Mechanisms controlling the deposition and dynamics of histone variant H2BE

Histone variants shape chromatin structure and gene regulation and their deposition and localization in chromatin are tightly controlled. H2BE is the only known widely expressed mammalian H2B variant and localizes to transcription start sites to control chromatin accessibility and cognitive function. However, the mechanisms governing H2B variant incorporation into chromatin remain unclear. Here, we define the regulatory framework controlling H2BE incorporation, localization, and eviction in neuronal chromatin. We identify the BAF remodeling complex and the transcription factor SP1 as key drivers of H2BE deposition at specific genomic loci. We further show that FACT maintains H2BE enrichment at transcription start sites by preventing its distribution into gene bodies, while the histone chaperone NAP1L4 mediates H2BE eviction from chromatin. Comparative analysis with H2A.Z reveals that BAF, SP1 and NAP1L4 exert H2BE-specific functions, while FACT functions more broadly across histone variants. Finally, we define the H2BE-dependent transcriptional effects of it chaperones. Together, these findings uncover the first chaperones governing H2B variant incorporation and define a highly complex mechanism responsible for H2BE regulation in chromatin. Highlights: The BAF complex controls H2BE incorporation.SP1 promotes locus-specific incorporation of H2BE.FACT prevents H2BE accumulation in genic regions.NAP1L4 mediates eviction of H2BE from chromatin.