Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells
2Department of Molecular Genetics, Weizmann Institute of Science, Israel
Exchange of histones within nucleosomes by newly synthesized or alternative variants is a central regulatory mechanism that influences DNA accessibility and gene expression. Yet, genetic determinants and regulatory consequences of this key process in mammals are largely unknown, due to limited temporal resolution of conventional methods. Here, we developed a molecular sensor that reports on steady-state replacement rate from a single sample. High temporal resolution is achieved via histone tagging such that tags are modified at each genomic position in a way that depends on residence time of histones on DNA. Utilizing the sensor system in mouse embryonic stem cells allowed robust charting of genome-wide histone incorporation and exchange rates for canonical and non-canonical variants. We confirmed highest exchange rates within transcriptionally active and regulatory regions. But we also identified variant-specific exchange within gene bodies and in association with Polycomb binding. Surprisingly, exchange of H3.1 and H2B variants is also evident within repetitive elements of heterochromatin in which H3.3 is stably incorporated. Apart from heterochromatin, high deposition of H3.3 at enhancers and promoters also correlates with the exchange of H3.1 and H2B variants. Depleting a H3.3 specific chaperon – HIRA, resulted in global reduction of exchange levels at open chromatin, suggesting that H3.3 deposition enhances nucleosome dynamics at these sites. Together, our work provides in-depth characterization of histone dynamics in mammals. The sensor system holds great potential for elucidating functional relationships between histone exchange and gene expression in multiple biological systems, including in vivo studies that were previously largely unapproachable.