UBR7 Promotes Accumulation of NASP‐Bound Pre‐Existing Histone H3

Abstract

The packaging of DNA into chromatin necessitates the assembly and disassembly of nucleosomes during DNA-based processes such as transcription and replication. Histone supply, deposition and reassembly depends on a class of histone binding proteins known as chaperones. Histone chaperones modulate the stability of histones from synthesis, through chromatin deposition, and during histone recycling during transcription and replication. Histone chaperones also interact with pre-existing soluble histones downstream of histone eviction from chromatin and upstream of histone degradation. The pathways that chaperone pre-existing histones are not as well characterized as the pathways that chaperone newly synthesized histones. We and others have demonstrated that histone H3.1 associates abundantly with the protein UBR7. Here we characterize UBR7 as a pre-existing histone H3.1 chaperone that modulates the stability of evicted soluble histone complexes. Immunofluorescence and biochemical fractionation show that UBR7 is a largely nuclear soluble protein. UBR7 contains two putative functional domains: the UBR-box and the PHD. Like several other PHD containing proteins, we find through an unbiased peptide array that UBR7 preferentially binds histone H3 that is di- or tri-methylated at H3K4 or tri-methylated at H3K9. We show that the UBR7 UBR-box and PHD are necessary for binding to modified histone H3 complexes. Consistent with the soluble nature of UBR7 protein, we demonstrate that UBR7 interacts with endogenous H3K4me3 and H3K9me3 histones in the soluble fraction of human cells. Through an unbiased BioID approach, we demonstrate that UBR7 interacts abundantly with the soluble histone chaperone NASP. NASP was previously shown to bind and preserve a soluble reservoir of histones H3/H4, such that soluble H3/H4 are degraded in the absence of NASP. We show that, like UBR7, NASP binds to soluble pre-existing histone H3/H4, but unlike UBR7, also binds newly synthesized histones. Through NASP pull-downs in wild-type and UBR7 KO cells, we demonstrate that NASP-bound H3/H4 accumulate in the absence of UBR7. We propose a model in which the interaction between the histone chaperones UBR7 and NASP and histones opposes NASP protection of soluble H3/H4 complexes and promotes loss of evicted soluble pre-existing histones.