The docking domain of histone H2A is required for H1 binding and RSC-mediated nucleosome remodeling

Abstract

Histone variants within the H2A family show high divergences in their C-terminal regions. In this work, we have studied how these divergences and in particular, how a part of the H2A COOH-terminus, the docking domain, is implicated in both structural and functional properties of the nucleosome. Using biochemical methods in combination with Atomic Force Microscopy and Electron Cryo-Microscopy, we show that the H2A-docking domain is a key structural feature within the nucleosome. Deletion of this domain or replacement with the incomplete docking domain from the variant H2A.Bbd results in significant structural alterations in the nucleosome, including an increase in overall accessibility to nucleases, un-wrapping of ∼10 bp of DNA from each end of the nucleosome and associated changes in the entry/exit angle of DNA ends. These structural alterations are associated with a reduced ability of the chromatin remodeler RSC to both remodel and mobilize the nucleosomes. Linker histone H1 binding is also abrogated in nucleosomes containing the incomplete docking domain of H2A.Bbd. Our data illustrate the unique role of the H2A-docking domain in coordinating the structural-functional aspects of the nucleosome properties. Moreover, our data suggest that incorporation of a ‘defective’ docking domain may be a primary structural role of H2A.Bbd in chromatin.

Integrated molecular mechanism directing nucleosome reorganization by human FACT

“…Taken together, we propose that H2A-H2B displacement by hMid-AID leads to DNA stripping. In agreement with this interpretation, the nucleosomal DNA ends are detached from nucleosomes, which contain H2A lacking the docking segment, similar to hexasomes (Shukla et al 2011;Arimura et al 2012).…”

“…The (H3-H4) 2 -binding loop of hMid also clashes with more residues of the H2A-docking segment, such as Ile87, Arg88, and residues of Gly105-Leu116. In addition, the previous report indicates that the extensive lack of the H2A-docking segment leads to prominent structural perturbations within nucleosomes (Shukla et al 2011). Taken together, it is convincing that the H2A-docking segment, which occupies the same site as the (H3-H4) 2 -binding loop, is detached from histones H3-H4 upon invasion of hMid-AID into nucleosomes, thereby inducing the conversion of nucleosomes into hexasomes.…”

Key Functional Regions in the Histone Variant H2A.Z C-Terminal Docking Domain

“…These data suggested that this region of the docking domain might play a similar role in chromatin anchoring of both histone H2A forms. Consistent with this, the Xenopus laevis H2A docking domain is critical to stabilize its interactions within the nucleosome in vitro (47), and the human H2A C terminus is required for proper nucleosome stability in vivo (50). The general functional requirement of this region is further supported by our own data showing that the H2A residues corresponding to H2A.Z H118, I119, and N120 were important in vivo.…”

Histone H2A variants in nucleosomes and chromatin: more or less stable?

“…Incorporation of H2A.X into nucleosomes exhibits only mild effects on interaction with H1, but phosphorylation of the H2A.X C-terminus leads to significant impairment of this binding (49). More pronounced reductions of interaction with H1 were reported for H2A.Z (102) and H2A.Bbd nucleosomes (127). In the case of H2A.Bbd, this has been further dissected, showing that reduced interaction with H1 can be attributed to the H2A.Bbd docking domain.…”

“…Interestingly, and counter-intuitively, H2A.Bbd is much less efficiently remodelled by a variety of ATP-dependent chromatin remodelling complexes like SWI/SNF (SWItch/Sucrose Non-Fermentable), ACF (ATP-utilizing Chromatin assembly and remodelling Factor) (124) and RSC (Remodels the Structure of Chromatin) (127). However, as H2A.Bbd is expressed more or less testis-specifically, it is possible that it is remodelled by, as yet, unidentified, tissue-specific, molecular machines.…”