The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity

M Daniel Ricketts,Nirmalya Dasgupta,Jiayi Fan,Joseph Han,Morgan Gerace,Yong Tang,Ben E Black,Peter D Adams,Ronen Marmorstein

doi:10.1074/jbc.ra119.007480

Abstract

The HIRA histone chaperone complex is composed of the proteins HIRA, UBN1, and CABIN1 and cooperates with the histone chaperone ASF1a to specifically bind and deposit H3.3/H4 into chromatin. We recently reported that the UBN1 Hpc2-related domain (HRD) specifically binds to H3.3/H4 over H3.1/H4. However, the mechanism for HIRA complex deposition of H3.3/H4 into nucleosomes remains unclear. Here, we characterize a central region of UBN1 (UBN1 middle domain) that is evolutionarily conserved and predicted to have helical secondary structure. We report that the UBN1 middle domain has dimer formation activity and binds to H3/H4 in a manner that does not discriminate between H3.1 and H3.3. We additionally identify a nearby DNA-binding domain in UBN1, located between the UBN1 HRD and middle domain, which binds DNA through electrostatic contacts involving several conserved lysine residues. Together, these observations suggest a mechanism for HIRA-mediated H3.3/H4 deposition whereby UBN1 associates with DNA and dimerizes to mediate formation of an (H3.3/H4)2 heterotetramer prior to chromatin deposition.

Highlights

The HIRA histone chaperone complex is composed of the proteins HIRA, UBN1, and CABIN1 and cooperates with the histone chaperone ASF1a to bind and deposit H3.3/H4 into chromatin
To identify regions of UBN1 that contribute to the biological function of the human HIRA histone chaperone complex, beyond the well-characterized Hpc2-related domain (HRD) and NHRD domains, we performed a multiple-sequence alignment of metazoan UBN1 homologs to hone in on additional regions of conservation to probe for functional significance (Fig. 1)
UBN1 is an essential member of the HIRA complex, but only the very small HRD and NHRD domains have been studied in any depth

Summary

Present address

Gle variant histone into chromatin (3, 4). The human HIRA histone chaperone complex binds to and deposits H3.3/H4 into chromatin in a replication-independent manner (5). Several studies have identified that dimerization of histone chaperones may contribute to formation of a (H3/H4)[2] tetramer for deposition onto DNA (2, 23–26). We recently reported that the C-terminal region of the HIRA subunit forms a stable trimer in solution, and trimerization is essential for HIRA histone chaperone activity in cells (27), whereas it is still unclear whether this timer contributes to formation an (H3.3/H4)[2] tetramer for deposition. We identify several vertebrate-specific conserved lysine residues in a very basic loop region of low predicted structure residing between the UBN1 HRD and middle domain. Our observations of H3/H4 binding and dimer formation by the UBN1 middle domain indicate that UBN1 may be capable of binding two H3.3/H4 molecules to facilitate (H3.3/H4)[2] tetramer formation in a pathway to nucleosome deposition that may involve UBN1-mediated DNA binding by the HIRA complex

Results

Discussion

Experimental procedures