The in vivo Interaction Landscape of Histones H3.1 and H3.3

Chromatin structure, transcription, DNA replication, and repair are regulated via locus-specific incorporation of histone variants and posttranslational modifications that guide effector chromatin-binding proteins. Here we report unbiased, quantitative interactomes for the replication -coupled (H3.1) and replication-independent (H3.3) histone H3 variants based on BioID proximity labeling, which al-lows interactions in intact, living cells to be detected. Along with a significant proportion of previously reported interactions detected by affinity purification followed by mass spectrometry, three quarters of the 608 histone-associated proteins that we identified are new, unchar-acterized histone associations. The data reveal important biological nuances not captured by traditional biochemical means. For example, we found that the chromatin as-sembly factor-1 histone chaperone not only deposits the replication-coupled H3.1 histone variant during S-phase but also associates with H3.3 throughout the cell cycle in vivo. We also identified other variant-specific associa-tions, such as with transcription factors, chromatin regulators, and with the mitotic machinery. Our proximity -based analysis is thus a rich resource that extends the H3 interactome and reveals new sets of variant-specific associations.

Automated summary

In this study, unbiased quantitative interactomes for histone H3 variants H3.1 and H3.3 were reported based on BioID proximity labeling, revealing a significant number of new histone-associated proteins and important biological nuances not captured by traditional biochemical means.