Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells

Eviction of histones from nucleosomes and their exchange with newly synthesized or alternative variants is a central mechanism shaping the epigenome. Here, we implemented a recently established sensor system that enables measuring genome-wide incorporation and exchange of canonical and non-canonical histone variants in mouse embryonic stem cells. While exchange of all measured variants scales with transcription, variant-specific patterns are associated with transcription elongation and Polycomb binding. We found considerable exchange rates of canonical H3.1 and H2B in heterochromatin and repeat elements where non-canonical H3.3 is stably incorporated but not exchanged. This unexpected association between H3.3 incorporation and the exchange of H3.1 and H2B is also evident in active promoters and enhancers, which we validated using HIRA knockout cells harboring the sensor system. The sensor system provides a powerful experimental framework with quantitative readout, facilitating functional studies of histone dynamics and epigenetic gene regulation in vivo. Overall design: ChIP-seq in WT or HIRA KO mESC cell lines carrying histone exchange sensor with two biological replicates per condition. Also, ChIP-seq of hepatocytes derived from transgenic mice carrying either H3.3- or H3.1-modified sensor and mouse embryonic fibroblasts derived from E12.5 embryos with H3.1-modified sensor.