The nucleosome core particle remembers its position through DNA replication and transcription

We tracked the fate of labelled nucleosomes through DNA replication, and established that nucleosomes present at a locus remembered their position during DNA replication. The replication-associated histone chaperones DPB3 and MCM2 were essential for nucleosome position memory, and in the absence of both DPB3 and MCM2 histone chaperone activity nucleosomes did not remember their position. Using the same approach, we tested the model that transcription results in retrograde transposition of nucleosomes along a transcription unit. We found no evidence of retrograde transposition. Our results suggest that nucleosomes have the capacity to transmit epigenetic memory across mitotic generations with exquisite spatial fidelity. Overall design: Nucleosomes were tagged with the 15aa AviTag, then the AviTag was biotinylated using various versions of TetR-BirA (including a split TetR-BirA obligate heterodimer). Site-specific biotinyaltion was stopped by adding doxycycline, and the labeled nucleosomes were detected before and after replication using streptavidin affinity purification and sequencing. In the same samples, we directly detected the localization of the TetR-BirA enzyme by using a V5-tagged allele of TetR-BirA, and precipitating the TetR-BirA-bound chromatin using anti-V5 agarose resin.