Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA

Abstract

H2A.Bbd is an unusual histone variant whose sequence is only 48% conserved compared to major H2A. The major sequence differences are in the docking domain that tethers the H2A-H2B dimer to the (H3-H4) 2 tetramer; in addition, the C-terminal tail is absent in H2A.Bbd. We assembled nucleosomes in which H2A is replaced by H2A.Bbd (Bbd-NCP), and found that Bbd-NCP had a more relaxed structure in which only 11872 bp of DNA is protected against digestion with micrococcal nuclease. The absence of fluorescence resonance energy transfer between the ends of the DNA in Bbd-NCP indicates that the distance between the DNA ends is increased significantly. The Bbd docking domain is largely responsible for this behavior, as shown by domain-swap experiments. Bbd-containing nucleosomal arrays repress transcription from a natural promoter, and this repression can be alleviated by transcriptional activators Tax and CREB. The structural properties of Bbd-NCP described here have important implications for the in vivo function of this histone variant and are consistent with its proposed role in transcriptionally active chromatin.

Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T

“…The H2AL2 nucleosome was quite susceptible to nucleases, suggesting that these nucleosomes have different structural properties, as compared to those of the conventional nucleosome (21). A possible human counterpart of H2AL2, H2A.Bbd, which is highly expressed in the testis, was also suggested to form a specific nucleosome structure with reduced stability (22)(23)(24). Furthermore, nucleosomes containing a testis-specific H2B variant, hTSH2B/TH2B, were reportedly unstable, as compared to the conventional nucleosome (25).…”

Histone chaperones in nucleosome eviction and histone exchange

“…H2A.Bbd (a H2A variant generally associated with transcriptionally active chromatin) lacks the carboxy-terminal tail as well as a signature acidic surface. H2A.Bbd incorporation results in a less compact nucleosome in which DNA may be more amenable to transcription factor binding [16,17]. These nucleosomal arrays have a more extended conformation and H2A.Bbd inhibits the folding of 30-nm fiber like structures [9].…”

Nucleosome Assembly Protein 1 Exchanges Histone H2A-H2B Dimers and Assists Nucleosome Sliding

“…Samples were analyzed by native PAGE. Identical amounts of N1 and N2 nucleosomes (ϳ6 g of DNA) were digested with 3.0 units of micrococcal nuclease (MNase) (Worthington) at 37°C (44). To analyze histone content, nucleosomes were first fractionated on a 5% native gel in 0.2 ϫ TBE, and the nucleosome species were electroeluted into 0.05 ϫ TBE for 45 min at 150 W and 4°C.…”