the DNA template. Together, we highlight fast histone-turnover rates and their regulatory roles.